openms_openswathworkflow: OpenSwathWorkflow.xml annotate

annotate OpenSwathWorkflow.xml @ 14:ec4490c65f95 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

author	galaxyp
date	Fri, 14 Jun 2024 21:38:33 +0000
parents	4a7b96835140
children

rev	line source
5 56988709dec6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: 1 diff changeset	1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2 <!--Proposed Tool Section: []-->
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	3 <tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	4 <description>Complete workflow to run OpenSWATH</description>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	5 <macros>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	6 <token name="@EXECUTABLE@">OpenSwathWorkflow</token>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	7 <import>macros.xml</import>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	8 </macros>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	9 <expand macro="requirements"/>
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	10 <expand macro="stdio"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	12 @EXT_FOO@
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	13 #import re
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	14
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	15 ## Preprocessing
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	16 mkdir in &&
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	18 mkdir tr &&
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	19 cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	20 #if $tr_irt:
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	21 mkdir tr_irt &&
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	22 cp '$tr_irt' 'tr_irt/${re.sub("[^\w\-_]", "_", $tr_irt.element_identifier)}.$gxy2omsext($tr_irt.ext)' &&
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	23 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	24 #if $tr_irt_nonlinear:
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	25 mkdir tr_irt_nonlinear &&
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	26 cp '$tr_irt_nonlinear' 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)' &&
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	27 #end if
11 48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	28 #if $swath_windows_file:
48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	29 mkdir swath_windows_file &&
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	30 cp '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' &&
11 48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	31 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	32 #if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	33 mkdir out_features &&
1 190554cf2195 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 galaxyp parents: 0 diff changeset	34 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	35 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	36 mkdir out_tsv &&
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	37 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	38 #if "out_osw_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	39 mkdir out_osw &&
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	40 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	41 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	42 mkdir out_chrom &&
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	43 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	44 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	45 mkdir out_qc &&
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	46 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	47 #if "irt_mzml_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	48 mkdir Debugging_irt_mzml &&
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	49 #end if
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	50 #if "irt_trafo_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	51 mkdir Debugging_irt_trafo &&
1 190554cf2195 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 galaxyp parents: 0 diff changeset	52 #end if
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	53 ## advanced options
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	54 #if $adv_opts.rt_norm:
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	55 mkdir adv_opts.rt_norm &&
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	56 cp '$adv_opts.rt_norm' 'adv_opts.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts.rt_norm.element_identifier)}.$gxy2omsext($adv_opts.rt_norm.ext)' &&
5 56988709dec6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: 1 diff changeset	57 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	58
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	59
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	60 ## Main program call
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	61
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	62 set -o pipefail &&
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	63 @EXECUTABLE@ -write_ctd ./ &&
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	64 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	65 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	66 -in
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	67 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	68 -tr
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	69 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	70 #if $tr_irt:
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	71 -tr_irt
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	72 'tr_irt/${re.sub("[^\w\-_]", "_", $tr_irt.element_identifier)}.$gxy2omsext($tr_irt.ext)'
5 56988709dec6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: 1 diff changeset	73 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	74 #if $tr_irt_nonlinear:
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	75 -tr_irt_nonlinear
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	76 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	77 #end if
11 48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	78 #if $swath_windows_file:
48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	79 -swath_windows_file
48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	80 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)'
48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	81 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	82 #if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	83 -out_features
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	84 'out_features/output.${gxy2omsext("featurexml")}'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	85 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	86 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	87 -out_tsv
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	88 'out_tsv/output.${gxy2omsext("tabular")}'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	89 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	90 #if "out_osw_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	91 -out_osw
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	92 'out_osw/output.${gxy2omsext("osw")}'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	93 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	94 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	95 -out_chrom
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	96 'out_chrom/output.${adv_opts.out_chrom_type}'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	97 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	98 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	99 -out_qc
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	100 'out_qc/output.${gxy2omsext("json")}'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	101 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	102 #if "irt_mzml_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	103 -Debugging:irt_mzml
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	104 'Debugging_irt_mzml/output.${gxy2omsext("mzml")}'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	105 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	106 #if "irt_trafo_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	107 -Debugging:irt_trafo
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	108 'Debugging_irt_trafo/output.${gxy2omsext("trafoxml")}'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	109 #end if
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	110 ## advanced options
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	111 #if $adv_opts.rt_norm:
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	112 -rt_norm
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	113 'adv_opts.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts.rt_norm.element_identifier)}.$gxy2omsext($adv_opts.rt_norm.ext)'
1 190554cf2195 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 galaxyp parents: 0 diff changeset	114 #end if
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	115
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	116 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	117 \| tee '$stdout'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	118 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	119
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	120 ## Postprocessing
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	121 #if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	122 && mv 'out_features/output.${gxy2omsext("featurexml")}' '$out_features'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	123 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	124 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	125 && mv 'out_tsv/output.${gxy2omsext("tabular")}' '$out_tsv'
1 190554cf2195 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 galaxyp parents: 0 diff changeset	126 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	127 #if "out_osw_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	128 && mv 'out_osw/output.${gxy2omsext("osw")}' '$out_osw'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	129 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	130 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	131 && mv 'out_chrom/output.${adv_opts.out_chrom_type}' '$out_chrom'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	132 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	133 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	134 && mv 'out_qc/output.${gxy2omsext("json")}' '$out_qc'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	135 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	136 #if "irt_mzml_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	137 && mv 'Debugging_irt_mzml/output.${gxy2omsext("mzml")}' '$Debugging_irt_mzml'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	138 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	139 #if "irt_trafo_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	140 && mv 'Debugging_irt_trafo/output.${gxy2omsext("trafoxml")}' '$Debugging_irt_trafo'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	141 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	142 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	143 && mv '@EXECUTABLE@.ctd' '$ctd_out'
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	144 #end if]]></command>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	145 <configfiles>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	146 <inputs name="args_json" data_style="paths"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	147 <configfile name="hardcoded_json"><![CDATA[{"tempDirectory": "\$TMP_DIR", "outer_loop_threads": "1", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	148 </configfiles>
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	149 <inputs>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	150 <param argument="-in" type="data" format="mzml,mzxml,sqmass" label="Input files separated by blank" help=" select mzml,mzxml,sqmass data sets(s)"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	151 <param argument="-tr" type="data" format="pqp,tabular,traml" label="transition file ('TraML','tsv','pqp')" help=" select pqp,tabular,traml data sets(s)"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	152 <param argument="-tr_irt" type="data" format="pqp,tabular,traml" optional="true" label="transition file ('TraML')" help=" select pqp,tabular,traml data sets(s)"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	153 <param argument="-tr_irt_nonlinear" type="data" format="pqp,tabular,traml" optional="true" label="additional nonlinear transition file ('TraML')" help=" select pqp,tabular,traml data sets(s)"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	154 <param argument="-swath_windows_file" type="data" format="txt" optional="true" label="Optional, tab-separated file containing the SWATH windows for extraction: lower_offset upper_offset" help="Note that the first line is a header and will be skipped select txt data sets(s)"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	155 <param argument="-sonar" type="boolean" truevalue="true" falsevalue="false" checked="false" label="data is scanning SWATH data" help=""/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	156 <param argument="-pasef" type="boolean" truevalue="true" falsevalue="false" checked="false" label="data is PASEF data" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	157 <param argument="-rt_extraction_window" type="float" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	158 <param argument="-ion_mobility_window" type="float" value="-1.0" label="Extraction window in ion mobility dimension (in 1/k0 or milliseconds depending on library)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side. -1 means extract over the whole range or ion mobility is not present. (Default for diaPASEF data: 0.06 1/k0)"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	159 <param argument="-mz_extraction_window" type="float" min="0.0" value="50.0" label="Extraction window in Thomson or ppm (see mz_extraction_window_unit)" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	160 <param argument="-mz_extraction_window_ms1" type="float" min="0.0" value="50.0" label="Extraction window used in MS1 in Thomson or ppm (see mz_extraction_window_ms1_unit)" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	161 <param argument="-im_extraction_window_ms1" type="float" value="-1.0" label="Extraction window in ion mobility dimension for MS1 (in 1/k0 or milliseconds depending on library)" help="-1 means this is not ion mobility data"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	162 <section name="Calibration" title="Parameters for the m/z and ion mobility calibration" help="" expanded="false">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	163 <param name="ms1_im_calibration" argument="-Calibration:ms1_im_calibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use MS1 precursor data for the ion mobility calibration (default = false, uses MS2 / fragment ions for calibration)" help=""/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	164 <param name="im_correction_function" argument="-Calibration:im_correction_function" type="select" label="Type of normalization function for IM calibration" help="">
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	165 <option value="none">none</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	166 <option value="linear" selected="true">linear</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	167 <expand macro="list_string_san" name="im_correction_function"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	168 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	169 <param name="debug_im_file" argument="-Calibration:debug_im_file" type="text" optional="true" value="" label="Debug file for Ion Mobility calibration" help="">
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	170 <expand macro="list_string_san" name="debug_im_file"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	171 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	172 <param name="debug_mz_file" argument="-Calibration:debug_mz_file" type="text" optional="true" value="" label="Debug file for m/z calibration" help="">
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	173 <expand macro="list_string_san" name="debug_mz_file"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	174 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	175 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	176 <section name="Library" title="Library parameters section" help="" expanded="false">
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	177 <param name="retentionTimeInterpretation" argument="-Library:retentionTimeInterpretation" type="select" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="">
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	178 <option value="iRT" selected="true">iRT</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	179 <option value="seconds">seconds</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	180 <option value="minutes">minutes</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	181 <expand macro="list_string_san" name="retentionTimeInterpretation"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	182 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	183 <param name="override_group_label_check" argument="-Library:override_group_label_check" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="Only turn this off if you know what you are doing"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	184 <param name="force_invalid_mods" argument="-Library:force_invalid_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	185 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	186 <section name="RTNormalization" title="Parameters for the RTNormalization for iRT petides" help="This specifies how the RT alignment is performed and how outlier detection is applied. Outlier detection can be done iteratively (by default) which removes one outlier per iteration or using the RANSAC algorithm" expanded="false">
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	187 <param name="alignmentMethod" argument="-RTNormalization:alignmentMethod" type="select" label="How to perform the alignment to the normalized RT space using anchor points" help="'linear': perform linear regression (for few anchor points). 'interpolated': Interpolate between anchor points (for few, noise-free anchor points). 'lowess' Use local regression (for many, noisy anchor points). 'b_spline' use b splines for smoothing">
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	188 <option value="linear" selected="true">linear</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	189 <option value="interpolated">interpolated</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	190 <option value="lowess">lowess</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	191 <option value="b_spline">b_spline</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	192 <expand macro="list_string_san" name="alignmentMethod"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	193 </param>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	194 <param name="outlierMethod" argument="-RTNormalization:outlierMethod" type="select" label="Which outlier detection method to use (valid: 'iter_residual', 'iter_jackknife', 'ransac', 'none')" help="Iterative methods remove one outlier at a time. Jackknife approach optimizes for maximum r-squared improvement while 'iter_residual' removes the datapoint with the largest residual error (removal by residual is computationally cheaper, use this with lots of peptides)">
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	195 <option value="iter_residual" selected="true">iter_residual</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	196 <option value="iter_jackknife">iter_jackknife</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	197 <option value="ransac">ransac</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	198 <option value="none">none</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	199 <expand macro="list_string_san" name="outlierMethod"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	200 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	201 <param name="useIterativeChauvenet" argument="-RTNormalization:useIterativeChauvenet" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use Chauvenet's criterion when using iterative methods" help="This should be used if the algorithm removes too many datapoints but it may lead to true outliers being retained"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	202 <param name="RANSACMaxIterations" argument="-RTNormalization:RANSACMaxIterations" type="integer" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	203 <param name="RANSACMaxPercentRTThreshold" argument="-RTNormalization:RANSACMaxPercentRTThreshold" type="integer" value="3" label="Maximum threshold in RT dimension for the RANSAC outlier detection algorithm (in percent of the total gradient)" help="Default is set to 3% which is around +/- 4 minutes on a 120 gradient"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	204 <param name="RANSACSamplingSize" argument="-RTNormalization:RANSACSamplingSize" type="integer" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help=""/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	205 <param name="estimateBestPeptides" argument="-RTNormalization:estimateBestPeptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether the algorithms should try to choose the best peptides based on their peak shape for normalization" help="Use this option you do not expect all your peptides to be detected in a sample and too many 'bad' peptides enter the outlier removal step (e.g. due to them being endogenous peptides or using a less curated list of peptides)"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	206 <param name="InitialQualityCutoff" argument="-RTNormalization:InitialQualityCutoff" type="float" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="-2 to 2)"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	207 <param name="OverallQualityCutoff" argument="-RTNormalization:OverallQualityCutoff" type="float" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="0 to 10)"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	208 <param name="NrRTBins" argument="-RTNormalization:NrRTBins" type="integer" value="10" label="Number of RT bins to use to compute coverage" help="This option should be used to ensure that there is a complete coverage of the RT space (this should detect cases where only a part of the RT gradient is actually covered by normalization peptides)"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	209 <param name="MinPeptidesPerBin" argument="-RTNormalization:MinPeptidesPerBin" type="integer" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	210 <param name="MinBinsFilled" argument="-RTNormalization:MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help=""/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	211 <section name="lowess" title="" help="" expanded="false">
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	212 <param name="span" argument="-RTNormalization:lowess:span" type="float" min="0.0" max="1.0" value="0.05" label="Span parameter for lowess" help=""/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	213 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	214 <section name="b_spline" title="" help="" expanded="false">
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	215 <param name="num_nodes" argument="-RTNormalization:b_spline:num_nodes" type="integer" min="0" value="5" label="Number of nodes for b spline" help=""/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	216 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	217 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	218 <section name="Scoring" title="Scoring parameters section" help="" expanded="false">
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	219 <param name="stop_report_after_feature" argument="-Scoring:stop_report_after_feature" type="integer" value="5" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	220 <param name="rt_normalization_factor" argument="-Scoring:rt_normalization_factor" type="float" value="100.0" label="The normalized RT is expected to be between 0 and 1" help="If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	221 <param name="quantification_cutoff" argument="-Scoring:quantification_cutoff" type="float" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	222 <param name="write_convex_hull" argument="-Scoring:write_convex_hull" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write out all points of all features into the featureXML" help=""/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	223 <param name="spectrum_addition_method" argument="-Scoring:spectrum_addition_method" type="select" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	224 <option value="simple" selected="true">simple</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	225 <option value="resample">resample</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	226 <expand macro="list_string_san" name="spectrum_addition_method"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	227 </param>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	228 <param name="add_up_spectra" argument="-Scoring:add_up_spectra" type="integer" min="1" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	229 <param name="spacing_for_spectra_resampling" argument="-Scoring:spacing_for_spectra_resampling" type="float" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	230 <param name="uis_threshold_sn" argument="-Scoring:uis_threshold_sn" type="integer" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	231 <param name="uis_threshold_peak_area" argument="-Scoring:uis_threshold_peak_area" type="integer" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	232 <param name="scoring_model" argument="-Scoring:scoring_model" type="select" label="Scoring model to use" help="">
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	233 <option value="default" selected="true">default</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	234 <option value="single_transition">single_transition</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	235 <expand macro="list_string_san" name="scoring_model"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	236 </param>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	237 <param name="im_extra_drift" argument="-Scoring:im_extra_drift" type="float" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	238 <param name="strict" argument="-Scoring:strict" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to error (true) or skip (false) if a transition in a transition group does not have a corresponding chromatogram" help=""/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	239 <section name="TransitionGroupPicker" title="" help="" expanded="false">
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	240 <param name="stop_after_feature" argument="-Scoring:TransitionGroupPicker:stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	241 <param name="min_peak_width" argument="-Scoring:TransitionGroupPicker:min_peak_width" type="float" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	242 <param name="peak_integration" argument="-Scoring:TransitionGroupPicker:peak_integration" type="select" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	243 <option value="original" selected="true">original</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	244 <option value="smoothed">smoothed</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	245 <expand macro="list_string_san" name="peak_integration"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	246 </param>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	247 <param name="background_subtraction" argument="-Scoring:TransitionGroupPicker:background_subtraction" type="select" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	248 <option value="none" selected="true">none</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	249 <option value="original">original</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	250 <option value="exact">exact</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	251 <expand macro="list_string_san" name="background_subtraction"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	252 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	253 <param name="recalculate_peaks" argument="-Scoring:TransitionGroupPicker:recalculate_peaks" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="Tries to use the consensus (median) peak border if the variation within the picked peaks is too large"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	254 <param name="use_precursors" argument="-Scoring:TransitionGroupPicker:use_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	255 <param name="use_consensus" argument="-Scoring:TransitionGroupPicker:use_consensus" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)" help=""/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	256 <param name="recalculate_peaks_max_z" argument="-Scoring:TransitionGroupPicker:recalculate_peaks_max_z" type="float" value="0.75" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	257 <param name="minimal_quality" argument="-Scoring:TransitionGroupPicker:minimal_quality" type="float" value="-1.5" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	258 <param name="resample_boundary" argument="-Scoring:TransitionGroupPicker:resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
11 48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	259 <param name="compute_peak_quality" argument="-Scoring:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	260 <param name="compute_peak_shape_metrics" argument="-Scoring:TransitionGroupPicker:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	261 <param name="compute_total_mi" argument="-Scoring:TransitionGroupPicker:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	262 <param name="boundary_selection_method" argument="-Scoring:TransitionGroupPicker:boundary_selection_method" type="select" label="Method to use when selecting the best boundaries for peaks" help="">
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	263 <option value="largest" selected="true">largest</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	264 <option value="widest">widest</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	265 <expand macro="list_string_san" name="boundary_selection_method"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	266 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	267 <section name="PeakPickerMRM" title="" help="" expanded="false">
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	268 <param name="sgolay_frame_length" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	269 <param name="sgolay_polynomial_order" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	270 <param name="gauss_width" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="float" value="30.0" label="Gaussian width in seconds, estimated peak size" help=""/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	271 <param name="use_gauss" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help=""/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	272 <param name="peak_width" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	273 <param name="signal_to_noise" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="float" min="0.0" value="0.1" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	274 <param name="write_sn_log_messages" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	275 <param name="remove_overlapping_peaks" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Try to remove overlapping peaks during peak picking" help=""/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	276 <param name="method" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:method" type="select" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	277 <option value="legacy">legacy</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	278 <option value="corrected" selected="true">corrected</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	279 <option value="crawdad">crawdad</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	280 <expand macro="list_string_san" name="method"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	281 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	282 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	283 <section name="PeakIntegrator" title="" help="" expanded="false">
