openms_openswathworkflow: OpenSwathWorkflow.xml annotate

annotate OpenSwathWorkflow.xml @ 9:3967f7cf35b9 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"

author	galaxyp
date	Wed, 09 Sep 2020 12:46:48 +0000
parents	091d4e82839a
children	887be35bc42e

rev	line source
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	1 <?xml version='1.0' encoding='UTF-8'?>
5 56988709dec6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: 1 diff changeset	2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	3 <!--Proposed Tool Section: [Utilities]-->
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	4 <tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	5 <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	6 <macros>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	7 <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	8 <import>macros.xml</import>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	9 <import>macros_autotest.xml</import>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	10 <import>macros_test.xml</import>
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	11 </macros>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	12 <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	13 <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	14 <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	15 @EXT_FOO@
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	16 #import re
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	17
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	18 ## Preprocessing
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	19 mkdir in &&
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	21 mkdir tr &&
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	22 ln -s '$tr' '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	23 #if $tr_irt:
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	24 mkdir tr_irt &&
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	25 ln -s '$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	26 #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	27 #if $tr_irt_nonlinear:
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	28 mkdir tr_irt_nonlinear &&
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	29 ln -s '$tr_irt_nonlinear' 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)' &&
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	30 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	31 #if "out_features_FLAG" in str($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	32 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	33 #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	34 #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	35 mkdir out_tsv &&
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	36 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	37 #if "out_osw_FLAG" in str($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	38 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	39 #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	40 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	41 mkdir out_chrom &&
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	42 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	43 #if "out_qc_FLAG" in str($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	44 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	45 #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	46 #if "irt_mzml_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	47 mkdir Debugging_irt_mzml &&
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	48 #end if
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	49 #if "irt_trafo_FLAG" in str($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	50 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	51 #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	52 #if $adv_opts_cond.adv_opts_selector=='advanced':
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	53 #if $adv_opts_cond.rt_norm:
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	54 mkdir adv_opts_cond.rt_norm &&
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	55 ln -s '$adv_opts_cond.rt_norm' 'adv_opts_cond.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts_cond.rt_norm.element_identifier)}.$gxy2omsext($adv_opts_cond.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	56 #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	57 #if $adv_opts_cond.swath_windows_file:
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	58 mkdir adv_opts_cond.swath_windows_file &&
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	59 ln -s '$adv_opts_cond.swath_windows_file' 'adv_opts_cond.swath_windows_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.swath_windows_file.element_identifier)}.$gxy2omsext($adv_opts_cond.swath_windows_file.ext)' &&
5 56988709dec6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: 1 diff changeset	60 #end if
56988709dec6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: 1 diff changeset	61 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	62
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	63 ## Main program call
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	64
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	65 set -o pipefail &&
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	66 @EXECUTABLE@ -write_ctd ./ &&
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	67 python3 '$__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	68 @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	69 -in
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	70 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	71 -tr
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	72 'tr/${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	73 #if $tr_irt:
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	74 -tr_irt
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	75 'tr_irt/${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	76 #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	77 #if $tr_irt_nonlinear:
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	78 -tr_irt_nonlinear
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	79 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	80 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	81 #if "out_features_FLAG" in str($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	82 -out_features
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/output.${gxy2omsext("featurexml")}'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	84 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	85 #if "out_tsv_FLAG" in str($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	86 -out_tsv
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/output.${gxy2omsext("tabular")}'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	88 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	89 #if "out_osw_FLAG" in str($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	90 -out_osw
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/output.${gxy2omsext("osw")}'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	92 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	93 #if "out_chrom_FLAG" in str($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	94 -out_chrom
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/output.${adv_opts_cond.out_chrom_type}'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	96 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	97 #if "out_qc_FLAG" in str($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	98 -out_qc
