openms_mssimulator: MSSimulator.xml annotate

annotate MSSimulator.xml @ 13:9e6a371d539b draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

author	galaxyp
date	Thu, 01 Dec 2022 19:08:01 +0000
parents	04228172e123
children

rev	line source
0 7c2b85eb3ccf 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 66f0ddeb23f3 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 7c2b85eb3ccf 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]-->
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	4 <tool id="MSSimulator" name="MSSimulator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	5 <description>A highly configurable simulator for mass spectrometry experiments.</description>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	6 <macros>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	7 <token name="@EXECUTABLE@">MSSimulator</token>
7c2b85eb3ccf 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>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	9 </macros>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	10 <expand macro="requirements"/>
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	11 <expand macro="stdio"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	13 @EXT_FOO@
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	14 #import re
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	15
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	16 ## Preprocessing
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	17 mkdir in_cond.in &&
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	18 #if $in_cond.in_select == "no"
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	20 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	21 #else
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	23 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	24 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	25 mkdir out &&
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	26 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	27 #if "out_pm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	28 mkdir out_pm &&
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	29 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	30 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	31 mkdir out_fm &&
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	32 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	33 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	34 mkdir out_cm &&
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	35 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	36 #if "out_lcm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	37 mkdir out_lcm &&
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	38 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	39 #if "out_cntm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	40 mkdir out_cntm &&
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	41 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	42 #if "out_id_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	43 mkdir out_id &&
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	44 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	45
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	46 ## Main program call
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	47
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	48 set -o pipefail &&
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	49 @EXECUTABLE@ -write_ctd ./ &&
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	50 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	51 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	52 -in
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	53 #if $in_cond.in_select == "no"
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	54 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	55 #else
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	56 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	57 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	58 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	59 -out
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	60 'out/output.${gxy2omsext("mzml")}'
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	61 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	62 #if "out_pm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	63 -out_pm
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	64 'out_pm/output.${gxy2omsext("mzml")}'
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	65 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	66 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	67 -out_fm
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	68 'out_fm/output.${gxy2omsext("featurexml")}'
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	69 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	70 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	71 -out_cm
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	72 'out_cm/output.${gxy2omsext("consensusxml")}'
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	73 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	74 #if "out_lcm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	75 -out_lcm
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	76 'out_lcm/output.${gxy2omsext("consensusxml")}'
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	77 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	78 #if "out_cntm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	79 -out_cntm
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	80 'out_cntm/output.${gxy2omsext("featurexml")}'
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	81 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	82 #if "out_id_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	83 -out_id
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	84 'out_id/output.${gxy2omsext("idxml")}'
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	85 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	86 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	87 \| tee '$stdout'
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	88 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	89
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	90 ## Postprocessing
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	91 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	92 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	93 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	94 #if "out_pm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	95 && mv 'out_pm/output.${gxy2omsext("mzml")}' '$out_pm'
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	96 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	97 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	98 && mv 'out_fm/output.${gxy2omsext("featurexml")}' '$out_fm'