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	284 <param name="integration_type" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	285 <option value="intensity_sum" selected="true">intensity_sum</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	286 <option value="simpson">simpson</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	287 <option value="trapezoid">trapezoid</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	288 <expand macro="list_string_san" name="integration_type"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	289 </param>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	290 <param name="baseline_type" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	291 <option value="base_to_base" selected="true">base_to_base</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	292 <option value="vertical_division">vertical_division</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	293 <option value="vertical_division_min">vertical_division_min</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	294 <option value="vertical_division_max">vertical_division_max</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	295 <expand macro="list_string_san" name="baseline_type"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	296 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	297 <param name="fit_EMG" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:fit_EMG" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit the chromatogram/spectrum to the EMG peak model" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	298 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	299 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	300 <section name="DIAScoring" title="" help="" expanded="false">
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	301 <param name="dia_extraction_window" argument="-Scoring:DIAScoring:dia_extraction_window" type="float" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	302 <param name="dia_extraction_unit" argument="-Scoring:DIAScoring:dia_extraction_unit" type="select" label="DIA extraction window unit" help="">
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	303 <option value="Th" selected="true">Th</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	304 <option value="ppm">ppm</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	305 <expand macro="list_string_san" name="dia_extraction_unit"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	306 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	307 <param name="dia_centroided" argument="-Scoring:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	308 <param name="dia_byseries_intensity_min" argument="-Scoring:DIAScoring:dia_byseries_intensity_min" type="float" min="0.0" value="300.0" label="DIA b/y series minimum intensity to conside" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	309 <param name="dia_byseries_ppm_diff" argument="-Scoring:DIAScoring:dia_byseries_ppm_diff" type="float" min="0.0" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	310 <param name="dia_nr_isotopes" argument="-Scoring:DIAScoring:dia_nr_isotopes" type="integer" min="0" value="4" label="DIA number of isotopes to conside" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	311 <param name="dia_nr_charges" argument="-Scoring:DIAScoring:dia_nr_charges" type="integer" min="0" value="4" label="DIA number of charges to conside" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	312 <param name="peak_before_mono_max_ppm_diff" argument="-Scoring:DIAScoring:peak_before_mono_max_ppm_diff" type="float" min="0.0" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help=""/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	313 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	314 <section name="EMGScoring" title="" help="" expanded="false">
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	315 <param name="max_iteration" argument="-Scoring:EMGScoring:max_iteration" type="integer" value="10" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help=""/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	316 <param name="init_mom" argument="-Scoring:EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Initialize parameters using method of moments estimators" help=""/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	317 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	318 <section name="Scores" title="" help="" expanded="false">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	319 <param name="use_shape_score" argument="-Scoring:Scores:use_shape_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	320 <param name="use_coelution_score" argument="-Scoring:Scores:use_coelution_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	321 <param name="use_rt_score" argument="-Scoring:Scores:use_rt_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the retention time score (this score measure the difference in retention time)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	322 <param name="use_library_score" argument="-Scoring:Scores:use_library_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the library score" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	323 <param name="use_intensity_score" argument="-Scoring:Scores:use_intensity_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the intensity score" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	324 <param name="use_nr_peaks_score" argument="-Scoring:Scores:use_nr_peaks_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the number of peaks score" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	325 <param name="use_total_xic_score" argument="-Scoring:Scores:use_total_xic_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the total XIC score" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	326 <param name="use_total_mi_score" argument="-Scoring:Scores:use_total_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the total MI score" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	327 <param name="use_sn_score" argument="-Scoring:Scores:use_sn_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the SN (signal to noise) score" help=""/>
11 48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	328 <param name="use_mi_score" argument="-Scoring:Scores:use_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the MI (mutual information) score" help=""/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	329 <param name="use_dia_scores" argument="-Scoring:Scores:use_dia_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the DIA (SWATH) scores" help="If turned off, will not use fragment ion spectra for scoring"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	330 <param name="use_ms1_correlation" argument="-Scoring:Scores:use_ms1_correlation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the correlation scores with the MS1 elution profiles" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	331 <param name="use_sonar_scores" argument="-Scoring:Scores:use_sonar_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for SONAR scans (scanning swath)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	332 <param name="use_ion_mobility_scores" argument="-Scoring:Scores:use_ion_mobility_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for Ion Mobility scans" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	333 <param name="use_ms1_fullscan" argument="-Scoring:Scores:use_ms1_fullscan" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help=""/>
11 48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	334 <param name="use_ms1_mi" argument="-Scoring:Scores:use_ms1_mi" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the MS1 MI score" help=""/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	335 <param name="use_uis_scores" argument="-Scoring:Scores:use_uis_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use UIS scores for peptidoform identification" help=""/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	336 <param name="use_ionseries_scores" argument="-Scoring:Scores:use_ionseries_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use MS2-level b/y ion-series scores for peptidoform identification" help=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	337 <param name="use_ms2_isotope_scores" argument="-Scoring:Scores:use_ms2_isotope_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use MS2-level isotope scores (pearson & manhattan) across product transitions (based on ID if annotated or averagine)" help=""/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	338 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	339 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	340 <expand macro="adv_opts_macro">
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	341 <param argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="If set, tr_irt may be omitted select trafoxml data sets(s)"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	342 <param argument="-sort_swath_maps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sort input SWATH files when matching to SWATH windows from swath_windows_file" help=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	343 <param argument="-enable_ms1" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Extract the precursor ion trace(s) and use for scoring if present" help=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	344 <param argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable additional scoring of identification assays using IPF (see online documentation)" help=""/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	345 <param name="out_chrom_type" type="select" label="File type of output out_chrom (Also output all computed chromatograms output in mzML (chrom.mzML) or sqMass (SQLite format))">
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	346 <option value="mzML">mzml</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	347 <option value="sqMass">sqmass</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	348 </param>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	349 <param argument="-min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the upper edge of a Swath window to still consider a precursor, in Thomson" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	350 <param argument="-extra_rt_extraction_window" type="float" min="0.0" value="0.0" label="Output an XIC with a RT-window by this much large" help="(e.g. to visually inspect a larger area of the chromatogram)"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	351 <param argument="-mz_extraction_window_unit" type="select" label="Unit for mz extraction" help="">
11 48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	352 <option value="Th">Th</option>
48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	353 <option value="ppm" selected="true">ppm</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	354 <expand macro="list_string_san" name="mz_extraction_window_unit"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	355 </param>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	356 <param argument="-mz_extraction_window_ms1_unit" type="select" label="Unit of the MS1 m/z extraction window" help="">
11 48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	357 <option value="ppm" selected="true">ppm</option>
48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	358 <option value="Th">Th</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	359 <expand macro="list_string_san" name="mz_extraction_window_ms1_unit"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	360 </param>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	361 <param argument="-use_ms1_ion_mobility" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Also perform precursor extraction using the same ion mobility window as for fragment ion extraction" help=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	362 <param argument="-matching_window_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assume the input data is targeted / PRM-like data with potentially overlapping DIA windows" help="Will only attempt to extract each assay from the best matching DIA window (instead of all matching windows)"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	363 <param argument="-irt_mz_extraction_window" type="float" min="0.0" value="50.0" label="Extraction window used for iRT and m/z correction in Thomson or ppm (see irt_mz_extraction_window_unit)" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	364 <param argument="-irt_mz_extraction_window_unit" type="select" label="Unit for mz extraction" help="">
11 48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	365 <option value="Th">Th</option>
48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	366 <option value="ppm" selected="true">ppm</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	367 <expand macro="list_string_san" name="irt_mz_extraction_window_unit"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	368 </param>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	369 <param argument="-irt_im_extraction_window" type="float" value="-1.0" label="Ion mobility extraction window used for iRT (in 1/K0 or milliseconds depending on library)" help="-1 means do not perform ion mobility calibration"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	370 <param argument="-min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	371 <param argument="-min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	372 <param argument="-split_file_input" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The input files each contain one single SWATH (alternatively: all SWATH are in separate files)" help=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	373 <param argument="-use_elution_model_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Turn on elution model score (EMG fit to peak)" help=""/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	374 <param argument="-readOptions" type="select" label="Whether to run OpenSWATH directly on the input data, cache data to disk first or to perform a datareduction step first" help="If you choose cache, make sure to also set tempDirectory">
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	375 <option value="normal" selected="true">normal</option>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	376 <option value="cache">cache</option>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	377 <option value="cacheWorkingInMemory">cacheWorkingInMemory</option>
1 190554cf2195 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 galaxyp parents: 0 diff changeset	378 <option value="workingInMemory">workingInMemory</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	379 <expand macro="list_string_san" name="readOptions"/>
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	380 </param>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	381 <param argument="-mz_correction_function" type="select" label="Use the retention time normalization peptide MS2 masses to perform a mass correction (linear, weighted by intensity linear or quadratic) of all spectra" help="">
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	382 <option value="none" selected="true">none</option>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	383 <option value="regression_delta_ppm">regression_delta_ppm</option>
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	384 <option value="unweighted_regression">unweighted_regression</option>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	385 <option value="weighted_regression">weighted_regression</option>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	386 <option value="quadratic_regression">quadratic_regression</option>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	387 <option value="weighted_quadratic_regression">weighted_quadratic_regression</option>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	388 <option value="weighted_quadratic_regression_delta_ppm">weighted_quadratic_regression_delta_ppm</option>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	389 <option value="quadratic_regression_delta_ppm">quadratic_regression_delta_ppm</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	390 <expand macro="list_string_san" name="mz_correction_function"/>
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	391 </param>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	392 <param argument="-extraction_function" type="select" label="Function used to extract the signal" help="">
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	393 <option value="tophat" selected="true">tophat</option>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	394 <option value="bartlett">bartlett</option>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	395 <expand macro="list_string_san" name="extraction_function"/>
1 190554cf2195 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 galaxyp parents: 0 diff changeset	396 </param>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	397 <param argument="-batchSize" type="integer" min="0" value="1000" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 250-1000)" help=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	398 <param argument="-ms1_isotopes" type="integer" min="0" value="3" label="The number of MS1 isotopes used for extraction" help=""/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	399 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	400 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	401 <expand macro="list_string_san" name="test"/>
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	402 </param>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	403 </expand>
11 48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	404 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	405 <option value="out_features_FLAG">out_features (output file)</option>
48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	406 <option value="out_tsv_FLAG">out_tsv (TSV output file (mProphet-compatible TSV file))</option>
48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	407 <option value="out_osw_FLAG">out_osw (OSW output file (PyProphet-compatible SQLite file))</option>
48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	408 <option value="out_chrom_FLAG">out_chrom (Also output all computed chromatograms output in mzML (chrom.mzML) or sqMass (SQLite format))</option>
48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	409 <option value="out_qc_FLAG">out_qc (Optional QC meta data (charge distribution in MS1))</option>
48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	410 <option value="irt_mzml_FLAG">irt_mzml (Chromatogram mzML containing the iRT peptides)</option>
48e2d8b51c8a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 10 diff changeset	411 <option value="irt_trafo_FLAG">irt_trafo (Transformation file for RT transform)</option>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	412 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	413 </param>
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	414 </inputs>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	415 <outputs>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	416 <data name="out_features" label="${tool.name} on ${on_string}: out_features" format="featurexml">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	417 <filter>OPTIONAL_OUTPUTS is not None and "out_features_FLAG" in OPTIONAL_OUTPUTS</filter>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	418 </data>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	419 <data name="out_tsv" label="${tool.name} on ${on_string}: out_tsv" format="tabular">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	420 <filter>OPTIONAL_OUTPUTS is not None and "out_tsv_FLAG" in OPTIONAL_OUTPUTS</filter>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	421 </data>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	422 <data name="out_osw" label="${tool.name} on ${on_string}: out_osw" format="osw">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	423 <filter>OPTIONAL_OUTPUTS is not None and "out_osw_FLAG" in OPTIONAL_OUTPUTS</filter>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	424 </data>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	425 <data name="out_chrom" label="${tool.name} on ${on_string}: out_chrom" format="mzml">
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	426 <change_format>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	427 <when input="adv_opts.out_chrom_type" value="sqMass" format="sqmass"/>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	428 </change_format>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	429 <filter>OPTIONAL_OUTPUTS is not None and "out_chrom_FLAG" in OPTIONAL_OUTPUTS</filter>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	430 </data>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	431 <data name="out_qc" label="${tool.name} on ${on_string}: out_qc" format="json">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	432 <filter>OPTIONAL_OUTPUTS is not None and "out_qc_FLAG" in OPTIONAL_OUTPUTS</filter>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	433 </data>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	434 <data name="Debugging_irt_mzml" label="${tool.name} on ${on_string}: Debugging:irt_mzml" format="mzml">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	435 <filter>OPTIONAL_OUTPUTS is not None and "irt_mzml_FLAG" in OPTIONAL_OUTPUTS</filter>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	436 </data>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	437 <data name="Debugging_irt_trafo" label="${tool.name} on ${on_string}: Debugging:irt_trafo" format="trafoxml">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	438 <filter>OPTIONAL_OUTPUTS is not None and "irt_trafo_FLAG" in OPTIONAL_OUTPUTS</filter>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	439 </data>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	440 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	441 <filter>OPTIONAL_OUTPUTS is None</filter>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	442 </data>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	443 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	444 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	445 </data>
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	446 </outputs>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	447 <tests>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	448 <!-- TOPP_OpenSwathWorkflow_1 -->
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	449 <test expect_num_outputs="4">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	450 <section name="adv_opts">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	451 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	452 <param name="sort_swath_maps" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	453 <param name="enable_ms1" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	454 <param name="enable_ipf" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	455 <param name="out_chrom_type" value="mzML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	456 <param name="min_upper_edge_dist" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	457 <param name="extra_rt_extraction_window" value="0.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	458 <param name="mz_extraction_window_unit" value="Th"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	459 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	460 <param name="use_ms1_ion_mobility" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	461 <param name="matching_window_only" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	462 <param name="irt_mz_extraction_window" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	463 <param name="irt_mz_extraction_window_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	464 <param name="irt_im_extraction_window" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	465 <param name="min_rsq" value="0.95"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	466 <param name="min_coverage" value="0.6"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	467 <param name="split_file_input" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	468 <param name="use_elution_model_score" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	469 <param name="readOptions" value="normal"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	470 <param name="mz_correction_function" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	471 <param name="extraction_function" value="tophat"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	472 <param name="batchSize" value="1000"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	473 <param name="ms1_isotopes" value="0"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	474 <param name="force" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	475 <param name="test" value="true"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	476 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	477 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	478 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	479 <output name="out_features" value="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	480 <output name="out_chrom" value="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	481 <output name="out_qc" value="OpenSwathWorkflow_1_output.json" compare="sim_size" delta_frac="0.7" ftype="json"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	482 <param name="sonar" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	483 <param name="pasef" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	484 <param name="rt_extraction_window" value="600.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	485 <param name="ion_mobility_window" value="-1.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	486 <param name="mz_extraction_window" value="0.05"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	487 <param name="mz_extraction_window_ms1" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	488 <param name="im_extraction_window_ms1" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	489 <section name="Debugging"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	490 <section name="Calibration">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	491 <param name="ms1_im_calibration" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	492 <param name="im_correction_function" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	493 <param name="debug_im_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	494 <param name="debug_mz_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	495 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	496 <section name="Library">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	497 <param name="retentionTimeInterpretation" value="iRT"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	498 <param name="override_group_label_check" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	499 <param name="force_invalid_mods" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	500 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	501 <section name="RTNormalization">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	502 <param name="alignmentMethod" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	503 <param name="outlierMethod" value="iter_residual"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	504 <param name="useIterativeChauvenet" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	505 <param name="RANSACMaxIterations" value="1000"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	506 <param name="RANSACMaxPercentRTThreshold" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	507 <param name="RANSACSamplingSize" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	508 <param name="estimateBestPeptides" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	509 <param name="InitialQualityCutoff" value="0.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	510 <param name="OverallQualityCutoff" value="5.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	511 <param name="NrRTBins" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	512 <param name="MinPeptidesPerBin" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	513 <param name="MinBinsFilled" value="8"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	514 <section name="lowess">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	515 <param name="span" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	516 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	517 <section name="b_spline">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	518 <param name="num_nodes" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	519 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	520 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	521 <section name="Scoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	522 <param name="stop_report_after_feature" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	523 <param name="rt_normalization_factor" value="100.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	524 <param name="quantification_cutoff" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	525 <param name="write_convex_hull" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	526 <param name="spectrum_addition_method" value="simple"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	527 <param name="add_up_spectra" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	528 <param name="spacing_for_spectra_resampling" value="0.005"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	529 <param name="uis_threshold_sn" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	530 <param name="uis_threshold_peak_area" value="0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	531 <param name="scoring_model" value="default"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	532 <param name="im_extra_drift" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	533 <param name="strict" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	534 <section name="TransitionGroupPicker">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	535 <param name="stop_after_feature" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	536 <param name="min_peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	537 <param name="peak_integration" value="original"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	538 <param name="background_subtraction" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	539 <param name="recalculate_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	540 <param name="use_precursors" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	541 <param name="use_consensus" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	542 <param name="recalculate_peaks_max_z" value="0.75"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	543 <param name="minimal_quality" value="-1.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	544 <param name="resample_boundary" value="15.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	545 <param name="compute_peak_quality" value="true"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	546 <param name="compute_peak_shape_metrics" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	547 <param name="compute_total_mi" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	548 <param name="boundary_selection_method" value="largest"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	549 <section name="PeakPickerMRM">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	550 <param name="sgolay_frame_length" value="11"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	551 <param name="sgolay_polynomial_order" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	552 <param name="gauss_width" value="30.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	553 <param name="use_gauss" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	554 <param name="peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	555 <param name="signal_to_noise" value="0.1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	556 <param name="write_sn_log_messages" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	557 <param name="remove_overlapping_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	558 <param name="method" value="corrected"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	559 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	560 <section name="PeakIntegrator">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	561 <param name="integration_type" value="intensity_sum"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	562 <param name="baseline_type" value="base_to_base"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	563 <param name="fit_EMG" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	564 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	565 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	566 <section name="DIAScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	567 <param name="dia_extraction_window" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	568 <param name="dia_extraction_unit" value="Th"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	569 <param name="dia_centroided" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	570 <param name="dia_byseries_intensity_min" value="300.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	571 <param name="dia_byseries_ppm_diff" value="10.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	572 <param name="dia_nr_isotopes" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	573 <param name="dia_nr_charges" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	574 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	575 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	576 <section name="EMGScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	577 <param name="max_iteration" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	578 <param name="init_mom" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	579 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	580 <section name="Scores">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	581 <param name="use_shape_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	582 <param name="use_coelution_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	583 <param name="use_rt_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	584 <param name="use_library_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	585 <param name="use_intensity_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	586 <param name="use_nr_peaks_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	587 <param name="use_total_xic_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	588 <param name="use_total_mi_score" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	589 <param name="use_sn_score" value="true"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	590 <param name="use_mi_score" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	591 <param name="use_dia_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	592 <param name="use_ms1_correlation" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	593 <param name="use_sonar_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	594 <param name="use_ion_mobility_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	595 <param name="use_ms1_fullscan" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	596 <param name="use_ms1_mi" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	597 <param name="use_uis_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	598 <param name="use_ionseries_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	599 <param name="use_ms2_isotope_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	600 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	601 </section>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	602 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,out_qc_FLAG"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	603 <output name="ctd_out" ftype="xml">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	604 <assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	605 <is_valid_xml/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	606 </assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	607 </output>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	608 <assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	609 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	610 </assert_stdout>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	611 </test>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	612 <!-- TOPP_OpenSwathWorkflow_2 -->