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/output.${gxy2omsext("json")}'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	100 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	101 #if "irt_mzml_FLAG" in str($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	102 -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	103 'Debugging_irt_mzml/output.${gxy2omsext("mzml")}'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	104 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	105 #if "irt_trafo_FLAG" in str($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	106 -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	107 '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	108 #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	109 #if $adv_opts_cond.adv_opts_selector=='advanced':
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	110 #if $adv_opts_cond.rt_norm:
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	111 -rt_norm
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	112 'adv_opts_cond.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts_cond.rt_norm.element_identifier)}.$gxy2omsext($adv_opts_cond.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	113 #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	114 #if $adv_opts_cond.swath_windows_file:
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	115 -swath_windows_file
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	116 'adv_opts_cond.swath_windows_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.swath_windows_file.element_identifier)}.$gxy2omsext($adv_opts_cond.swath_windows_file.ext)'
1 190554cf2195 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 galaxyp parents: 0 diff changeset	117 #end if
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	118 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	119 #if len(str($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	120 \| tee '$stdout'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	121 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	122
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	123 ## Postprocessing
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	124 #if "out_features_FLAG" in str($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	125 && 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	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_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	128 && mv 'out_tsv/output.${gxy2omsext("tabular")}' '$out_tsv'
1 190554cf2195 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 galaxyp parents: 0 diff changeset	129 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	130 #if "out_osw_FLAG" in str($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	131 && 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	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_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	134 && mv 'out_chrom/output.${adv_opts_cond.out_chrom_type}' '$out_chrom'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	135 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	136 #if "out_qc_FLAG" in str($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	137 && 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	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_mzml_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	140 && mv 'Debugging_irt_mzml/output.${gxy2omsext("mzml")}' '$Debugging_irt_mzml'
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	141 #end if
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	142 #if "irt_trafo_FLAG" in str($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	143 && 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	144 #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	145 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	146 && mv '@EXECUTABLE@.ctd' '$ctd_out'
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	147 #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	148 <configfiles>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	149 <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	150 <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	151 </configfiles>
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	152 <inputs>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	153 <param name="in" argument="-in" type="data" format="mzml,mzxml,sqmass" optional="false" label="Input files separated by blank" help=" select mzml,mzxml,sqmass data sets(s)"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	154 <param name="tr" argument="-tr" type="data" format="pqp,tabular,traml" optional="false" label="transition file ('TraML','tsv','pqp')" help=" select pqp,tabular,traml data sets(s)"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	155 <param name="tr_irt" argument="-tr_irt" type="data" format="pqp,tabular,traml" optional="true" label="transition file ('TraML')" help=" select pqp,tabular,traml data sets(s)"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	156 <param name="tr_irt_nonlinear" 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)"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	157 <param name="sonar" argument="-sonar" type="boolean" truevalue="true" falsevalue="false" checked="false" label="data is scanning SWATH data" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	158 <param name="rt_extraction_window" argument="-rt_extraction_window" type="float" optional="true" 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=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	159 <param name="ion_mobility_window" argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	160 <param name="mz_extraction_window" argument="-mz_extraction_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window in Thomson or ppm (see mz_extraction_window_unit)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	161 <param name="mz_extraction_window_ms1" argument="-mz_extraction_window_ms1" type="float" optional="true" min="0.0" value="0.05" label="Extraction window used in MS1 in Thomson or ppm (see mz_extraction_window_ms1_unit)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	162 <param name="im_extraction_window_ms1" argument="-im_extraction_window_ms1" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension for MS1 (in milliseconds)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	163 <section name="Debugging" title="Debugging" 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	164 <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	165 <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=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	166 <param name="im_correction_function" argument="-Calibration:im_correction_function" display="radio" type="select" optional="false" label="Type of normalization function for IM calibration" help="">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	167 <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	168 <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	169 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	170 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	171 <param name="debug_im_file" argument="-Calibration:debug_im_file" type="text" optional="true" value="" label="Debug file for Ion Mobility calibration" help="">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	172 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	173 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	174 <param name="debug_mz_file" argument="-Calibration:debug_mz_file" type="text" optional="true" value="" label="Debug file for m/z calibration" help="">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	175 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	176 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	177 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	178 <section name="Library" title="Library parameters section" 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	179 <param name="retentionTimeInterpretation" argument="-Library:retentionTimeInterpretation" display="radio" type="select" optional="false" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="">