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	99 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	100 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	101 && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	102 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	103 #if "out_lcm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	104 && mv 'out_lcm/output.${gxy2omsext("consensusxml")}' '$out_lcm'
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	105 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	106 #if "out_cntm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	107 && mv 'out_cntm/output.${gxy2omsext("featurexml")}' '$out_cntm'
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	108 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	109 #if "out_id_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	110 && mv 'out_id/output.${gxy2omsext("idxml")}' '$out_id'
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	111 #end if
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	112 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	113 && mv '@EXECUTABLE@.ctd' '$ctd_out'
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	114 #end if]]></command>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	115 <configfiles>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	116 <inputs name="args_json" data_style="paths"/>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	117 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "algorithm": {"MSSim": {"RT": {"HPLC": {"model_file": "SIMULATION/RTPredict.model"}}, "Detectability": {"dt_model_file": "SIMULATION/DTPredict.model"}}}}]]></configfile>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	118 </configfiles>
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	119 <inputs>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	120 <conditional name="in_cond">
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	121 <param name="in_select" type="select" label="Run tool in batch mode for -in">
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	122 <option value="no">No: process all datasets jointly</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	123 <option value="yes">Yes: process each dataset in an independent job</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	124 </param>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	125 <when value="no">
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	126 <param argument="-in" type="data" format="fasta" multiple="true" optional="false" label="Input protein sequences" help=" select fasta data sets(s)"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	127 </when>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	128 <when value="yes">
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	129 <param argument="-in" type="data" format="fasta" multiple="false" optional="false" label="Input protein sequences" help=" select fasta data sets(s)"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	130 </when>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	131 </conditional>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	132 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	133 <section name="MSSim" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	134 <section name="Digestion" title="" help="" expanded="false">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	135 <param name="enzyme" argument="-algorithm:MSSim:Digestion:enzyme" type="select" optional="true" label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" help="">
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	136 <option value="Asp-N/B">Asp-N/B</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	137 <option value="Asp-N_ambic">Asp-N_ambic</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	138 <option value="Chymotrypsin">Chymotrypsin</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	139 <option value="2-iodobenzoate">2-iodobenzoate</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	140 <option value="iodosobenzoate">iodosobenzoate</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	141 <option value="Arg-C">Arg-C</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	142 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	143 <option value="CNBr">CNBr</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	144 <option value="Formic_acid">Formic_acid</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	145 <option value="Arg-C/P">Arg-C/P</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	146 <option value="Asp-N">Asp-N</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	147 <option value="cyanogen-bromide">cyanogen-bromide</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	148 <option value="Clostripain/P">Clostripain/P</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	149 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	150 <option value="no cleavage">no cleavage</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	151 <option value="unspecific cleavage">unspecific cleavage</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	152 <option value="Lys-C">Lys-C</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	153 <option value="Lys-N">Lys-N</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	154 <option value="Lys-C/P">Lys-C/P</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	155 <option value="PepsinA">PepsinA</option>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	156 <option value="TrypChymo">TrypChymo</option>
11 04228172e123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	157 <option value="Trypsin/P">Trypsin/P</option>
04228172e123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	158 <option value="V8-DE">V8-DE</option>
04228172e123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	159 <option value="V8-E">V8-E</option>
04228172e123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	160 <option value="leukocyte elastase">leukocyte elastase</option>
04228172e123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	161 <option value="proline endopeptidase">proline endopeptidase</option>
04228172e123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	162 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