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	613 <test expect_num_outputs="3">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	614 <section name="adv_opts">
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	615 <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	616 <param name="sort_swath_maps" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	617 <param name="enable_ms1" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	618 <param name="enable_ipf" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	619 <param name="out_chrom_type" value="mzML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	620 <param name="min_upper_edge_dist" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	621 <param name="extra_rt_extraction_window" value="0.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	622 <param name="mz_extraction_window_unit" value="Th"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	623 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	624 <param name="use_ms1_ion_mobility" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	625 <param name="matching_window_only" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	626 <param name="irt_mz_extraction_window" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	627 <param name="irt_mz_extraction_window_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	628 <param name="irt_im_extraction_window" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	629 <param name="min_rsq" value="0.95"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	630 <param name="min_coverage" value="0.6"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	631 <param name="split_file_input" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	632 <param name="use_elution_model_score" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	633 <param name="readOptions" value="normal"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	634 <param name="mz_correction_function" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	635 <param name="extraction_function" value="tophat"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	636 <param name="batchSize" value="1000"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	637 <param name="ms1_isotopes" value="0"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	638 <param name="force" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	639 <param name="test" value="true"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	640 </section>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	641 <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	642 <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	643 <output name="out_features" value="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	644 <output name="out_chrom" value="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	645 <param name="sonar" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	646 <param name="pasef" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	647 <param name="rt_extraction_window" value="600.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	648 <param name="ion_mobility_window" value="-1.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	649 <param name="mz_extraction_window" value="0.05"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	650 <param name="mz_extraction_window_ms1" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	651 <param name="im_extraction_window_ms1" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	652 <section name="Debugging"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	653 <section name="Calibration">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	654 <param name="ms1_im_calibration" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	655 <param name="im_correction_function" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	656 <param name="debug_im_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	657 <param name="debug_mz_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	658 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	659 <section name="Library">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	660 <param name="retentionTimeInterpretation" value="iRT"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	661 <param name="override_group_label_check" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	662 <param name="force_invalid_mods" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	663 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	664 <section name="RTNormalization">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	665 <param name="alignmentMethod" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	666 <param name="outlierMethod" value="iter_residual"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	667 <param name="useIterativeChauvenet" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	668 <param name="RANSACMaxIterations" value="1000"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	669 <param name="RANSACMaxPercentRTThreshold" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	670 <param name="RANSACSamplingSize" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	671 <param name="estimateBestPeptides" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	672 <param name="InitialQualityCutoff" value="0.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	673 <param name="OverallQualityCutoff" value="5.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	674 <param name="NrRTBins" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	675 <param name="MinPeptidesPerBin" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	676 <param name="MinBinsFilled" value="8"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	677 <section name="lowess">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	678 <param name="span" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	679 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	680 <section name="b_spline">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	681 <param name="num_nodes" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	682 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	683 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	684 <section name="Scoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	685 <param name="stop_report_after_feature" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	686 <param name="rt_normalization_factor" value="100.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	687 <param name="quantification_cutoff" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	688 <param name="write_convex_hull" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	689 <param name="spectrum_addition_method" value="simple"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	690 <param name="add_up_spectra" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	691 <param name="spacing_for_spectra_resampling" value="0.005"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	692 <param name="uis_threshold_sn" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	693 <param name="uis_threshold_peak_area" value="0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	694 <param name="scoring_model" value="default"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	695 <param name="im_extra_drift" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	696 <param name="strict" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	697 <section name="TransitionGroupPicker">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	698 <param name="stop_after_feature" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	699 <param name="min_peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	700 <param name="peak_integration" value="original"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	701 <param name="background_subtraction" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	702 <param name="recalculate_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	703 <param name="use_precursors" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	704 <param name="use_consensus" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	705 <param name="recalculate_peaks_max_z" value="0.75"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	706 <param name="minimal_quality" value="-1.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	707 <param name="resample_boundary" value="15.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	708 <param name="compute_peak_quality" value="true"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	709 <param name="compute_peak_shape_metrics" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	710 <param name="compute_total_mi" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	711 <param name="boundary_selection_method" value="largest"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	712 <section name="PeakPickerMRM">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	713 <param name="sgolay_frame_length" value="11"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	714 <param name="sgolay_polynomial_order" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	715 <param name="gauss_width" value="30.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	716 <param name="use_gauss" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	717 <param name="peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	718 <param name="signal_to_noise" value="0.1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	719 <param name="write_sn_log_messages" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	720 <param name="remove_overlapping_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	721 <param name="method" value="corrected"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	722 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	723 <section name="PeakIntegrator">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	724 <param name="integration_type" value="intensity_sum"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	725 <param name="baseline_type" value="base_to_base"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	726 <param name="fit_EMG" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	727 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	728 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	729 <section name="DIAScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	730 <param name="dia_extraction_window" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	731 <param name="dia_extraction_unit" value="Th"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	732 <param name="dia_centroided" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	733 <param name="dia_byseries_intensity_min" value="300.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	734 <param name="dia_byseries_ppm_diff" value="10.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	735 <param name="dia_nr_isotopes" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	736 <param name="dia_nr_charges" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	737 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	738 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	739 <section name="EMGScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	740 <param name="max_iteration" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	741 <param name="init_mom" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	742 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	743 <section name="Scores">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	744 <param name="use_shape_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	745 <param name="use_coelution_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	746 <param name="use_rt_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	747 <param name="use_library_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	748 <param name="use_intensity_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	749 <param name="use_nr_peaks_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	750 <param name="use_total_xic_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	751 <param name="use_total_mi_score" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	752 <param name="use_sn_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	753 <param name="use_mi_score" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	754 <param name="use_dia_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	755 <param name="use_ms1_correlation" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	756 <param name="use_sonar_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	757 <param name="use_ion_mobility_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	758 <param name="use_ms1_fullscan" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	759 <param name="use_ms1_mi" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	760 <param name="use_uis_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	761 <param name="use_ionseries_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	762 <param name="use_ms2_isotope_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	763 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	764 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	765 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	766 <output name="ctd_out" ftype="xml">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	767 <assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	768 <is_valid_xml/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	769 </assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	770 </output>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	771 <assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	772 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	773 </assert_stdout>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	774 </test>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	775 <!-- TOPP_OpenSwathWorkflow_3 -->
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	776 <test expect_num_outputs="3">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	777 <section name="adv_opts">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	778 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	779 <param name="sort_swath_maps" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	780 <param name="enable_ms1" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	781 <param name="enable_ipf" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	782 <param name="out_chrom_type" value="mzML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	783 <param name="min_upper_edge_dist" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	784 <param name="extra_rt_extraction_window" value="0.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	785 <param name="mz_extraction_window_unit" value="Th"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	786 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	787 <param name="use_ms1_ion_mobility" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	788 <param name="matching_window_only" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	789 <param name="irt_mz_extraction_window" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	790 <param name="irt_mz_extraction_window_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	791 <param name="irt_im_extraction_window" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	792 <param name="min_rsq" value="0.95"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	793 <param name="min_coverage" value="0.6"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	794 <param name="split_file_input" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	795 <param name="use_elution_model_score" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	796 <param name="readOptions" value="normal"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	797 <param name="mz_correction_function" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	798 <param name="extraction_function" value="tophat"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	799 <param name="batchSize" value="1000"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	800 <param name="ms1_isotopes" value="0"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	801 <param name="force" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	802 <param name="test" value="true"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	803 </section>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	804 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	805 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	806 <output name="out_features" value="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	807 <output name="out_chrom" value="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	808 <param name="sonar" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	809 <param name="pasef" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	810 <param name="rt_extraction_window" value="600.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	811 <param name="ion_mobility_window" value="-1.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	812 <param name="mz_extraction_window" value="0.05"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	813 <param name="mz_extraction_window_ms1" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	814 <param name="im_extraction_window_ms1" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	815 <section name="Debugging"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	816 <section name="Calibration">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	817 <param name="ms1_im_calibration" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	818 <param name="im_correction_function" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	819 <param name="debug_im_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	820 <param name="debug_mz_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	821 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	822 <section name="Library">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	823 <param name="retentionTimeInterpretation" value="iRT"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	824 <param name="override_group_label_check" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	825 <param name="force_invalid_mods" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	826 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	827 <section name="RTNormalization">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	828 <param name="alignmentMethod" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	829 <param name="outlierMethod" value="iter_residual"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	830 <param name="useIterativeChauvenet" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	831 <param name="RANSACMaxIterations" value="1000"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	832 <param name="RANSACMaxPercentRTThreshold" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	833 <param name="RANSACSamplingSize" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	834 <param name="estimateBestPeptides" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	835 <param name="InitialQualityCutoff" value="0.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	836 <param name="OverallQualityCutoff" value="5.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	837 <param name="NrRTBins" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	838 <param name="MinPeptidesPerBin" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	839 <param name="MinBinsFilled" value="8"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	840 <section name="lowess">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	841 <param name="span" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	842 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	843 <section name="b_spline">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	844 <param name="num_nodes" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	845 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	846 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	847 <section name="Scoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	848 <param name="stop_report_after_feature" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	849 <param name="rt_normalization_factor" value="100.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	850 <param name="quantification_cutoff" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	851 <param name="write_convex_hull" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	852 <param name="spectrum_addition_method" value="simple"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	853 <param name="add_up_spectra" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	854 <param name="spacing_for_spectra_resampling" value="0.005"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	855 <param name="uis_threshold_sn" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	856 <param name="uis_threshold_peak_area" value="0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	857 <param name="scoring_model" value="default"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	858 <param name="im_extra_drift" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	859 <param name="strict" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	860 <section name="TransitionGroupPicker">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	861 <param name="stop_after_feature" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	862 <param name="min_peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	863 <param name="peak_integration" value="original"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	864 <param name="background_subtraction" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	865 <param name="recalculate_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	866 <param name="use_precursors" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	867 <param name="use_consensus" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	868 <param name="recalculate_peaks_max_z" value="0.75"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	869 <param name="minimal_quality" value="-1.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	870 <param name="resample_boundary" value="15.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	871 <param name="compute_peak_quality" value="true"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	872 <param name="compute_peak_shape_metrics" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	873 <param name="compute_total_mi" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	874 <param name="boundary_selection_method" value="largest"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	875 <section name="PeakPickerMRM">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	876 <param name="sgolay_frame_length" value="11"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	877 <param name="sgolay_polynomial_order" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	878 <param name="gauss_width" value="30.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	879 <param name="use_gauss" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	880 <param name="peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	881 <param name="signal_to_noise" value="0.1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	882 <param name="write_sn_log_messages" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	883 <param name="remove_overlapping_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	884 <param name="method" value="corrected"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	885 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	886 <section name="PeakIntegrator">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	887 <param name="integration_type" value="intensity_sum"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	888 <param name="baseline_type" value="base_to_base"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	889 <param name="fit_EMG" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	890 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	891 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	892 <section name="DIAScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	893 <param name="dia_extraction_window" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	894 <param name="dia_extraction_unit" value="Th"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	895 <param name="dia_centroided" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	896 <param name="dia_byseries_intensity_min" value="300.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	897 <param name="dia_byseries_ppm_diff" value="10.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	898 <param name="dia_nr_isotopes" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	899 <param name="dia_nr_charges" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	900 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	901 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	902 <section name="EMGScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	903 <param name="max_iteration" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	904 <param name="init_mom" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	905 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	906 <section name="Scores">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	907 <param name="use_shape_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	908 <param name="use_coelution_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	909 <param name="use_rt_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	910 <param name="use_library_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	911 <param name="use_intensity_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	912 <param name="use_nr_peaks_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	913 <param name="use_total_xic_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	914 <param name="use_total_mi_score" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	915 <param name="use_sn_score" value="true"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	916 <param name="use_mi_score" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	917 <param name="use_dia_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	918 <param name="use_ms1_correlation" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	919 <param name="use_sonar_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	920 <param name="use_ion_mobility_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	921 <param name="use_ms1_fullscan" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	922 <param name="use_ms1_mi" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	923 <param name="use_uis_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	924 <param name="use_ionseries_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	925 <param name="use_ms2_isotope_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	926 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	927 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	928 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	929 <output name="ctd_out" ftype="xml">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	930 <assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	931 <is_valid_xml/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	932 </assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	933 </output>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	934 <assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	935 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	936 </assert_stdout>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	937 </test>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	938 <!-- TOPP_OpenSwathWorkflow_4 -->
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	939 <test expect_num_outputs="3">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	940 <section name="adv_opts">