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="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	181 <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	182 <option value="minutes">minutes</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	183 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	184 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	185 <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	186 <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	187 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	188 <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">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	189 <param name="alignmentMethod" argument="-RTNormalization:alignmentMethod" display="radio" type="select" optional="false" 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">
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="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	191 <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	192 <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	193 <option value="b_spline">b_spline</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	194 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	195 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	196 <param name="outlierMethod" argument="-RTNormalization:outlierMethod" display="radio" type="select" optional="false" 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)">
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="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	198 <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	199 <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	200 <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	201 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	202 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	203 <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"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	204 <param name="RANSACMaxIterations" argument="-RTNormalization:RANSACMaxIterations" type="integer" optional="true" value="1000" label="Maximum iterations for the RANSAC outlier detection algorithm" help=""/>
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="RANSACMaxPercentRTThreshold" argument="-RTNormalization:RANSACMaxPercentRTThreshold" type="integer" optional="true" 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"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	206 <param name="RANSACSamplingSize" argument="-RTNormalization:RANSACSamplingSize" type="integer" optional="true" value="10" label="Sampling size of data points per iteration for the RANSAC outlier detection algorithm" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	207 <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)"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	208 <param name="InitialQualityCutoff" argument="-RTNormalization:InitialQualityCutoff" type="float" optional="true" value="0.5" label="The initial overall quality cutoff for a peak to be scored (range ca" help="-2 to 2)"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	209 <param name="OverallQualityCutoff" argument="-RTNormalization:OverallQualityCutoff" type="float" optional="true" value="5.5" label="The overall quality cutoff for a peak to go into the retention time estimation (range ca" help="0 to 10)"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	210 <param name="NrRTBins" argument="-RTNormalization:NrRTBins" type="integer" optional="true" 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)"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	211 <param name="MinPeptidesPerBin" argument="-RTNormalization:MinPeptidesPerBin" type="integer" optional="true" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	212 <param name="MinBinsFilled" argument="-RTNormalization:MinBinsFilled" type="integer" optional="true" value="8" label="Minimal number of bins required to be covered" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	213 <section name="lowess" 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	214 <param name="span" argument="-RTNormalization:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Span parameter for lowess" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	215 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	216 <section name="b_spline" 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	217 <param name="num_nodes" argument="-RTNormalization:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for b spline" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	218 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	219 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	220 <section name="Scoring" title="Scoring parameters section" 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	221 <param name="stop_report_after_feature" argument="-Scoring:stop_report_after_feature" type="integer" optional="true" value="5" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help=""/>
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="rt_normalization_factor" argument="-Scoring:rt_normalization_factor" type="float" optional="true" 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)"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	223 <param name="quantification_cutoff" argument="-Scoring:quantification_cutoff" type="float" optional="true" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	224 <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=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	225 <param name="spectrum_addition_method" argument="-Scoring:spectrum_addition_method" display="radio" type="select" optional="false" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	226 <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	227 <option value="resample">resample</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	228 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	229 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	230 <param name="add_up_spectra" argument="-Scoring:add_up_spectra" type="integer" optional="true" min="1" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	231 <param name="spacing_for_spectra_resampling" argument="-Scoring:spacing_for_spectra_resampling" type="float" optional="true" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	232 <param name="uis_threshold_sn" argument="-Scoring:uis_threshold_sn" type="integer" optional="true" value="0" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	233 <param name="uis_threshold_peak_area" argument="-Scoring:uis_threshold_peak_area" type="integer" optional="true" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	234 <param name="scoring_model" argument="-Scoring:scoring_model" display="radio" type="select" optional="false" label="Scoring