04228172e123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	163 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	164 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	165 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	166 <option value="Glu-C+P">Glu-C+P</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	167 <option value="PepsinA + P">PepsinA + P</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	168 <option value="Trypsin" selected="true">Trypsin</option>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	169 <expand macro="list_string_san" name="enzyme"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	170 </param>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	171 <param name="model" argument="-algorithm:MSSim:Digestion:model" type="select" optional="true" label="The cleavage model to use for digestion" help="'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)">
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	172 <option value="trained">trained</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	173 <option value="naive" selected="true">naive</option>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	174 <expand macro="list_string_san" name="model"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	175 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	176 <param name="min_peptide_length" argument="-algorithm:MSSim:Digestion:min_peptide_length" type="integer" optional="true" min="1" value="3" label="Minimum peptide length after digestion (shorter ones will be discarded)" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	177 <section name="model_trained" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	178 <param name="threshold" argument="-algorithm:MSSim:Digestion:model_trained:threshold" type="float" optional="true" min="-2.0" max="4.0" value="0.5" label="Model threshold for calling a cleavage" help="Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	179 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	180 <section name="model_naive" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	181 <param name="missed_cleavages" argument="-algorithm:MSSim:Digestion:model_naive:missed_cleavages" type="integer" optional="true" min="0" value="1" label="Maximum number of missed cleavages considered" help="All possible resulting peptides will be created"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	182 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	183 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	184 <section name="RT" title="" help="" expanded="false">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	185 <param name="rt_column" argument="-algorithm:MSSim:RT:rt_column" type="select" optional="true" label="Modelling of an RT or CE column" help="">
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	186 <option value="none">none</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	187 <option value="HPLC" selected="true">HPLC</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	188 <option value="CE">CE</option>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	189 <expand macro="list_string_san" name="rt_column"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	190 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	191 <param name="auto_scale" argument="-algorithm:MSSim:RT:auto_scale" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Scale predicted RT's/MT's to given 'total_gradient_time'" help="If 'true', for CE this means that 'CE:lenght_d', 'CE:length_total', 'CE:voltage' have no influence"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	192 <param name="total_gradient_time" argument="-algorithm:MSSim:RT:total_gradient_time" type="float" optional="true" min="1e-05" value="2500.0" label="The duration [s] of the gradient" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	193 <param name="sampling_rate" argument="-algorithm:MSSim:RT:sampling_rate" type="float" optional="true" min="0.01" max="60.0" value="2.0" label="Time interval [s] between consecutive scans" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	194 <section name="scan_window" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	195 <param name="min" argument="-algorithm:MSSim:RT:scan_window:min" type="float" optional="true" min="0.0" value="500.0" label="Start of RT Scan Window [s]" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	196 <param name="max" argument="-algorithm:MSSim:RT:scan_window:max" type="float" optional="true" min="1.0" value="1500.0" label="End of RT Scan Window [s]" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	197 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	198 <section name="variation" title="Random component that simulates technical/biological variation" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	199 <param name="feature_stddev" argument="-algorithm:MSSim:RT:variation:feature_stddev" type="integer" optional="true" value="3" label="Standard deviation of shift in retention time [s] from predicted model (applied to every single feature independently)" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	200 <param name="affine_offset" argument="-algorithm:MSSim:RT:variation:affine_offset" type="integer" optional="true" value="0" label="Global offset in retention time [s] from predicted model" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	201 <param name="affine_scale" argument="-algorithm:MSSim:RT:variation:affine_scale" type="integer" optional="true" value="1" label="Global scaling in retention time from predicted model" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	202 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	203 <section name="column_condition" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	204 <param name="distortion" argument="-algorithm:MSSim:RT:column_condition:distortion" type="integer" optional="true" min="0" max="10" value="0" label="Distortion of the elution profiles" help="Good presets are 0 for a perfect elution profile, 1 for a slightly distorted elution profile etc... For trapping instruments (e.g. Orbitrap) distortion should be >4"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	205 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	206 <section name="profile_shape" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	207 <section name="width" title="Width of the EGH elution shape" help="i.e. the sigma^2 parameter, which is computed using 'value' + rnd_cauchy('variance')" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	208 <param name="value" argument="-algorithm:MSSim:RT:profile_shape:width:value" type="float" optional="true" min="0.0" value="9.0" label="Width of the Exponential Gaussian Hybrid distribution shape of the elution profile" help="This does not correspond directly to the width in [s]"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	209 <param name="variance" argument="-algorithm:MSSim:RT:profile_shape:width:variance" type="float" optional="true" min="0.0" value="1.6" label="Random component of the width (set to 0 to disable randomness)" help="i.e. scale parameter for the lorentzian variation of the variance (Note: The scale parameter has to be >= 0)"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	