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	941 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	942 <param name="sort_swath_maps" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	943 <param name="enable_ms1" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	944 <param name="enable_ipf" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	945 <param name="out_chrom_type" value="mzML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	946 <param name="min_upper_edge_dist" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	947 <param name="extra_rt_extraction_window" value="0.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	948 <param name="mz_extraction_window_unit" value="Th"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	949 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	950 <param name="use_ms1_ion_mobility" value="true"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	951 <param name="matching_window_only" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	952 <param name="irt_mz_extraction_window" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	953 <param name="irt_mz_extraction_window_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	954 <param name="irt_im_extraction_window" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	955 <param name="min_rsq" value="0.95"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	956 <param name="min_coverage" value="0.6"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	957 <param name="split_file_input" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	958 <param name="use_elution_model_score" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	959 <param name="readOptions" value="normal"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	960 <param name="mz_correction_function" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	961 <param name="extraction_function" value="tophat"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	962 <param name="batchSize" value="1000"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	963 <param name="ms1_isotopes" value="0"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	964 <param name="force" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	965 <param name="test" value="true"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	966 </section>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	967 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	968 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	969 <output name="out_tsv" value="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	970 <output name="out_chrom" value="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	971 <param name="sonar" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	972 <param name="pasef" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	973 <param name="rt_extraction_window" value="600.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	974 <param name="ion_mobility_window" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	975 <param name="mz_extraction_window" value="0.05"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	976 <param name="mz_extraction_window_ms1" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	977 <param name="im_extraction_window_ms1" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	978 <section name="Debugging"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	979 <section name="Calibration">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	980 <param name="ms1_im_calibration" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	981 <param name="im_correction_function" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	982 <param name="debug_im_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	983 <param name="debug_mz_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	984 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	985 <section name="Library">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	986 <param name="retentionTimeInterpretation" value="iRT"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	987 <param name="override_group_label_check" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	988 <param name="force_invalid_mods" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	989 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	990 <section name="RTNormalization">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	991 <param name="alignmentMethod" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	992 <param name="outlierMethod" value="iter_residual"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	993 <param name="useIterativeChauvenet" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	994 <param name="RANSACMaxIterations" value="1000"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	995 <param name="RANSACMaxPercentRTThreshold" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	996 <param name="RANSACSamplingSize" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	997 <param name="estimateBestPeptides" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	998 <param name="InitialQualityCutoff" value="0.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	999 <param name="OverallQualityCutoff" value="5.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1000 <param name="NrRTBins" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1001 <param name="MinPeptidesPerBin" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1002 <param name="MinBinsFilled" value="8"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1003 <section name="lowess">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1004 <param name="span" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1005 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1006 <section name="b_spline">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1007 <param name="num_nodes" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1008 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1009 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1010 <section name="Scoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1011 <param name="stop_report_after_feature" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1012 <param name="rt_normalization_factor" value="100.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1013 <param name="quantification_cutoff" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1014 <param name="write_convex_hull" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1015 <param name="spectrum_addition_method" value="simple"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1016 <param name="add_up_spectra" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1017 <param name="spacing_for_spectra_resampling" value="0.005"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1018 <param name="uis_threshold_sn" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1019 <param name="uis_threshold_peak_area" value="0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1020 <param name="scoring_model" value="default"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1021 <param name="im_extra_drift" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1022 <param name="strict" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1023 <section name="TransitionGroupPicker">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1024 <param name="stop_after_feature" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1025 <param name="min_peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1026 <param name="peak_integration" value="original"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1027 <param name="background_subtraction" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1028 <param name="recalculate_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1029 <param name="use_precursors" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1030 <param name="use_consensus" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1031 <param name="recalculate_peaks_max_z" value="0.75"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1032 <param name="minimal_quality" value="-1.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1033 <param name="resample_boundary" value="15.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1034 <param name="compute_peak_quality" value="true"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1035 <param name="compute_peak_shape_metrics" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1036 <param name="compute_total_mi" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1037 <param name="boundary_selection_method" value="largest"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1038 <section name="PeakPickerMRM">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1039 <param name="sgolay_frame_length" value="11"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1040 <param name="sgolay_polynomial_order" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1041 <param name="gauss_width" value="30.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1042 <param name="use_gauss" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1043 <param name="peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1044 <param name="signal_to_noise" value="0.1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1045 <param name="write_sn_log_messages" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1046 <param name="remove_overlapping_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1047 <param name="method" value="corrected"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1048 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1049 <section name="PeakIntegrator">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1050 <param name="integration_type" value="intensity_sum"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1051 <param name="baseline_type" value="base_to_base"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1052 <param name="fit_EMG" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1053 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1054 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1055 <section name="DIAScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1056 <param name="dia_extraction_window" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1057 <param name="dia_extraction_unit" value="Th"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1058 <param name="dia_centroided" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1059 <param name="dia_byseries_intensity_min" value="300.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1060 <param name="dia_byseries_ppm_diff" value="10.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1061 <param name="dia_nr_isotopes" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1062 <param name="dia_nr_charges" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1063 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1064 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1065 <section name="EMGScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1066 <param name="max_iteration" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1067 <param name="init_mom" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1068 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1069 <section name="Scores">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1070 <param name="use_shape_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1071 <param name="use_coelution_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1072 <param name="use_rt_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1073 <param name="use_library_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1074 <param name="use_intensity_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1075 <param name="use_nr_peaks_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1076 <param name="use_total_xic_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1077 <param name="use_total_mi_score" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1078 <param name="use_sn_score" value="true"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1079 <param name="use_mi_score" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1080 <param name="use_dia_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1081 <param name="use_ms1_correlation" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1082 <param name="use_sonar_scores" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1083 <param name="use_ion_mobility_scores" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1084 <param name="use_ms1_fullscan" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1085 <param name="use_ms1_mi" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1086 <param name="use_uis_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1087 <param name="use_ionseries_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1088 <param name="use_ms2_isotope_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1089 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1090 </section>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1091 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG,out_chrom_FLAG"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1092 <output name="ctd_out" ftype="xml">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1093 <assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1094 <is_valid_xml/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1095 </assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1096 </output>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1097 <assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1098 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1099 </assert_stdout>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1100 </test>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1101 <!-- TOPP_OpenSwathWorkflow_5 -->
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1102 <test expect_num_outputs="3">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1103 <section name="adv_opts">
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1104 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1105 <param name="sort_swath_maps" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1106 <param name="enable_ms1" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1107 <param name="enable_ipf" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1108 <param name="out_chrom_type" value="mzML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1109 <param name="min_upper_edge_dist" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1110 <param name="extra_rt_extraction_window" value="0.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1111 <param name="mz_extraction_window_unit" value="Th"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1112 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1113 <param name="use_ms1_ion_mobility" value="true"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1114 <param name="matching_window_only" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1115 <param name="irt_mz_extraction_window" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1116 <param name="irt_mz_extraction_window_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1117 <param name="irt_im_extraction_window" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1118 <param name="min_rsq" value="0.95"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1119 <param name="min_coverage" value="0.6"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1120 <param name="split_file_input" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1121 <param name="use_elution_model_score" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1122 <param name="readOptions" value="cache"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1123 <param name="mz_correction_function" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1124 <param name="extraction_function" value="tophat"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1125 <param name="batchSize" value="1000"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1126 <param name="ms1_isotopes" value="0"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1127 <param name="force" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1128 <param name="test" value="true"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1129 </section>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1130 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1131 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1132 <output name="out_features" value="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1133 <output name="out_chrom" value="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1134 <param name="sonar" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1135 <param name="pasef" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1136 <param name="rt_extraction_window" value="600.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1137 <param name="ion_mobility_window" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1138 <param name="mz_extraction_window" value="0.05"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1139 <param name="mz_extraction_window_ms1" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1140 <param name="im_extraction_window_ms1" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1141 <section name="Debugging"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1142 <section name="Calibration">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1143 <param name="ms1_im_calibration" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1144 <param name="im_correction_function" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1145 <param name="debug_im_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1146 <param name="debug_mz_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1147 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1148 <section name="Library">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1149 <param name="retentionTimeInterpretation" value="iRT"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1150 <param name="override_group_label_check" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1151 <param name="force_invalid_mods" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1152 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1153 <section name="RTNormalization">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1154 <param name="alignmentMethod" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1155 <param name="outlierMethod" value="iter_residual"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1156 <param name="useIterativeChauvenet" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1157 <param name="RANSACMaxIterations" value="1000"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1158 <param name="RANSACMaxPercentRTThreshold" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1159 <param name="RANSACSamplingSize" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1160 <param name="estimateBestPeptides" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1161 <param name="InitialQualityCutoff" value="0.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1162 <param name="OverallQualityCutoff" value="5.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1163 <param name="NrRTBins" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1164 <param name="MinPeptidesPerBin" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1165 <param name="MinBinsFilled" value="8"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1166 <section name="lowess">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1167 <param name="span" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1168 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1169 <section name="b_spline">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1170 <param name="num_nodes" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1171 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1172 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1173 <section name="Scoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1174 <param name="stop_report_after_feature" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1175 <param name="rt_normalization_factor" value="100.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1176 <param name="quantification_cutoff" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1177 <param name="write_convex_hull" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1178 <param name="spectrum_addition_method" value="simple"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1179 <param name="add_up_spectra" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1180 <param name="spacing_for_spectra_resampling" value="0.005"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1181 <param name="uis_threshold_sn" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1182 <param name="uis_threshold_peak_area" value="0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1183 <param name="scoring_model" value="default"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1184 <param name="im_extra_drift" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1185 <param name="strict" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1186 <section name="TransitionGroupPicker">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1187 <param name="stop_after_feature" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1188 <param name="min_peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1189 <param name="peak_integration" value="original"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1190 <param name="background_subtraction" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1191 <param name="recalculate_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1192 <param name="use_precursors" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1193 <param name="use_consensus" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1194 <param name="recalculate_peaks_max_z" value="0.75"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1195 <param name="minimal_quality" value="-1.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1196 <param name="resample_boundary" value="15.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1197 <param name="compute_peak_quality" value="true"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1198 <param name="compute_peak_shape_metrics" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1199 <param name="compute_total_mi" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1200 <param name="boundary_selection_method" value="largest"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1201 <section name="PeakPickerMRM">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1202 <param name="sgolay_frame_length" value="11"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1203 <param name="sgolay_polynomial_order" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1204 <param name="gauss_width" value="30.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1205 <param name="use_gauss" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1206 <param name="peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1207 <param name="signal_to_noise" value="0.1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1208 <param name="write_sn_log_messages" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1209 <param name="remove_overlapping_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1210 <param name="method" value="corrected"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1211 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1212 <section name="PeakIntegrator">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1213 <param name="integration_type" value="intensity_sum"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1214 <param name="baseline_type" value="base_to_base"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1215 <param name="fit_EMG" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1216 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1217 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1218 <section name="DIAScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1219 <param name="dia_extraction_window" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1220 <param name="dia_extraction_unit" value="Th"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1221 <param name="dia_centroided" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1222 <param name="dia_byseries_intensity_min" value="300.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1223 <param name="dia_byseries_ppm_diff" value="10.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1224 <param name="dia_nr_isotopes" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1225 <param name="dia_nr_charges" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1226 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1227 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1228 <section name="EMGScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1229 <param name="max_iteration" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1230 <param name="init_mom" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1231 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1232 <section name="Scores">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1233 <param name="use_shape_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1234 <param name="use_coelution_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1235 <param name="use_rt_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1236 <param name="use_library_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1237 <param name="use_intensity_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1238 <param name="use_nr_peaks_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1239 <param name="use_total_xic_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1240 <param name="use_total_mi_score" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1241 <param name="use_sn_score" value="true"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1242 <param name="use_mi_score" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1243 <param name="use_dia_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1244 <param name="use_ms1_correlation" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1245 <param name="use_sonar_scores" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1246 <param name="use_ion_mobility_scores" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1247 <param name="use_ms1_fullscan" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1248 <param name="use_ms1_mi" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1249 <param name="use_uis_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1250 <param name="use_ionseries_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1251 <param name="use_ms2_isotope_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1252 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1253 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1254 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1255 <output name="ctd_out" ftype="xml">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1256 <assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1257 <is_valid_xml/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1258 </assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1259 </output>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1260 <assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1261 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1262 </assert_stdout>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1263 </test>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1264 <!-- TOPP_OpenSwathWorkflow_6 -->
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1265 <test expect_num_outputs="3">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1266 <section name="adv_opts">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1267 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1268 <param name="sort_swath_maps" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1269 <param name="enable_ms1" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1270 <param name="enable_ipf" value="true"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1271 <param name="out_chrom_type" value="mzML"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1272 <param name="min_upper_edge_dist" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1273 <param name="extra_rt_extraction_window" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1274 <param name="mz_extraction_window_unit" value="Th"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1275 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1276 <param name="use_ms1_ion_mobility" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1277 <param name="matching_window_only" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1278 <param name="irt_mz_extraction_window" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1279 <param name="irt_mz_extraction_window_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1280 <param name="irt_im_extraction_window" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1281 <param name="min_rsq" value="0.95"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1282 <param name="min_coverage" value="0.6"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1283 <param name="split_file_input" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1284 <param name="use_elution_model_score" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1285 <param name="readOptions" value="cacheWorkingInMemory"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1286 <param name="mz_correction_function" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1287 <param name="extraction_function" value="tophat"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1288 <param name="batchSize" value="1000"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1289 <param name="ms1_isotopes" value="0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1290 <param name="force" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1291 <param name="test" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1292 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1293 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1294 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1295 <output name="out_features" value="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1296 <output name="out_chrom" value="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1297 <param name="sonar" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1298 <param name="pasef" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1299 <param name="rt_extraction_window" value="600.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1300 <param name="ion_mobility_window" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1301 <param name="mz_extraction_window" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1302 <param name="mz_extraction_window_ms1" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1303 <param name="im_extraction_window_ms1" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1304 <section name="Debugging"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1305 <section name="Calibration">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1306 <param name="ms1_im_calibration" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1307 <param name="im_correction_function" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1308 <param name="debug_im_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1309 <param name="debug_mz_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1310 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1311 <section name="Library">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1312 <param name="retentionTimeInterpretation" value="iRT"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1313 <param name="override_group_label_check" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1314 <param name="force_invalid_mods" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1315 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1316 <section name="RTNormalization">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1317 <param name="alignmentMethod" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1318 <param name="outlierMethod" value="iter_residual"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1319 <param name="useIterativeChauvenet" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1320 <param name="RANSACMaxIterations" value="1000"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1321 <param name="RANSACMaxPercentRTThreshold" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1322 <param name="RANSACSamplingSize" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1323 <param name="estimateBestPeptides" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1324 <param name="InitialQualityCutoff" value="0.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1325 <param name="OverallQualityCutoff" value="5.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1326 <param name="NrRTBins" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1327 <param name="MinPeptidesPerBin" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1328 <param name="MinBinsFilled" value="8"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1329 <section name="lowess">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1330 <param name="span" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1331 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1332 <section name="b_spline">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1333 <param name="num_nodes" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1334 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1335 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1336 <section name="Scoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1337 <param name="stop_report_after_feature" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1338 <param name="rt_normalization_factor" value="100.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1339 <param name="quantification_cutoff" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1340 <param name="write_convex_hull" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1341 <param name="spectrum_addition_method" value="simple"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1342 <param name="add_up_spectra" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1343 <param name="spacing_for_spectra_resampling" value="0.005"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1344 <param name="uis_threshold_sn" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1345 <param name="uis_threshold_peak_area" value="0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1346 <param name="scoring_model" value="default"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1347 <param name="im_extra_drift" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1348 <param name="strict" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1349 <section name="TransitionGroupPicker">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1350 <param name="stop_after_feature" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1351 <param name="min_peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1352 <param name="peak_integration" value="original"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1353 <param name="background_subtraction" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1354 <param name="recalculate_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1355 <param name="use_precursors" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1356 <param name="use_consensus" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1357 <param name="recalculate_peaks_max_z" value="0.75"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1358 <param name="minimal_quality" value="-1.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1359 <param name="resample_boundary" value="15.