model to use" help="">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	235 <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	236 <option value="single_transition">single_transition</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	237 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	238 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	239 <param name="im_extra_drift" argument="-Scoring:im_extra_drift" type="float" optional="true" 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)"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	240 <section name="TransitionGroupPicker" 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	241 <param name="stop_after_feature" argument="-Scoring:TransitionGroupPicker:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	242 <param name="min_peak_width" argument="-Scoring:TransitionGroupPicker:min_peak_width" type="float" optional="true" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	243 <param name="peak_integration" argument="-Scoring:TransitionGroupPicker:peak_integration" display="radio" type="select" optional="false" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
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="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	245 <option value="smoothed">smoothed</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	246 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	247 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	248 <param name="background_subtraction" argument="-Scoring:TransitionGroupPicker:background_subtraction" display="radio" type="select" optional="false" 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">
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="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	250 <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	251 <option value="exact">exact</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	252 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	253 </param>
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="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	255 <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	256 <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=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	257 <param name="recalculate_peaks_max_z" argument="-Scoring:TransitionGroupPicker:recalculate_peaks_max_z" type="float" optional="true" 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)"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	258 <param name="minimal_quality" argument="-Scoring:TransitionGroupPicker:minimal_quality" type="float" optional="true" value="-1.5" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	259 <param name="resample_boundary" argument="-Scoring:TransitionGroupPicker:resample_boundary" type="float" optional="true" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
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_quality" argument="-Scoring:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="true" 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"/>
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_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	262 <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=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	263 <param name="boundary_selection_method" argument="-Scoring:TransitionGroupPicker:boundary_selection_method" display="radio" type="select" optional="false" label="Method to use when selecting the best boundaries for peaks" help="">
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="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	265 <option value="widest">widest</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	266 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	267 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	268 <section name="PeakPickerMRM" 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	269 <param name="sgolay_frame_length" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length" type="integer" optional="true" 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"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	270 <param name="sgolay_polynomial_order" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order" type="integer" optional="true" value="3" label="Order of the polynomial that is fitted" help=""/>
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="gauss_width" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="float" optional="true" value="30.0" label="Gaussian width in seconds, estimated peak size" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	272 <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=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	273 <param name="peak_width" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width" type="float" optional="true" 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"/>
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="signal_to_noise" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="float" optional="true" 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"/>
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="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	276 <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=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	277 <param name="method" argument="-Scoring:TransitionGroupPicker:PeakPickerMRM:method" display="radio" type="select" optional="false" 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="">
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="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	279 <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	280 <option value="crawdad">crawdad</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	281 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	282 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	283 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	284 <section name="PeakIntegrator" 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	285 <param name="integration_type" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:integration_type" display="radio" type="select" optional="false" 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="">
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="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	287 <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	288 <option value="trapezoid">trapezoid</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	289 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	290 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	291 <param name="baseline_type" argument="-Scoring:TransitionGroupPicker:PeakIntegrator:baseline_type" display="radio" type="select" optional="false" 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)">
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="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	293 <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	294 <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	295 <option value="vertical_division_max">vertical_division_max</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	296 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	297 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	298 <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	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>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	301 <section name="DIAScoring" 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	302 <param name="dia_extraction_window" argument="-Scoring:DIAScoring:dia_extraction_window" type="float" optional="true" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	303 <param name="dia_extraction_unit" argument="-Scoring:DIAScoring:dia_extraction_unit" display="radio" type="select" optional="false" label="DIA extraction window unit" help="">