210 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	211 <section name="skewness" title="Skewness of the EGH elution shape" help="i.e. the tau parameter, which is computed using 'value' + rnd_cauchy('variance')" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	212 <param name="value" argument="-algorithm:MSSim:RT:profile_shape:skewness:value" type="float" optional="true" value="0.1" label="Asymmetric component of the EGH" help="Higher absolute(!) values lead to more skewness (negative values cause fronting, positive values cause tailing). Tau parameter of the EGH, i.e. time constant of the exponential decay of the Exponential Gaussian Hybrid distribution shape of the elution profile"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	213 <param name="variance" argument="-algorithm:MSSim:RT:profile_shape:skewness:variance" type="float" optional="true" min="0.0" value="0.3" label="Random component of skewness (set to 0 to disable randomness)" help="i.e. scale parameter for the lorentzian variation of the time constant (Note: The scale parameter has to be > 0)"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	214 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	215 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	216 <section name="CE" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	217 <param name="pH" argument="-algorithm:MSSim:RT:CE:pH" type="float" optional="true" min="0.0" max="14.0" value="3.0" label="pH of buffe" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	218 <param name="alpha" argument="-algorithm:MSSim:RT:CE:alpha" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Exponent Alpha used to calculate mobility" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	219 <param name="mu_eo" argument="-algorithm:MSSim:RT:CE:mu_eo" type="float" optional="true" min="0.0" max="5.0" value="0.0" label="Electroosmotic flow" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	220 <param name="lenght_d" argument="-algorithm:MSSim:RT:CE:lenght_d" type="float" optional="true" min="0.0" max="1000.0" value="70.0" label="Length of capillary [cm] from injection site to MS" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	221 <param name="length_total" argument="-algorithm:MSSim:RT:CE:length_total" type="float" optional="true" min="0.0" max="1000.0" value="75.0" label="Total length of capillary [cm]" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	222 <param name="voltage" argument="-algorithm:MSSim:RT:CE:voltage" type="float" optional="true" min="0.0" value="1000.0" label="Voltage applied to capillary" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	223 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	224 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	225 <section name="Detectability" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	226 <param name="dt_simulation_on" argument="-algorithm:MSSim:Detectability:dt_simulation_on" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Modelling detectibility enabled" help="This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	227 <param name="min_detect" argument="-algorithm:MSSim:Detectability:min_detect" type="float" optional="true" value="0.5" label="Minimum peptide detectability accepted" help="Peptides with a lower score will be removed"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	228 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	229 <section name="Ionization" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	230 <section name="esi" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	231 <param name="ionized_residues" argument="-algorithm:MSSim:Ionization:esi:ionized_residues" multiple="true" type="select" optional="true" label="List of residues (as three letter code) that will be considered during ES ionization" help="The N-term is always assumed to carry a charge. This parameter will be ignored during MALDI ionization">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	232 <option value="Ala">Ala</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	233 <option value="Cys">Cys</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	234 <option value="Asp">Asp</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	235 <option value="Glu">Glu</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	236 <option value="Phe">Phe</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	237 <option value="Gly">Gly</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	238 <option value="His" selected="true">His</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	239 <option value="Ile">Ile</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	240 <option value="Lys" selected="true">Lys</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	241 <option value="Leu">Leu</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	242 <option value="Met">Met</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	243 <option value="Asn">Asn</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	244 <option value="Pro">Pro</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	245 <option value="Gln">Gln</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	246 <option value="Arg" selected="true">Arg</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	247 <option value="Sec">Sec</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	248 <option value="Ser">Ser</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	249 <option value="Thr">Thr</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	250 <option value="Val">Val</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	251 <option value="Trp">Trp</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	252 <option value="Tyr">Tyr</option>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	253 <expand macro="list_string_san" name="ionized_residues"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	254 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	255 <param name="charge_impurity" argument="-algorithm:MSSim:Ionization:esi:charge_impurity" type="text" optional="true" value="H+:1" label="List of charged ions that contribute to charge with weight of occurrence (their sum is scaled to 1 internally)" help="e.g. ['H:1'] or ['H:0.7' 'Na:0.3'], ['H:4' 'Na:1'] (which internally translates to ['H:0.8' 'Na:0.2']) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	256 <expand macro="list_string_val" name="charge_impurity"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	257 <expand macro="list_string_san" name="charge_impurity"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	258 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	259 <param name="max_impurity_set_size" argument="-algorithm:MSSim:Ionization:esi:max_impurity_set_size" type="integer" optional="true" value="3" label="Maximal #combinations of charge impurities allowed (each generating one feature) per charge state" help="E.g. assuming charge=3 and this parameter is 2, then we could choose to allow '3H+, 2H+Na+' features (given a certain 'charge_impurity' constraints), but no '3H+, 2H+Na+, 3Na+'"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	260 <param name="ionization_probability" argument="-algorithm:MSSim:Ionization:esi:ionization_probability" type="float" optional="true" value="0.8" label="Probability for the binomial distribution of the ESI charge states" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	261 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	262 <section name="maldi" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	263 <param name="ionization_probabilities" argument="-algorithm:MSSim:Ionization:maldi:ionization_probabilities" type="text" optional="true" value="0.9 0.1 0.0" label="List of probabilities for different charge states (starting at charge=1, 2, ...) during MALDI ionization (the list must sum up to 1.0)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	264 <expand macro="list_float_valsan" name="ionization_probabilities"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	265 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	266 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	267 <section name="mz" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	268 <param name="lower_measurement_limit" argument="-algorithm:MSSim:Ionization:mz:lower_measurement_limit" type="float" optional="true" min="0.0" value="200.0" label="Lower m/z detector limit" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	269 <param name="upper_measurement_limit" argument="-algorithm:MSSim:Ionization:mz:upper_measurement_limit" type="float" optional="true" min="0.0" value="1200.0" label="Upper m/z detector limit" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	270 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	271 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	272 <section name="RawSignal" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	273 <param name="enabled" argument="-algorithm:MSSim:RawSignal:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable RAW signal simulation" help="(select 'false' if you only need feature-maps)"/>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	274 <param name="peak_shape" argument="-algorithm:MSSim:RawSignal:peak_shape" type="select" optional="true" label="Peak Shape used around each isotope peak (be aware that the area under the curve is constant for both types, but the maximal height will differ (~ 2:3 = Lorentz:Gaussian) due to the wider base of the Lorentzian" help="">
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	275 <option value="Gaussian" selected="true">Gaussian</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	276 <option value="Lorentzian">Lorentzian</option>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	277 <expand macro="list_string_san" name="peak_shape"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	278 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	279 <section name="resolution" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	280 <param name="value" argument="-algorithm:MSSim:RawSignal:resolution:value" type="integer" optional="true" value="50000" label="Instrument resolution at 400 Th" help=""/>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	281 <param name="type" argument="-algorithm:MSSim:RawSignal:resolution:type" type="select" optional="true" label="How does resolution change with increasing m/z" help="QTOFs usually show 'constant' behavior, FTs have linear degradation, and on Orbitraps the resolution decreases with square root of mass">
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	282 <option value="constant">constant</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	283 <option value="linear" selected="true">linear</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	284 <option value="sqrt">sqrt</option>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	285 <expand macro="list_string_san" name="type"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	286 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	287 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	288 <section name="baseline" title="Baseline modeling for MALDI ionization" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	289 <param name="scaling" argument="-algorithm:MSSim:RawSignal:baseline:scaling" type="float" optional="true" min="0.0" value="0.0" label="Scale of baseline" help="Set to 0 to disable simulation of baseline"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	290 <param name="shape" argument="-algorithm:MSSim:RawSignal:baseline:shape" type="float" optional="true" min="0.0" value="0.5" label="The baseline is modeled by an exponential probability density function (pdf) with f(x) = shapee^(- shapex)" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	291 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	292 <section name="mz" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	293 <param name="sampling_points" argument="-algorithm:MSSim:RawSignal:mz:sampling_points" type="integer" optional="true" min="2" value="3" label="Number of raw data points per FWHM of the peak" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	294 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	295 <section name="contaminants" title="" help="" expanded="false">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	296 <param name="file" argument="-algorithm:MSSim:RawSignal:contaminants:file" type="text" optional="true" value="SIMULATION/contaminants.csv" label="Contaminants file with sum formula and absolute RT interval" help="See 'share/OpenMS/SIMULATION/contaminants.txt' for details">