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1360 <param name="compute_peak_quality" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1361 <param name="compute_peak_shape_metrics" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1362 <param name="compute_total_mi" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1363 <param name="boundary_selection_method" value="largest"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1364 <section name="PeakPickerMRM">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1365 <param name="sgolay_frame_length" value="11"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1366 <param name="sgolay_polynomial_order" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1367 <param name="gauss_width" value="30.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1368 <param name="use_gauss" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1369 <param name="peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1370 <param name="signal_to_noise" value="0.1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1371 <param name="write_sn_log_messages" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1372 <param name="remove_overlapping_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1373 <param name="method" value="corrected"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1374 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1375 <section name="PeakIntegrator">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1376 <param name="integration_type" value="intensity_sum"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1377 <param name="baseline_type" value="base_to_base"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1378 <param name="fit_EMG" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1379 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1380 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1381 <section name="DIAScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1382 <param name="dia_extraction_window" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1383 <param name="dia_extraction_unit" value="Th"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1384 <param name="dia_centroided" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1385 <param name="dia_byseries_intensity_min" value="300.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1386 <param name="dia_byseries_ppm_diff" value="10.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1387 <param name="dia_nr_isotopes" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1388 <param name="dia_nr_charges" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1389 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1390 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1391 <section name="EMGScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1392 <param name="max_iteration" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1393 <param name="init_mom" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1394 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1395 <section name="Scores">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1396 <param name="use_shape_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1397 <param name="use_coelution_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1398 <param name="use_rt_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1399 <param name="use_library_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1400 <param name="use_intensity_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1401 <param name="use_nr_peaks_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1402 <param name="use_total_xic_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1403 <param name="use_total_mi_score" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1404 <param name="use_sn_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1405 <param name="use_mi_score" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1406 <param name="use_dia_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1407 <param name="use_ms1_correlation" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1408 <param name="use_sonar_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1409 <param name="use_ion_mobility_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1410 <param name="use_ms1_fullscan" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1411 <param name="use_ms1_mi" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1412 <param name="use_uis_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1413 <param name="use_ionseries_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1414 <param name="use_ms2_isotope_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1415 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1416 </section>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1417 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1418 <output name="ctd_out" ftype="xml">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1419 <assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1420 <is_valid_xml/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1421 </assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1422 </output>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1423 <assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1424 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1425 </assert_stdout>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1426 </test>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1427 <!-- TOPP_OpenSwathWorkflow_7 -->
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1428 <test expect_num_outputs="3">
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1429 <section name="adv_opts">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1430 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1431 <param name="sort_swath_maps" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1432 <param name="enable_ms1" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1433 <param name="enable_ipf" value="true"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1434 <param name="out_chrom_type" value="mzML"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1435 <param name="min_upper_edge_dist" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1436 <param name="extra_rt_extraction_window" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1437 <param name="mz_extraction_window_unit" value="Th"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1438 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1439 <param name="use_ms1_ion_mobility" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1440 <param name="matching_window_only" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1441 <param name="irt_mz_extraction_window" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1442 <param name="irt_mz_extraction_window_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1443 <param name="irt_im_extraction_window" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1444 <param name="min_rsq" value="0.95"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1445 <param name="min_coverage" value="0.6"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1446 <param name="split_file_input" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1447 <param name="use_elution_model_score" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1448 <param name="readOptions" value="normal"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1449 <param name="mz_correction_function" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1450 <param name="extraction_function" value="tophat"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1451 <param name="batchSize" value="1000"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1452 <param name="ms1_isotopes" value="0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1453 <param name="force" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1454 <param name="test" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1455 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1456 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1457 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1458 <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1459 <output name="out_features" value="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1460 <output name="out_chrom" value="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1461 <param name="sonar" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1462 <param name="pasef" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1463 <param name="rt_extraction_window" value="600.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1464 <param name="ion_mobility_window" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1465 <param name="mz_extraction_window" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1466 <param name="mz_extraction_window_ms1" value="50.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1467 <param name="im_extraction_window_ms1" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1468 <section name="Debugging"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1469 <section name="Calibration">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1470 <param name="ms1_im_calibration" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1471 <param name="im_correction_function" value="linear"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1472 <param name="debug_im_file" value=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1473 <param name="debug_mz_file" value=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1474 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1475 <section name="Library">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1476 <param name="retentionTimeInterpretation" value="iRT"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1477 <param name="override_group_label_check" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1478 <param name="force_invalid_mods" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1479 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1480 <section name="RTNormalization">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1481 <param name="alignmentMethod" value="linear"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1482 <param name="outlierMethod" value="iter_residual"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1483 <param name="useIterativeChauvenet" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1484 <param name="RANSACMaxIterations" value="1000"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1485 <param name="RANSACMaxPercentRTThreshold" value="3"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1486 <param name="RANSACSamplingSize" value="10"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1487 <param name="estimateBestPeptides" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1488 <param name="InitialQualityCutoff" value="0.5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1489 <param name="OverallQualityCutoff" value="5.5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1490 <param name="NrRTBins" value="10"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1491 <param name="MinPeptidesPerBin" value="1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1492 <param name="MinBinsFilled" value="8"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1493 <section name="lowess">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1494 <param name="span" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1495 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1496 <section name="b_spline">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1497 <param name="num_nodes" value="5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1498 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1499 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1500 <section name="Scoring">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1501 <param name="stop_report_after_feature" value="5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1502 <param name="rt_normalization_factor" value="100.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1503 <param name="quantification_cutoff" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1504 <param name="write_convex_hull" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1505 <param name="spectrum_addition_method" value="simple"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1506 <param name="add_up_spectra" value="1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1507 <param name="spacing_for_spectra_resampling" value="0.005"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1508 <param name="uis_threshold_sn" value="-1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1509 <param name="uis_threshold_peak_area" value="0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1510 <param name="scoring_model" value="default"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1511 <param name="im_extra_drift" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1512 <param name="strict" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1513 <section name="TransitionGroupPicker">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1514 <param name="stop_after_feature" value="-1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1515 <param name="min_peak_width" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1516 <param name="peak_integration" value="original"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1517 <param name="background_subtraction" value="none"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1518 <param name="recalculate_peaks" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1519 <param name="use_precursors" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1520 <param name="use_consensus" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1521 <param name="recalculate_peaks_max_z" value="0.75"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1522 <param name="minimal_quality" value="-1.5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1523 <param name="resample_boundary" value="15.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1524 <param name="compute_peak_quality" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1525 <param name="compute_peak_shape_metrics" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1526 <param name="compute_total_mi" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1527 <param name="boundary_selection_method" value="largest"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1528 <section name="PeakPickerMRM">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1529 <param name="sgolay_frame_length" value="11"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1530 <param name="sgolay_polynomial_order" value="3"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1531 <param name="gauss_width" value="30.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1532 <param name="use_gauss" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1533 <param name="peak_width" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1534 <param name="signal_to_noise" value="0.1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1535 <param name="write_sn_log_messages" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1536 <param name="remove_overlapping_peaks" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1537 <param name="method" value="corrected"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1538 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1539 <section name="PeakIntegrator">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1540 <param name="integration_type" value="intensity_sum"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1541 <param name="baseline_type" value="base_to_base"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1542 <param name="fit_EMG" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1543 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1544 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1545 <section name="DIAScoring">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1546 <param name="dia_extraction_window" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1547 <param name="dia_extraction_unit" value="Th"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1548 <param name="dia_centroided" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1549 <param name="dia_byseries_intensity_min" value="300.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1550 <param name="dia_byseries_ppm_diff" value="10.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1551 <param name="dia_nr_isotopes" value="4"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1552 <param name="dia_nr_charges" value="4"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1553 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1554 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1555 <section name="EMGScoring">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1556 <param name="max_iteration" value="10"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1557 <param name="init_mom" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1558 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1559 <section name="Scores">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1560 <param name="use_shape_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1561 <param name="use_coelution_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1562 <param name="use_rt_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1563 <param name="use_library_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1564 <param name="use_intensity_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1565 <param name="use_nr_peaks_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1566 <param name="use_total_xic_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1567 <param name="use_total_mi_score" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1568 <param name="use_sn_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1569 <param name="use_mi_score" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1570 <param name="use_dia_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1571 <param name="use_ms1_correlation" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1572 <param name="use_sonar_scores" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1573 <param name="use_ion_mobility_scores" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1574 <param name="use_ms1_fullscan" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1575 <param name="use_ms1_mi" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1576 <param name="use_uis_scores" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1577 <param name="use_ionseries_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1578 <param name="use_ms2_isotope_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1579 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1580 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1581 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1582 <output name="ctd_out" ftype="xml">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1583 <assert_contents>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1584 <is_valid_xml/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1585 </assert_contents>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1586 </output>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1587 <assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1588 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1589 </assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1590 </test>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1591 <!-- TOPP_OpenSwathWorkflow_10 -->
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1592 <test expect_num_outputs="3">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1593 <section name="adv_opts">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1594 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1595 <param name="sort_swath_maps" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1596 <param name="enable_ms1" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1597 <param name="enable_ipf" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1598 <param name="out_chrom_type" value="mzML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1599 <param name="min_upper_edge_dist" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1600 <param name="extra_rt_extraction_window" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1601 <param name="mz_extraction_window_unit" value="Th"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1602 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1603 <param name="use_ms1_ion_mobility" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1604 <param name="matching_window_only" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1605 <param name="irt_mz_extraction_window" value="50.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1606 <param name="irt_mz_extraction_window_unit" value="ppm"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1607 <param name="irt_im_extraction_window" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1608 <param name="min_rsq" value="0.95"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1609 <param name="min_coverage" value="0.6"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1610 <param name="split_file_input" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1611 <param name="use_elution_model_score" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1612 <param name="readOptions" value="normal"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1613 <param name="mz_correction_function" value="none"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1614 <param name="extraction_function" value="tophat"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1615 <param name="batchSize" value="1000"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1616 <param name="ms1_isotopes" value="0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1617 <param name="force" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1618 <param name="test" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1619 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1620 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1621 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1622 <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1623 <output name="out_features" value="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1624 <output name="out_chrom" value="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1625 <param name="sonar" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1626 <param name="pasef" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1627 <param name="rt_extraction_window" value="600.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1628 <param name="ion_mobility_window" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1629 <param name="mz_extraction_window" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1630 <param name="mz_extraction_window_ms1" value="50.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1631 <param name="im_extraction_window_ms1" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1632 <section name="Debugging"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1633 <section name="Calibration">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1634 <param name="ms1_im_calibration" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1635 <param name="im_correction_function" value="linear"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1636 <param name="debug_im_file" value=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1637 <param name="debug_mz_file" value=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1638 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1639 <section name="Library">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1640 <param name="retentionTimeInterpretation" value="iRT"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1641 <param name="override_group_label_check" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1642 <param name="force_invalid_mods" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1643 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1644 <section name="RTNormalization">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1645 <param name="alignmentMethod" value="linear"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1646 <param name="outlierMethod" value="iter_residual"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1647 <param name="useIterativeChauvenet" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1648 <param name="RANSACMaxIterations" value="1000"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1649 <param name="RANSACMaxPercentRTThreshold" value="3"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1650 <param name="RANSACSamplingSize" value="10"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1651 <param name="estimateBestPeptides" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1652 <param name="InitialQualityCutoff" value="0.5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1653 <param name="OverallQualityCutoff" value="5.5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1654 <param name="NrRTBins" value="10"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1655 <param name="MinPeptidesPerBin" value="1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1656 <param name="MinBinsFilled" value="8"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1657 <section name="lowess">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1658 <param name="span" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1659 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1660 <section name="b_spline">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1661 <param name="num_nodes" value="5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1662 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1663 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1664 <section name="Scoring">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1665 <param name="stop_report_after_feature" value="5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1666 <param name="rt_normalization_factor" value="100.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1667 <param name="quantification_cutoff" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1668 <param name="write_convex_hull" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1669 <param name="spectrum_addition_method" value="simple"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1670 <param name="add_up_spectra" value="1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1671 <param name="spacing_for_spectra_resampling" value="0.005"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1672 <param name="uis_threshold_sn" value="-1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1673 <param name="uis_threshold_peak_area" value="0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1674 <param name="scoring_model" value="default"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1675 <param name="im_extra_drift" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1676 <param name="strict" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1677 <section name="TransitionGroupPicker">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1678 <param name="stop_after_feature" value="-1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1679 <param name="min_peak_width" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1680 <param name="peak_integration" value="original"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1681 <param name="background_subtraction" value="none"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1682 <param name="recalculate_peaks" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1683 <param name="use_precursors" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1684 <param name="use_consensus" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1685 <param name="recalculate_peaks_max_z" value="0.75"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1686 <param name="minimal_quality" value="-1.5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1687 <param name="resample_boundary" value="15.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1688 <param name="compute_peak_quality" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1689 <param name="compute_peak_shape_metrics" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1690 <param name="compute_total_mi" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1691 <param name="boundary_selection_method" value="largest"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1692 <section name="PeakPickerMRM">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1693 <param name="sgolay_frame_length" value="11"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1694 <param name="sgolay_polynomial_order" value="3"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1695 <param name="gauss_width" value="30.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1696 <param name="use_gauss" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1697 <param name="peak_width" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1698 <param name="signal_to_noise" value="0.1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1699 <param name="write_sn_log_messages" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1700 <param name="remove_overlapping_peaks" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1701 <param name="method" value="corrected"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1702 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1703 <section name="PeakIntegrator">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1704 <param name="integration_type" value="intensity_sum"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1705 <param name="baseline_type" value="base_to_base"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1706 <param name="fit_EMG" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1707 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1708 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1709 <section name="DIAScoring">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1710 <param name="dia_extraction_window" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1711 <param name="dia_extraction_unit" value="Th"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1712 <param name="dia_centroided" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1713 <param name="dia_byseries_intensity_min" value="300.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1714 <param name="dia_byseries_ppm_diff" value="10.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1715 <param name="dia_nr_isotopes" value="4"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1716 <param name="dia_nr_charges" value="4"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1717 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1718 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1719 <section name="EMGScoring">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1720 <param name="max_iteration" value="10"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1721 <param name="init_mom" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1722 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1723 <section name="Scores">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1724 <param name="use_shape_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1725 <param name="use_coelution_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1726 <param name="use_rt_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1727 <param name="use_library_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1728 <param name="use_intensity_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1729 <param name="use_nr_peaks_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1730 <param name="use_total_xic_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1731 <param name="use_total_mi_score" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1732 <param name="use_sn_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1733 <param name="use_mi_score" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1734 <param name="use_dia_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1735 <param name="use_ms1_correlation" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1736 <param name="use_sonar_scores" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1737 <param name="use_ion_mobility_scores" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1738 <param name="use_ms1_fullscan" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1739 <param name="use_ms1_mi" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1740 <param name="use_uis_scores" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1741 <param name="use_ionseries_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1742 <param name="use_ms2_isotope_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1743 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1744 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1745 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1746 <output name="ctd_out" ftype="xml">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1747 <assert_contents>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1748 <is_valid_xml/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1749 </assert_contents>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1750 </output>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1751 <assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1752 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1753 </assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1754 </test>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1755 <!-- TOPP_OpenSwathWorkflow_13 -->