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="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	305 <option value="ppm">ppm</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	306 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	307 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	308 <param name="dia_centroided" argument="-Scoring:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	309 <param name="dia_byseries_intensity_min" argument="-Scoring:DIAScoring:dia_byseries_intensity_min" type="float" optional="true" min="0.0" value="300.0" label="DIA b/y series minimum intensity to conside" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	310 <param name="dia_byseries_ppm_diff" argument="-Scoring:DIAScoring:dia_byseries_ppm_diff" type="float" optional="true" min="0.0" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	311 <param name="dia_nr_isotopes" argument="-Scoring:DIAScoring:dia_nr_isotopes" type="integer" optional="true" min="0" value="4" label="DIA number of isotopes to conside" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	312 <param name="dia_nr_charges" argument="-Scoring:DIAScoring:dia_nr_charges" type="integer" optional="true" min="0" value="4" label="DIA number of charges to conside" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	313 <param name="peak_before_mono_max_ppm_diff" argument="-Scoring:DIAScoring:peak_before_mono_max_ppm_diff" type="float" optional="true" 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=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	314 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	315 <section name="EMGScoring" 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	316 <param name="max_iteration" argument="-Scoring:EMGScoring:max_iteration" type="integer" optional="true" value="10" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help=""/>
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=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	328 <param name="use_mi_score" argument="-Scoring:Scores:use_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MI (mutual information) score" help=""/>
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=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	334 <param name="use_ms1_mi" argument="-Scoring:Scores:use_ms1_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MS1 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	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=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	336 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	337 </section>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	338 <expand macro="adv_opts_macro">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	339 <param name="rt_norm" 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)"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	340 <param name="swath_windows_file" 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)"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	341 <param name="sort_swath_maps" 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=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	342 <param name="use_ms1_traces" argument="-use_ms1_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the precursor ion trace(s) and use for scoring" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	343 <param name="enable_uis_scoring" argument="-enable_uis_scoring" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable additional scoring of identification assays" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	344 <param name="out_chrom_type" type="select" optional="false" label="File type of output out_chrom (Also output all computed chromatograms output in mzML (chrom.mzML) or sqMass (SQLite format))">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	345 <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	346 <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	347 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	348 <param name="min_upper_edge_dist" argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the upper edge of a Swath window to still consider a precursor, in Thomson" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	349 <param name="extra_rt_extraction_window" argument="-extra_rt_extraction_window" type="float" optional="true" 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)"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	350 <param name="mz_extraction_window_unit" argument="-mz_extraction_window_unit" display="radio" type="select" optional="false" label="Unit for mz extraction" help="">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	351 <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	352 <option value="ppm">ppm</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	353 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	354 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	355 <param name="mz_extraction_window_ms1_unit" argument="-mz_extraction_window_ms1_unit" display="radio" type="select" optional="false" label="Unit of the MS1 m/z extraction window" help="">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	356 <option value="ppm">ppm</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	357 <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	358 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	359 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	360 <param name="use_ms1_ion_mobility" 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=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	361 <param name="matching_window_only" 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)"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	362 <param name="irt_mz_extraction_window" argument="-irt_mz_extraction_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window used for iRT and m/z correction in Thomson or ppm (see irt_mz_extraction_window_unit)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	363 <param name="irt_mz_extraction_window_unit" argument="-irt_mz_extraction_window_unit" display="radio" type="select" optional="false" label="Unit for mz extraction" help="">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	364 <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	365 <option value="ppm">ppm</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	366 <expand macro="list_string_san"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	367 </param>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	368 <param name="irt_im_extraction_window" argument="-irt_im_extraction_window" type="float" optional="true" value="-1.0" label="Ion mobility extraction window used for iRT (in 1/K0 or milliseconds)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	369 <param name="min_rsq" argument="-min_rsq" type="float" optional="true" value="0.95" label="Minimum r-squared of RT peptides regression" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	370 <param name="min_coverage" argument="-min_coverage" type="float" optional="true" value="0.6" label="Minimum relative amount of RT peptides to keep" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	371 <param name="split_file_input" 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=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	372 <param name="use_elution_model_score" argument="-use_elution_model_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Turn on elution model score (EMG fit to peak)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	373 <param name="readOptions" argument="-readOptions" display="radio" type="select" optional="false" 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	374 <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	375 <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	376 <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	377 <option value="workingInMemory">workingInMemory</option>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	378 <expand macro="list_string_san"/>