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1756 <test expect_num_outputs="3">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1757 <section name="adv_opts">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1758 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1759 <param name="sort_swath_maps" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1760 <param name="enable_ms1" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1761 <param name="enable_ipf" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1762 <param name="out_chrom_type" value="mzML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1763 <param name="min_upper_edge_dist" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1764 <param name="extra_rt_extraction_window" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1765 <param name="mz_extraction_window_unit" value="Th"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1766 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1767 <param name="use_ms1_ion_mobility" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1768 <param name="matching_window_only" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1769 <param name="irt_mz_extraction_window" value="50.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1770 <param name="irt_mz_extraction_window_unit" value="ppm"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1771 <param name="irt_im_extraction_window" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1772 <param name="min_rsq" value="0.95"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1773 <param name="min_coverage" value="0.6"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1774 <param name="split_file_input" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1775 <param name="use_elution_model_score" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1776 <param name="readOptions" value="normal"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1777 <param name="mz_correction_function" value="none"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1778 <param name="extraction_function" value="tophat"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1779 <param name="batchSize" value="1000"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1780 <param name="ms1_isotopes" value="0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1781 <param name="force" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1782 <param name="test" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1783 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1784 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1785 <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1786 <output name="out_osw" value="OpenSwathWorkflow_13.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1787 <output name="out_chrom" value="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1788 <param name="sonar" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1789 <param name="pasef" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1790 <param name="rt_extraction_window" value="600.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1791 <param name="ion_mobility_window" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1792 <param name="mz_extraction_window" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1793 <param name="mz_extraction_window_ms1" value="50.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1794 <param name="im_extraction_window_ms1" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1795 <section name="Debugging"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1796 <section name="Calibration">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1797 <param name="ms1_im_calibration" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1798 <param name="im_correction_function" value="linear"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1799 <param name="debug_im_file" value=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1800 <param name="debug_mz_file" value=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1801 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1802 <section name="Library">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1803 <param name="retentionTimeInterpretation" value="iRT"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1804 <param name="override_group_label_check" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1805 <param name="force_invalid_mods" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1806 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1807 <section name="RTNormalization">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1808 <param name="alignmentMethod" value="linear"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1809 <param name="outlierMethod" value="iter_residual"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1810 <param name="useIterativeChauvenet" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1811 <param name="RANSACMaxIterations" value="1000"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1812 <param name="RANSACMaxPercentRTThreshold" value="3"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1813 <param name="RANSACSamplingSize" value="10"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1814 <param name="estimateBestPeptides" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1815 <param name="InitialQualityCutoff" value="0.5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1816 <param name="OverallQualityCutoff" value="5.5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1817 <param name="NrRTBins" value="10"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1818 <param name="MinPeptidesPerBin" value="1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1819 <param name="MinBinsFilled" value="8"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1820 <section name="lowess">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1821 <param name="span" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1822 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1823 <section name="b_spline">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1824 <param name="num_nodes" value="5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1825 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1826 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1827 <section name="Scoring">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1828 <param name="stop_report_after_feature" value="5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1829 <param name="rt_normalization_factor" value="100.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1830 <param name="quantification_cutoff" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1831 <param name="write_convex_hull" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1832 <param name="spectrum_addition_method" value="simple"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1833 <param name="add_up_spectra" value="1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1834 <param name="spacing_for_spectra_resampling" value="0.005"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1835 <param name="uis_threshold_sn" value="-1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1836 <param name="uis_threshold_peak_area" value="0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1837 <param name="scoring_model" value="default"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1838 <param name="im_extra_drift" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1839 <param name="strict" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1840 <section name="TransitionGroupPicker">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1841 <param name="stop_after_feature" value="-1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1842 <param name="min_peak_width" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1843 <param name="peak_integration" value="original"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1844 <param name="background_subtraction" value="none"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1845 <param name="recalculate_peaks" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1846 <param name="use_precursors" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1847 <param name="use_consensus" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1848 <param name="recalculate_peaks_max_z" value="0.75"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1849 <param name="minimal_quality" value="-1.5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1850 <param name="resample_boundary" value="15.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1851 <param name="compute_peak_quality" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1852 <param name="compute_peak_shape_metrics" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1853 <param name="compute_total_mi" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1854 <param name="boundary_selection_method" value="largest"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1855 <section name="PeakPickerMRM">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1856 <param name="sgolay_frame_length" value="11"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1857 <param name="sgolay_polynomial_order" value="3"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1858 <param name="gauss_width" value="30.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1859 <param name="use_gauss" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1860 <param name="peak_width" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1861 <param name="signal_to_noise" value="0.1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1862 <param name="write_sn_log_messages" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1863 <param name="remove_overlapping_peaks" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1864 <param name="method" value="corrected"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1865 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1866 <section name="PeakIntegrator">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1867 <param name="integration_type" value="intensity_sum"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1868 <param name="baseline_type" value="base_to_base"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1869 <param name="fit_EMG" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1870 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1871 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1872 <section name="DIAScoring">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1873 <param name="dia_extraction_window" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1874 <param name="dia_extraction_unit" value="Th"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1875 <param name="dia_centroided" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1876 <param name="dia_byseries_intensity_min" value="300.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1877 <param name="dia_byseries_ppm_diff" value="10.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1878 <param name="dia_nr_isotopes" value="4"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1879 <param name="dia_nr_charges" value="4"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1880 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1881 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1882 <section name="EMGScoring">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1883 <param name="max_iteration" value="10"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1884 <param name="init_mom" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1885 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1886 <section name="Scores">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1887 <param name="use_shape_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1888 <param name="use_coelution_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1889 <param name="use_rt_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1890 <param name="use_library_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1891 <param name="use_intensity_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1892 <param name="use_nr_peaks_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1893 <param name="use_total_xic_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1894 <param name="use_total_mi_score" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1895 <param name="use_sn_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1896 <param name="use_mi_score" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1897 <param name="use_dia_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1898 <param name="use_ms1_correlation" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1899 <param name="use_sonar_scores" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1900 <param name="use_ion_mobility_scores" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1901 <param name="use_ms1_fullscan" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1902 <param name="use_ms1_mi" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1903 <param name="use_uis_scores" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1904 <param name="use_ionseries_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1905 <param name="use_ms2_isotope_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1906 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1907 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1908 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1909 <output name="ctd_out" ftype="xml">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1910 <assert_contents>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1911 <is_valid_xml/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1912 </assert_contents>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1913 </output>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1914 <assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1915 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1916 </assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1917 </test>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1918 <!-- TOPP_OpenSwathWorkflow_14 -->
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1919 <test expect_num_outputs="3">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1920 <section name="adv_opts">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1921 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1922 <param name="sort_swath_maps" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1923 <param name="enable_ms1" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1924 <param name="enable_ipf" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1925 <param name="out_chrom_type" value="sqMass"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1926 <param name="min_upper_edge_dist" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1927 <param name="extra_rt_extraction_window" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1928 <param name="mz_extraction_window_unit" value="Th"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1929 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1930 <param name="use_ms1_ion_mobility" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1931 <param name="matching_window_only" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1932 <param name="irt_mz_extraction_window" value="50.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1933 <param name="irt_mz_extraction_window_unit" value="ppm"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1934 <param name="irt_im_extraction_window" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1935 <param name="min_rsq" value="0.95"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1936 <param name="min_coverage" value="0.6"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1937 <param name="split_file_input" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1938 <param name="use_elution_model_score" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1939 <param name="readOptions" value="normal"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1940 <param name="mz_correction_function" value="none"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1941 <param name="extraction_function" value="tophat"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1942 <param name="batchSize" value="1000"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1943 <param name="ms1_isotopes" value="0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1944 <param name="force" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1945 <param name="test" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1946 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1947 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1948 <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1949 <output name="out_osw" value="OpenSwathWorkflow_14.osw" compare="sim_size" delta_frac="0.7" ftype="osw"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1950 <output name="out_chrom" value="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta_frac="0.7" ftype="sqmass"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1951 <param name="sonar" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	1952 <param name="pasef" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1953 <param name="rt_extraction_window" value="600.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1954 <param name="ion_mobility_window" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1955 <param name="mz_extraction_window" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1956 <param name="mz_extraction_window_ms1" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1957 <param name="im_extraction_window_ms1" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1958 <section name="Debugging"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1959 <section name="Calibration">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1960 <param name="ms1_im_calibration" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1961 <param name="im_correction_function" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1962 <param name="debug_im_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1963 <param name="debug_mz_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1964 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1965 <section name="Library">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1966 <param name="retentionTimeInterpretation" value="iRT"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1967 <param name="override_group_label_check" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1968 <param name="force_invalid_mods" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1969 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1970 <section name="RTNormalization">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1971 <param name="alignmentMethod" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1972 <param name="outlierMethod" value="iter_residual"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1973 <param name="useIterativeChauvenet" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1974 <param name="RANSACMaxIterations" value="1000"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1975 <param name="RANSACMaxPercentRTThreshold" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1976 <param name="RANSACSamplingSize" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1977 <param name="estimateBestPeptides" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1978 <param name="InitialQualityCutoff" value="0.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1979 <param name="OverallQualityCutoff" value="5.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1980 <param name="NrRTBins" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1981 <param name="MinPeptidesPerBin" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1982 <param name="MinBinsFilled" value="8"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1983 <section name="lowess">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1984 <param name="span" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1985 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1986 <section name="b_spline">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1987 <param name="num_nodes" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1988 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1989 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1990 <section name="Scoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1991 <param name="stop_report_after_feature" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1992 <param name="rt_normalization_factor" value="100.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1993 <param name="quantification_cutoff" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1994 <param name="write_convex_hull" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1995 <param name="spectrum_addition_method" value="simple"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1996 <param name="add_up_spectra" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1997 <param name="spacing_for_spectra_resampling" value="0.005"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1998 <param name="uis_threshold_sn" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	1999 <param name="uis_threshold_peak_area" value="0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2000 <param name="scoring_model" value="default"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2001 <param name="im_extra_drift" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2002 <param name="strict" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2003 <section name="TransitionGroupPicker">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2004 <param name="stop_after_feature" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2005 <param name="min_peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2006 <param name="peak_integration" value="original"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2007 <param name="background_subtraction" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2008 <param name="recalculate_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2009 <param name="use_precursors" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2010 <param name="use_consensus" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2011 <param name="recalculate_peaks_max_z" value="0.75"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2012 <param name="minimal_quality" value="-1.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2013 <param name="resample_boundary" value="15.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2014 <param name="compute_peak_quality" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2015 <param name="compute_peak_shape_metrics" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2016 <param name="compute_total_mi" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2017 <param name="boundary_selection_method" value="largest"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2018 <section name="PeakPickerMRM">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2019 <param name="sgolay_frame_length" value="11"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2020 <param name="sgolay_polynomial_order" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2021 <param name="gauss_width" value="30.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2022 <param name="use_gauss" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2023 <param name="peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2024 <param name="signal_to_noise" value="0.1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2025 <param name="write_sn_log_messages" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2026 <param name="remove_overlapping_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2027 <param name="method" value="corrected"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2028 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2029 <section name="PeakIntegrator">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2030 <param name="integration_type" value="intensity_sum"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2031 <param name="baseline_type" value="base_to_base"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2032 <param name="fit_EMG" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2033 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2034 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2035 <section name="DIAScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2036 <param name="dia_extraction_window" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2037 <param name="dia_extraction_unit" value="Th"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2038 <param name="dia_centroided" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2039 <param name="dia_byseries_intensity_min" value="300.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2040 <param name="dia_byseries_ppm_diff" value="10.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2041 <param name="dia_nr_isotopes" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2042 <param name="dia_nr_charges" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2043 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2044 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2045 <section name="EMGScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2046 <param name="max_iteration" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2047 <param name="init_mom" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2048 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2049 <section name="Scores">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2050 <param name="use_shape_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2051 <param name="use_coelution_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2052 <param name="use_rt_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2053 <param name="use_library_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2054 <param name="use_intensity_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2055 <param name="use_nr_peaks_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2056 <param name="use_total_xic_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2057 <param name="use_total_mi_score" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2058 <param name="use_sn_score" value="true"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2059 <param name="use_mi_score" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2060 <param name="use_dia_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2061 <param name="use_ms1_correlation" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2062 <param name="use_sonar_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2063 <param name="use_ion_mobility_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2064 <param name="use_ms1_fullscan" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2065 <param name="use_ms1_mi" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2066 <param name="use_uis_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2067 <param name="use_ionseries_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2068 <param name="use_ms2_isotope_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2069 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2070 </section>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2071 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2072 <output name="ctd_out" ftype="xml">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2073 <assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2074 <is_valid_xml/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2075 </assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2076 </output>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2077 <assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2078 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2079 </assert_stdout>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2080 </test>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2081 <!-- TOPP_OpenSwathWorkflow_16 -->
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2082 <test expect_num_outputs="3">