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	379 </param>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	380 <param name="mz_correction_function" argument="-mz_correction_function" type="select" optional="false" 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	381 <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	382 <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	383 <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	384 <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	385 <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	386 <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	387 <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	388 <option value="quadratic_regression_delta_ppm">quadratic_regression_delta_ppm</option>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	389 <expand macro="list_string_san"/>
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	390 </param>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	391 <param name="extraction_function" argument="-extraction_function" display="radio" type="select" optional="false" 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	392 <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	393 <option value="bartlett">bartlett</option>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	394 <expand macro="list_string_san"/>
1 190554cf2195 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14 galaxyp parents: 0 diff changeset	395 </param>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	396 <param name="batchSize" argument="-batchSize" type="integer" optional="true" min="0" value="250" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 250-1000)" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	397 <param name="ms1_isotopes" argument="-ms1_isotopes" type="integer" optional="true" min="0" value="0" label="The number of MS1 isotopes used for extraction" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	398 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	399 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	400 <expand macro="list_string_san"/>
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	401 </param>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	402 </expand>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	403 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	404 <option value="out_features_FLAG">out_features (Use UIS scores for peptidoform identification)</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	405 <option value="out_tsv_FLAG">out_tsv (Use UIS scores for peptidoform identification)</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	406 <option value="out_osw_FLAG">out_osw (Use UIS scores for peptidoform identification)</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	407 <option value="out_chrom_FLAG">out_chrom (Use UIS scores for peptidoform identification)</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	408 <option value="out_qc_FLAG">out_qc (Use UIS scores for peptidoform identification)</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	409 <option value="irt_mzml_FLAG">irt_mzml (Use UIS scores for peptidoform identification)</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	410 <option value="irt_trafo_FLAG">irt_trafo (Use UIS scores for peptidoform identification)</option>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	411 <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	412 </param>
0 380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	413 </inputs>
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	414 <outputs>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	415 <data name="out_features" label="${tool.name} on ${on_string}: out_features" format="featurexml">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	416 <filter>OPTIONAL_OUTPUTS is not None and "out_features_FLAG" in OPTIONAL_OUTPUTS</filter>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	417 </data>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	418 <data name="out_tsv" label="${tool.name} on ${on_string}: out_tsv" format="tabular">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	419 <filter>OPTIONAL_OUTPUTS is not None and "out_tsv_FLAG" in OPTIONAL_OUTPUTS</filter>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	420 </data>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	421 <data name="out_osw" label="${tool.name} on ${on_string}: out_osw" format="osw">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	422 <filter>OPTIONAL_OUTPUTS is not None and "out_osw_FLAG" in OPTIONAL_OUTPUTS</filter>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	423 </data>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	424 <data name="out_chrom" label="${tool.name} on ${on_string}: out_chrom">
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	425 <change_format>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	426 <when input="adv_opts_cond.out_chrom_type" value="mzML" format="mzml"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	427 <when input="adv_opts_cond.out_chrom_type" value="sqMass" format="sqmass"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	428 </change_format>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	429 <filter>OPTIONAL_OUTPUTS is not None and "out_chrom_FLAG" in OPTIONAL_OUTPUTS</filter>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	430 </data>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	431 <data name="out_qc" label="${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>
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	447 <tests>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	448 <expand macro="autotest_OpenSwathWorkflow"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	449 <expand macro="manutest_OpenSwathWorkflow"/>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	450 </tests>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	451 <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	452
380ced982ec7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	453
9 3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	454 For more information, visit http://www.openms.de/documentation/UTILS_OpenSwathWorkflow.html]]></help>
3967f7cf35b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	455 <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	456 </tool>

Mercurial > repos > galaxyp > openms_openswathworkflow

annotate OpenSwathWorkflow.xml @ 9:3967f7cf35b9 draft