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2083 <section name="adv_opts">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2084 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2085 <param name="sort_swath_maps" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2086 <param name="enable_ms1" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2087 <param name="enable_ipf" value="true"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2088 <param name="out_chrom_type" value="mzML"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2089 <param name="min_upper_edge_dist" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2090 <param name="extra_rt_extraction_window" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2091 <param name="mz_extraction_window_unit" value="Th"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2092 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2093 <param name="use_ms1_ion_mobility" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2094 <param name="matching_window_only" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2095 <param name="irt_mz_extraction_window" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2096 <param name="irt_mz_extraction_window_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2097 <param name="irt_im_extraction_window" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2098 <param name="min_rsq" value="0.95"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2099 <param name="min_coverage" value="0.6"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2100 <param name="split_file_input" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2101 <param name="use_elution_model_score" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2102 <param name="readOptions" value="workingInMemory"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2103 <param name="mz_correction_function" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2104 <param name="extraction_function" value="tophat"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2105 <param name="batchSize" value="1000"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2106 <param name="ms1_isotopes" value="2"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2107 <param name="force" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2108 <param name="test" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2109 </section>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2110 <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2111 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2112 <output name="out_features" value="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2113 <output name="out_chrom" value="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2114 <param name="sonar" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2115 <param name="pasef" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2116 <param name="rt_extraction_window" value="600.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2117 <param name="ion_mobility_window" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2118 <param name="mz_extraction_window" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2119 <param name="mz_extraction_window_ms1" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2120 <param name="im_extraction_window_ms1" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2121 <section name="Debugging"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2122 <section name="Calibration">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2123 <param name="ms1_im_calibration" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2124 <param name="im_correction_function" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2125 <param name="debug_im_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2126 <param name="debug_mz_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2127 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2128 <section name="Library">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2129 <param name="retentionTimeInterpretation" value="iRT"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2130 <param name="override_group_label_check" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2131 <param name="force_invalid_mods" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2132 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2133 <section name="RTNormalization">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2134 <param name="alignmentMethod" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2135 <param name="outlierMethod" value="iter_residual"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2136 <param name="useIterativeChauvenet" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2137 <param name="RANSACMaxIterations" value="1000"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2138 <param name="RANSACMaxPercentRTThreshold" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2139 <param name="RANSACSamplingSize" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2140 <param name="estimateBestPeptides" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2141 <param name="InitialQualityCutoff" value="0.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2142 <param name="OverallQualityCutoff" value="5.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2143 <param name="NrRTBins" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2144 <param name="MinPeptidesPerBin" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2145 <param name="MinBinsFilled" value="8"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2146 <section name="lowess">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2147 <param name="span" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2148 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2149 <section name="b_spline">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2150 <param name="num_nodes" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2151 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2152 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2153 <section name="Scoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2154 <param name="stop_report_after_feature" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2155 <param name="rt_normalization_factor" value="100.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2156 <param name="quantification_cutoff" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2157 <param name="write_convex_hull" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2158 <param name="spectrum_addition_method" value="simple"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2159 <param name="add_up_spectra" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2160 <param name="spacing_for_spectra_resampling" value="0.005"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2161 <param name="uis_threshold_sn" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2162 <param name="uis_threshold_peak_area" value="0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2163 <param name="scoring_model" value="default"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2164 <param name="im_extra_drift" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2165 <param name="strict" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2166 <section name="TransitionGroupPicker">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2167 <param name="stop_after_feature" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2168 <param name="min_peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2169 <param name="peak_integration" value="original"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2170 <param name="background_subtraction" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2171 <param name="recalculate_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2172 <param name="use_precursors" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2173 <param name="use_consensus" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2174 <param name="recalculate_peaks_max_z" value="0.75"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2175 <param name="minimal_quality" value="-1.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2176 <param name="resample_boundary" value="15.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2177 <param name="compute_peak_quality" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2178 <param name="compute_peak_shape_metrics" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2179 <param name="compute_total_mi" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2180 <param name="boundary_selection_method" value="largest"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2181 <section name="PeakPickerMRM">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2182 <param name="sgolay_frame_length" value="11"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2183 <param name="sgolay_polynomial_order" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2184 <param name="gauss_width" value="30.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2185 <param name="use_gauss" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2186 <param name="peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2187 <param name="signal_to_noise" value="0.1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2188 <param name="write_sn_log_messages" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2189 <param name="remove_overlapping_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2190 <param name="method" value="corrected"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2191 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2192 <section name="PeakIntegrator">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2193 <param name="integration_type" value="intensity_sum"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2194 <param name="baseline_type" value="base_to_base"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2195 <param name="fit_EMG" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2196 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2197 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2198 <section name="DIAScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2199 <param name="dia_extraction_window" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2200 <param name="dia_extraction_unit" value="Th"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2201 <param name="dia_centroided" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2202 <param name="dia_byseries_intensity_min" value="300.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2203 <param name="dia_byseries_ppm_diff" value="10.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2204 <param name="dia_nr_isotopes" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2205 <param name="dia_nr_charges" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2206 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2207 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2208 <section name="EMGScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2209 <param name="max_iteration" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2210 <param name="init_mom" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2211 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2212 <section name="Scores">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2213 <param name="use_shape_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2214 <param name="use_coelution_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2215 <param name="use_rt_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2216 <param name="use_library_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2217 <param name="use_intensity_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2218 <param name="use_nr_peaks_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2219 <param name="use_total_xic_score" value="true"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2220 <param name="use_total_mi_score" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2221 <param name="use_sn_score" value="true"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2222 <param name="use_mi_score" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2223 <param name="use_dia_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2224 <param name="use_ms1_correlation" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2225 <param name="use_sonar_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2226 <param name="use_ion_mobility_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2227 <param name="use_ms1_fullscan" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2228 <param name="use_ms1_mi" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2229 <param name="use_uis_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2230 <param name="use_ionseries_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2231 <param name="use_ms2_isotope_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2232 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2233 </section>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2234 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2235 <output name="ctd_out" ftype="xml">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2236 <assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2237 <is_valid_xml/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2238 </assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2239 </output>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2240 <assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2241 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2242 </assert_stdout>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2243 </test>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2244 <!-- TOPP_OpenSwathWorkflow_17_cache -->
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2245 <test expect_num_outputs="3">
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2246 <section name="adv_opts">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2247 <param name="sort_swath_maps" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2248 <param name="enable_ms1" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2249 <param name="enable_ipf" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2250 <param name="out_chrom_type" value="mzML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2251 <param name="min_upper_edge_dist" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2252 <param name="extra_rt_extraction_window" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2253 <param name="mz_extraction_window_unit" value="Th"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2254 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2255 <param name="use_ms1_ion_mobility" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2256 <param name="matching_window_only" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2257 <param name="irt_mz_extraction_window" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2258 <param name="irt_mz_extraction_window_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2259 <param name="irt_im_extraction_window" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2260 <param name="min_rsq" value="0.95"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2261 <param name="min_coverage" value="0.6"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2262 <param name="split_file_input" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2263 <param name="use_elution_model_score" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2264 <param name="readOptions" value="cache"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2265 <param name="mz_correction_function" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2266 <param name="extraction_function" value="tophat"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2267 <param name="batchSize" value="1000"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2268 <param name="ms1_isotopes" value="0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2269 <param name="force" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2270 <param name="test" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2271 </section>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2272 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2273 <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2274 <output name="out_features" value="OpenSwathWorkflow_17_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2275 <output name="out_chrom" value="OpenSwathWorkflow_17_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2276 <param name="sonar" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2277 <param name="pasef" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2278 <param name="rt_extraction_window" value="600.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2279 <param name="ion_mobility_window" value="0.05"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2280 <param name="mz_extraction_window" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2281 <param name="mz_extraction_window_ms1" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2282 <param name="im_extraction_window_ms1" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2283 <section name="Debugging"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2284 <section name="Calibration">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2285 <param name="ms1_im_calibration" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2286 <param name="im_correction_function" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2287 <param name="debug_im_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2288 <param name="debug_mz_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2289 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2290 <section name="Library">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2291 <param name="retentionTimeInterpretation" value="iRT"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2292 <param name="override_group_label_check" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2293 <param name="force_invalid_mods" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2294 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2295 <section name="RTNormalization">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2296 <param name="alignmentMethod" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2297 <param name="outlierMethod" value="iter_residual"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2298 <param name="useIterativeChauvenet" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2299 <param name="RANSACMaxIterations" value="1000"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2300 <param name="RANSACMaxPercentRTThreshold" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2301 <param name="RANSACSamplingSize" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2302 <param name="estimateBestPeptides" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2303 <param name="InitialQualityCutoff" value="0.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2304 <param name="OverallQualityCutoff" value="5.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2305 <param name="NrRTBins" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2306 <param name="MinPeptidesPerBin" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2307 <param name="MinBinsFilled" value="8"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2308 <section name="lowess">
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2309 <param name="span" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2310 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2311 <section name="b_spline">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2312 <param name="num_nodes" value="5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2313 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2314 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2315 <section name="Scoring">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2316 <param name="stop_report_after_feature" value="5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2317 <param name="rt_normalization_factor" value="100.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2318 <param name="quantification_cutoff" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2319 <param name="write_convex_hull" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2320 <param name="spectrum_addition_method" value="simple"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2321 <param name="add_up_spectra" value="1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2322 <param name="spacing_for_spectra_resampling" value="0.005"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2323 <param name="uis_threshold_sn" value="-1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2324 <param name="uis_threshold_peak_area" value="0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2325 <param name="scoring_model" value="default"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2326 <param name="im_extra_drift" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2327 <param name="strict" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2328 <section name="TransitionGroupPicker">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2329 <param name="stop_after_feature" value="-1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2330 <param name="min_peak_width" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2331 <param name="peak_integration" value="original"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2332 <param name="background_subtraction" value="none"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2333 <param name="recalculate_peaks" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2334 <param name="use_precursors" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2335 <param name="use_consensus" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2336 <param name="recalculate_peaks_max_z" value="0.75"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2337 <param name="minimal_quality" value="-1.5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2338 <param name="resample_boundary" value="15.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2339 <param name="compute_peak_quality" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2340 <param name="compute_peak_shape_metrics" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2341 <param name="compute_total_mi" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2342 <param name="boundary_selection_method" value="largest"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2343 <section name="PeakPickerMRM">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2344 <param name="sgolay_frame_length" value="11"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2345 <param name="sgolay_polynomial_order" value="3"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2346 <param name="gauss_width" value="30.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2347 <param name="use_gauss" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2348 <param name="peak_width" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2349 <param name="signal_to_noise" value="0.1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2350 <param name="write_sn_log_messages" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2351 <param name="remove_overlapping_peaks" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2352 <param name="method" value="corrected"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2353 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2354 <section name="PeakIntegrator">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2355 <param name="integration_type" value="intensity_sum"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2356 <param name="baseline_type" value="base_to_base"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2357 <param name="fit_EMG" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2358 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2359 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2360 <section name="DIAScoring">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2361 <param name="dia_extraction_window" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2362 <param name="dia_extraction_unit" value="Th"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2363 <param name="dia_centroided" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2364 <param name="dia_byseries_intensity_min" value="300.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2365 <param name="dia_byseries_ppm_diff" value="10.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2366 <param name="dia_nr_isotopes" value="4"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2367 <param name="dia_nr_charges" value="4"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2368 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2369 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2370 <section name="EMGScoring">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2371 <param name="max_iteration" value="10"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2372 <param name="init_mom" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2373 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2374 <section name="Scores">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2375 <param name="use_shape_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2376 <param name="use_coelution_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2377 <param name="use_rt_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2378 <param name="use_library_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2379 <param name="use_intensity_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2380 <param name="use_nr_peaks_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2381 <param name="use_total_xic_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2382 <param name="use_total_mi_score" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2383 <param name="use_sn_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2384 <param name="use_mi_score" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2385 <param name="use_dia_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2386 <param name="use_ms1_correlation" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2387 <param name="use_sonar_scores" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2388 <param name="use_ion_mobility_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2389 <param name="use_ms1_fullscan" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2390 <param name="use_ms1_mi" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2391 <param name="use_uis_scores" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2392 <param name="use_ionseries_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2393 <param name="use_ms2_isotope_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2394 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2395 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2396 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2397 <output name="ctd_out" ftype="xml">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2398 <assert_contents>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2399 <is_valid_xml/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2400 </assert_contents>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2401 </output>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2402 <assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2403 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2404 </assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2405 </test>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2406 <!-- TOPP_OpenSwathWorkflow_17_b -->
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2407 <test expect_num_outputs="3">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2408 <section name="adv_opts">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2409 <param name="sort_swath_maps" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2410 <param name="enable_ms1" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2411 <param name="enable_ipf" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2412 <param name="out_chrom_type" value="mzML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2413 <param name="min_upper_edge_dist" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2414 <param name="extra_rt_extraction_window" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2415 <param name="mz_extraction_window_unit" value="Th"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2416 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2417 <param name="use_ms1_ion_mobility" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2418 <param name="matching_window_only" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2419 <param name="irt_mz_extraction_window" value="50.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2420 <param name="irt_mz_extraction_window_unit" value="ppm"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2421 <param name="irt_im_extraction_window" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2422 <param name="min_rsq" value="0.95"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2423 <param name="min_coverage" value="0.6"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2424 <param name="split_file_input" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2425 <param name="use_elution_model_score" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2426 <param name="readOptions" value="workingInMemory"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2427 <param name="mz_correction_function" value="none"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2428 <param name="extraction_function" value="tophat"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2429 <param name="batchSize" value="1000"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2430 <param name="ms1_isotopes" value="0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2431 <param name="force" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2432 <param name="test" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2433 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2434 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2435 <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2436 <output name="out_features" value="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2437 <output name="out_chrom" value="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2438 <param name="sonar" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2439 <param name="pasef" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2440 <param name="rt_extraction_window" value="600.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2441 <param name="ion_mobility_window" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2442 <param name="mz_extraction_window" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2443 <param name="mz_extraction_window_ms1" value="50.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2444 <param name="im_extraction_window_ms1" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2445 <section name="Debugging"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2446 <section name="Calibration">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2447 <param name="ms1_im_calibration" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2448 <param name="im_correction_function" value="linear"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2449 <param name="debug_im_file" value=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2450 <param name="debug_mz_file" value=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2451 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2452 <section name="Library">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2453 <param name="retentionTimeInterpretation" value="iRT"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2454 <param name="override_group_label_check" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2455 <param name="force_invalid_mods" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2456 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2457 <section name="RTNormalization">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2458 <param name="alignmentMethod" value="linear"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2459 <param name="outlierMethod" value="iter_residual"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2460 <param name="useIterativeChauvenet" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2461 <param name="RANSACMaxIterations" value="1000"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2462 <param name="RANSACMaxPercentRTThreshold" value="3"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2463 <param name="RANSACSamplingSize" value="10"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2464 <param name="estimateBestPeptides" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2465 <param name="InitialQualityCutoff" value="0.5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2466 <param name="OverallQualityCutoff" value="5.5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2467 <param name="NrRTBins" value="10"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2468 <param name="MinPeptidesPerBin" value="1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2469 <param name="MinBinsFilled" value="8"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2470 <section name="lowess">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2471 <param name="span" value="0.05"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2472 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2473 <section name="b_spline">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2474 <param name="num_nodes" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2475 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2476 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2477 <section name="Scoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2478 <param name="stop_report_after_feature" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2479 <param name="rt_normalization_factor" value="100.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2480 <param name="quantification_cutoff" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2481 <param name="write_convex_hull" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2482 <param name="spectrum_addition_method" value="simple"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2483 <param name="add_up_spectra" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2484 <param name="spacing_for_spectra_resampling" value="0.005"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2485 <param name="uis_threshold_sn" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2486 <param name="uis_threshold_peak_area" value="0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2487 <param name="scoring_model" value="default"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2488 <param name="im_extra_drift" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2489 <param name="strict" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2490 <section name="TransitionGroupPicker">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2491 <param name="stop_after_feature" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2492 <param name="min_peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2493 <param name="peak_integration" value="original"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2494 <param name="background_subtraction" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2495 <param name="recalculate_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2496 <param name="use_precursors" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2497 <param name="use_consensus" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2498 <param name="recalculate_peaks_max_z" value="0.75"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2499 <param name="minimal_quality" value="-1.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2500 <param name="resample_boundary" value="15.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2501 <param name="compute_peak_quality" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2502 <param name="compute_peak_shape_metrics" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2503 <param name="compute_total_mi" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2504 <param name="boundary_selection_method" value="largest"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2505 <section name="PeakPickerMRM">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2506 <param name="sgolay_frame_length" value="11"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2507 <param name="sgolay_polynomial_order" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2508 <param name="gauss_width" value="30.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2509 <param name="use_gauss" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2510 <param name="peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2511 <param name="signal_to_noise" value="0.1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2512 <param name="write_sn_log_messages" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2513 <param name="remove_overlapping_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2514 <param name="method" value="corrected"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2515 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2516 <section name="PeakIntegrator">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2517 <param name="integration_type" value="intensity_sum"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2518 <param name="baseline_type" value="base_to_base"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2519 <param name="fit_EMG" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2520 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2521 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2522 <section name="DIAScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2523 <param name="dia_extraction_window" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2524 <param name="dia_extraction_unit" value="Th"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2525 <param name="dia_centroided" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2526 <param name="dia_byseries_intensity_min" value="300.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2527 <param name="dia_byseries_ppm_diff" value="10.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2528 <param name="dia_nr_isotopes" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2529 <param name="dia_nr_charges" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2530 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2531 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2532 <section name="EMGScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2533 <param name="max_iteration" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2534 <param name="init_mom" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2535 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2536 <section name="Scores">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2537 <param name="use_shape_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2538 <param name="use_coelution_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2539 <param name="use_rt_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2540 <param name="use_library_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2541 <param name="use_intensity_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2542 <param name="use_nr_peaks_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2543 <param name="use_total_xic_score" value="true"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2544 <param name="use_total_mi_score" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2545 <param name="use_sn_score" value="true"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2546 <param name="use_mi_score" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2547 <param name="use_dia_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2548 <param name="use_ms1_correlation" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2549 <param name="use_sonar_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2550 <param name="use_ion_mobility_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2551 <param name="use_ms1_fullscan" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2552 <param name="use_ms1_mi" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2553 <param name="use_uis_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2554 <param name="use_ionseries_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2555 <param name="use_ms2_isotope_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2556 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2557 </section>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2558 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2559 <output name="ctd_out" ftype="xml">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2560 <assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2561 <is_valid_xml/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2562 </assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2563 </output>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2564 <assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2565 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2566 </assert_stdout>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2567 </test>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2568 <!-- TOPP_OpenSwathWorkflow_22 -->
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2569 <test expect_num_outputs="3">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2570 <section name="adv_opts">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2571 <param name="sort_swath_maps" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2572 <param name="enable_ms1" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2573 <param name="enable_ipf" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2574 <param name="out_chrom_type" value="mzML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2575 <param name="min_upper_edge_dist" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2576 <param name="extra_rt_extraction_window" value="0.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2577 <param name="mz_extraction_window_unit" value="Th"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2578 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2579 <param name="use_ms1_ion_mobility" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2580 <param name="matching_window_only" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2581 <param name="irt_mz_extraction_window" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2582 <param name="irt_mz_extraction_window_unit" value="ppm"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2583 <param name="irt_im_extraction_window" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2584 <param name="min_rsq" value="0.95"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2585 <param name="min_coverage" value="0.6"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2586 <param name="split_file_input" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2587 <param name="use_elution_model_score" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2588 <param name="readOptions" value="workingInMemory"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2589 <param name="mz_correction_function" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2590 <param name="extraction_function" value="tophat"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2591 <param name="batchSize" value="1000"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2592 <param name="ms1_isotopes" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2593 <param name="force" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2594 <param name="test" value="true"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2595 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2596 <param name="in" value="OpenSwathWorkflow_22_input.mzML"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2597 <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2598 <output name="out_features" value="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2599 <output name="out_chrom" value="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2600 <param name="sonar" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2601 <param name="pasef" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2602 <param name="rt_extraction_window" value="600.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2603 <param name="ion_mobility_window" value="-1.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2604 <param name="mz_extraction_window" value="0.05"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2605 <param name="mz_extraction_window_ms1" value="50.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2606 <param name="im_extraction_window_ms1" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2607 <section name="Debugging"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2608 <section name="Calibration">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2609 <param name="ms1_im_calibration" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2610 <param name="im_correction_function" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2611 <param name="debug_im_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2612 <param name="debug_mz_file" value=""/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2613 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2614 <section name="Library">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2615 <param name="retentionTimeInterpretation" value="iRT"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2616 <param name="override_group_label_check" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2617 <param name="force_invalid_mods" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2618 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2619 <section name="RTNormalization">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2620 <param name="alignmentMethod" value="linear"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2621 <param name="outlierMethod" value="iter_residual"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2622 <param name="useIterativeChauvenet" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2623 <param name="RANSACMaxIterations" value="1000"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2624 <param name="RANSACMaxPercentRTThreshold" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2625 <param name="RANSACSamplingSize" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2626 <param name="estimateBestPeptides" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2627 <param name="InitialQualityCutoff" value="0.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2628 <param name="OverallQualityCutoff" value="5.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2629 <param name="NrRTBins" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2630 <param name="MinPeptidesPerBin" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2631 <param name="MinBinsFilled" value="8"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2632 <section name="lowess">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2633 <param name="span" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2634 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2635 <section name="b_spline">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2636 <param name="num_nodes" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2637 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2638 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2639 <section name="Scoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2640 <param name="stop_report_after_feature" value="5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2641 <param name="rt_normalization_factor" value="100.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2642 <param name="quantification_cutoff" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2643 <param name="write_convex_hull" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2644 <param name="spectrum_addition_method" value="simple"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2645 <param name="add_up_spectra" value="1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2646 <param name="spacing_for_spectra_resampling" value="0.005"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2647 <param name="uis_threshold_sn" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2648 <param name="uis_threshold_peak_area" value="0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2649 <param name="scoring_model" value="default"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2650 <param name="im_extra_drift" value="0.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2651 <param name="strict" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2652 <section name="TransitionGroupPicker">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2653 <param name="stop_after_feature" value="-1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2654 <param name="min_peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2655 <param name="peak_integration" value="original"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2656 <param name="background_subtraction" value="none"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2657 <param name="recalculate_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2658 <param name="use_precursors" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2659 <param name="use_consensus" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2660 <param name="recalculate_peaks_max_z" value="0.75"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2661 <param name="minimal_quality" value="-1.5"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2662 <param name="resample_boundary" value="15.0"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2663 <param name="compute_peak_quality" value="true"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2664 <param name="compute_peak_shape_metrics" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2665 <param name="compute_total_mi" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2666 <param name="boundary_selection_method" value="largest"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2667 <section name="PeakPickerMRM">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2668 <param name="sgolay_frame_length" value="11"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2669 <param name="sgolay_polynomial_order" value="3"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2670 <param name="gauss_width" value="30.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2671 <param name="use_gauss" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2672 <param name="peak_width" value="-1.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2673 <param name="signal_to_noise" value="0.1"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2674 <param name="write_sn_log_messages" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2675 <param name="remove_overlapping_peaks" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2676 <param name="method" value="corrected"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2677 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2678 <section name="PeakIntegrator">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2679 <param name="integration_type" value="intensity_sum"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2680 <param name="baseline_type" value="base_to_base"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2681 <param name="fit_EMG" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2682 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2683 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2684 <section name="DIAScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2685 <param name="dia_extraction_window" value="0.05"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2686 <param name="dia_extraction_unit" value="Th"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2687 <param name="dia_centroided" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2688 <param name="dia_byseries_intensity_min" value="300.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2689 <param name="dia_byseries_ppm_diff" value="10.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2690 <param name="dia_nr_isotopes" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2691 <param name="dia_nr_charges" value="4"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2692 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2693 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2694 <section name="EMGScoring">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2695 <param name="max_iteration" value="10"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2696 <param name="init_mom" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2697 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2698 <section name="Scores">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2699 <param name="use_shape_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2700 <param name="use_coelution_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2701 <param name="use_rt_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2702 <param name="use_library_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2703 <param name="use_intensity_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2704 <param name="use_nr_peaks_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2705 <param name="use_total_xic_score" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2706 <param name="use_total_mi_score" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2707 <param name="use_sn_score" value="true"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2708 <param name="use_mi_score" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2709 <param name="use_dia_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2710 <param name="use_ms1_correlation" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2711 <param name="use_sonar_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2712 <param name="use_ion_mobility_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2713 <param name="use_ms1_fullscan" value="false"/>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2714 <param name="use_ms1_mi" value="false"/>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2715 <param name="use_uis_scores" value="false"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2716 <param name="use_ionseries_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2717 <param name="use_ms2_isotope_scores" value="true"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2718 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2719 </section>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2720 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2721 <output name="ctd_out" ftype="xml">
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2722 <assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2723 <is_valid_xml/>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2724 </assert_contents>
4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2725 </output>
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2726 <assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2727 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2728 </assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2729 </test>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2730 <!-- TOPP_OpenSwathWorkflow_23 -->
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2731 <test expect_num_outputs="3">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2732 <section name="adv_opts">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2733 <param name="sort_swath_maps" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2734 <param name="enable_ms1" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2735 <param name="enable_ipf" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2736 <param name="out_chrom_type" value="mzML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2737 <param name="min_upper_edge_dist" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2738 <param name="extra_rt_extraction_window" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2739 <param name="mz_extraction_window_unit" value="Th"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2740 <param name="mz_extraction_window_ms1_unit" value="ppm"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2741 <param name="use_ms1_ion_mobility" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2742 <param name="matching_window_only" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2743 <param name="irt_mz_extraction_window" value="50.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2744 <param name="irt_mz_extraction_window_unit" value="ppm"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2745 <param name="irt_im_extraction_window" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2746 <param name="min_rsq" value="0.95"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2747 <param name="min_coverage" value="0.6"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2748 <param name="split_file_input" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2749 <param name="use_elution_model_score" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2750 <param name="readOptions" value="workingInMemory"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2751 <param name="mz_correction_function" value="none"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2752 <param name="extraction_function" value="tophat"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2753 <param name="batchSize" value="1000"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2754 <param name="ms1_isotopes" value="0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2755 <param name="force" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2756 <param name="test" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2757 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2758 <param name="in" value="OpenSwathWorkflow_23_input.mzML"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2759 <param name="tr" value="OpenSwathWorkflow_23_input.tsv" ftype="tabular"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2760 <output name="out_features" value="OpenSwathWorkflow_23_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2761 <output name="out_chrom" value="OpenSwathWorkflow_23_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2762 <param name="sonar" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2763 <param name="pasef" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2764 <param name="rt_extraction_window" value="600.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2765 <param name="ion_mobility_window" value="0.1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2766 <param name="mz_extraction_window" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2767 <param name="mz_extraction_window_ms1" value="50.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2768 <param name="im_extraction_window_ms1" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2769 <section name="Debugging"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2770 <section name="Calibration">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2771 <param name="ms1_im_calibration" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2772 <param name="im_correction_function" value="linear"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2773 <param name="debug_im_file" value=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2774 <param name="debug_mz_file" value=""/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2775 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2776 <section name="Library">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2777 <param name="retentionTimeInterpretation" value="iRT"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2778 <param name="override_group_label_check" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2779 <param name="force_invalid_mods" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2780 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2781 <section name="RTNormalization">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2782 <param name="alignmentMethod" value="linear"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2783 <param name="outlierMethod" value="iter_residual"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2784 <param name="useIterativeChauvenet" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2785 <param name="RANSACMaxIterations" value="1000"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2786 <param name="RANSACMaxPercentRTThreshold" value="3"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2787 <param name="RANSACSamplingSize" value="10"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2788 <param name="estimateBestPeptides" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2789 <param name="InitialQualityCutoff" value="0.5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2790 <param name="OverallQualityCutoff" value="5.5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2791 <param name="NrRTBins" value="10"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2792 <param name="MinPeptidesPerBin" value="1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2793 <param name="MinBinsFilled" value="8"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2794 <section name="lowess">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2795 <param name="span" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2796 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2797 <section name="b_spline">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2798 <param name="num_nodes" value="5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2799 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2800 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2801 <section name="Scoring">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2802 <param name="stop_report_after_feature" value="5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2803 <param name="rt_normalization_factor" value="100.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2804 <param name="quantification_cutoff" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2805 <param name="write_convex_hull" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2806 <param name="spectrum_addition_method" value="simple"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2807 <param name="add_up_spectra" value="1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2808 <param name="spacing_for_spectra_resampling" value="0.005"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2809 <param name="uis_threshold_sn" value="-1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2810 <param name="uis_threshold_peak_area" value="0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2811 <param name="scoring_model" value="default"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2812 <param name="im_extra_drift" value="0.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2813 <param name="strict" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2814 <section name="TransitionGroupPicker">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2815 <param name="stop_after_feature" value="-1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2816 <param name="min_peak_width" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2817 <param name="peak_integration" value="original"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2818 <param name="background_subtraction" value="none"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2819 <param name="recalculate_peaks" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2820 <param name="use_precursors" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2821 <param name="use_consensus" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2822 <param name="recalculate_peaks_max_z" value="0.75"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2823 <param name="minimal_quality" value="-1.5"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2824 <param name="resample_boundary" value="15.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2825 <param name="compute_peak_quality" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2826 <param name="compute_peak_shape_metrics" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2827 <param name="compute_total_mi" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2828 <param name="boundary_selection_method" value="largest"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2829 <section name="PeakPickerMRM">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2830 <param name="sgolay_frame_length" value="11"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2831 <param name="sgolay_polynomial_order" value="3"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2832 <param name="gauss_width" value="30.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2833 <param name="use_gauss" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2834 <param name="peak_width" value="-1.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2835 <param name="signal_to_noise" value="0.1"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2836 <param name="write_sn_log_messages" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2837 <param name="remove_overlapping_peaks" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2838 <param name="method" value="corrected"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2839 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2840 <section name="PeakIntegrator">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2841 <param name="integration_type" value="intensity_sum"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2842 <param name="baseline_type" value="base_to_base"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2843 <param name="fit_EMG" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2844 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2845 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2846 <section name="DIAScoring">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2847 <param name="dia_extraction_window" value="0.05"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2848 <param name="dia_extraction_unit" value="Th"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2849 <param name="dia_centroided" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2850 <param name="dia_byseries_intensity_min" value="300.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2851 <param name="dia_byseries_ppm_diff" value="10.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2852 <param name="dia_nr_isotopes" value="4"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2853 <param name="dia_nr_charges" value="4"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2854 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2855 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2856 <section name="EMGScoring">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2857 <param name="max_iteration" value="10"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2858 <param name="init_mom" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2859 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2860 <section name="Scores">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2861 <param name="use_shape_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2862 <param name="use_coelution_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2863 <param name="use_rt_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2864 <param name="use_library_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2865 <param name="use_intensity_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2866 <param name="use_nr_peaks_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2867 <param name="use_total_xic_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2868 <param name="use_total_mi_score" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2869 <param name="use_sn_score" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2870 <param name="use_mi_score" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2871 <param name="use_dia_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2872 <param name="use_ms1_correlation" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2873 <param name="use_sonar_scores" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2874 <param name="use_ion_mobility_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2875 <param name="use_ms1_fullscan" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2876 <param name="use_ms1_mi" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2877 <param name="use_uis_scores" value="false"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2878 <param name="use_ionseries_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2879 <param name="use_ms2_isotope_scores" value="true"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2880 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2881 </section>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2882 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2883 <output name="ctd_out" ftype="xml">
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2884 <assert_contents>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2885 <is_valid_xml/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2886 </assert_contents>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2887 </output>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2888 <assert_stdout>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2889 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2890 </assert_stdout>
13 4a7b96835140 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	2891 </test>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	2892 </tests>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	2893 <help><![CDATA[Complete workflow to run OpenSWATH
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	2894
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	2895
14 ec4490c65f95 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2896 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathWorkflow.html]]></help>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	2897 <expand macro="references"/>
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	2898 </tool>

Mercurial > repos > galaxyp > openms_openswathworkflow

annotate OpenSwathWorkflow.xml @ 14:ec4490c65f95 draft default tip