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	297 <expand macro="list_string_san" name="file"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	298 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	299 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	300 <section name="variation" title="Random components that simulate biological and technical variations of the simulated data" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	301 <section name="mz" title="Shifts in mass to charge dimension of the simulated signals" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	302 <param name="error_mean" argument="-algorithm:MSSim:RawSignal:variation:mz:error_mean" type="float" optional="true" value="0.0" label="Average systematic m/z error (in Da)" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	303 <param name="error_stddev" argument="-algorithm:MSSim:RawSignal:variation:mz:error_stddev" type="float" optional="true" value="0.0" label="Standard deviation for m/z errors" help="Set to 0 to disable simulation of m/z errors"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	304 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	305 <section name="intensity" title="Variations in intensity to model randomness in feature intensity" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	306 <param name="scale" argument="-algorithm:MSSim:RawSignal:variation:intensity:scale" type="float" optional="true" min="0.0" value="100.0" label="Constant scale factor of the feature intensity" help="Set to 1.0 to get the real intensity values provided in the FASTA file"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	307 <param name="scale_stddev" argument="-algorithm:MSSim:RawSignal:variation:intensity:scale_stddev" type="float" optional="true" min="0.0" value="0.0" label="Standard deviation of peak intensity (relative to the scaled peak height)" help="Set to 0 to get simple rescaled intensities"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	308 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	309 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	310 <section name="noise" title="Parameters modeling noise in mass spectrometry measurements" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	311 <section name="shot" title="Parameters of Poisson and Exponential for shot noise modeling (set :rate OR :mean = 0 to disable)" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	312 <param name="rate" argument="-algorithm:MSSim:RawSignal:noise:shot:rate" type="float" optional="true" min="0.0" value="0.0" label="Poisson rate of shot noise per unit m/z (random peaks in m/z, where the number of peaks per unit m/z follows a Poisson distribution)" help="Set this to 0 to disable simulation of shot noise"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	313 <param name="intensity_mean" argument="-algorithm:MSSim:RawSignal:noise:shot:intensity-mean" type="float" optional="true" value="1.0" label="Shot noise intensity mean (exponentially distributed with given mean)" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	314 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	315 <section name="white" title="Parameters of Gaussian distribution for white noise modeling (set :mean AND :stddev = 0 to disable)" help="No new peaks are generated; only intensity of existing ones is changed" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	316 <param name="mean" argument="-algorithm:MSSim:RawSignal:noise:white:mean" type="float" optional="true" value="0.0" label="Mean value of white noise (Gaussian) being added to each measured signal intensity" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	317 <param name="stddev" argument="-algorithm:MSSim:RawSignal:noise:white:stddev" type="float" optional="true" value="0.0" label="Standard deviation of white noise being added to each measured signal intensity" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	318 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	319 <section name="detector" title="Parameters of Gaussian distribution for detector noise modeling (set :mean AND :stddev = 0 to disable)" help="If enabled, ALL possible m/z positions (up to sampling frequency of detector) will receive an intensity increase/decrease according to the specified Gaussian intensity distribution (similar to a noisy baseline)" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	320 <param name="mean" argument="-algorithm:MSSim:RawSignal:noise:detector:mean" type="float" optional="true" value="0.0" label="Mean intensity value of the detector noise (Gaussian distribution)" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	321 <param name="stddev" argument="-algorithm:MSSim:RawSignal:noise:detector:stddev" type="float" optional="true" value="0.0" label="Standard deviation of the detector noise (Gaussian distribution)" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	322 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	323 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	324 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	325 <section name="RawTandemSignal" title="" help="" expanded="false">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	326 <param name="status" argument="-algorithm:MSSim:RawTandemSignal:status" type="select" optional="true" label="Create Tandem-MS scans?" help="">
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	327 <option value="disabled" selected="true">disabled</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	328 <option value="precursor">precursor</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	329 <option value="MS^E">MS^E</option>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	330 <expand macro="list_string_san" name="status"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	331 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	332 <param name="tandem_mode" argument="-algorithm:MSSim:RawTandemSignal:tandem_mode" type="integer" optional="true" min="0" max="2" value="0" label="Algorithm to generate the tandem-MS spectra" help="0 - fixed intensities, 1 - SVC prediction (abundant/missing), 2 - SVR prediction of peak intensity . "/>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	333 <param name="svm_model_set_file" argument="-algorithm:MSSim:RawTandemSignal:svm_model_set_file" type="text" optional="true" value="SIMULATION/SvmModelSet.model" label="File containing the filenames of SVM Models for different charge variants" help="">
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	334 <expand macro="list_string_san" name="svm_model_set_file"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	335 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	336 <section name="Precursor" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	337 <param name="ms2_spectra_per_rt_bin" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ms2_spectra_per_rt_bin" type="integer" optional="true" min="1" value="5" label="Number of allowed MS/MS spectra in a retention time bin" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	338 <param name="min_mz_peak_distance" argument="-algorithm:MSSim:RawTandemSignal:Precursor:min_mz_peak_distance" type="float" optional="true" min="0.0001" value="2.0" label="The minimal distance (in Th) between two peaks for concurrent selection for fragmentation" help="Also used to define the m/z width of an exclusion window (distance +/- from m/z of precursor). If you set this lower than the isotopic envelope of a peptide, you might get multiple fragment spectra pointing to the same precursor"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	339 <param name="mz_isolation_window" argument="-algorithm:MSSim:RawTandemSignal:Precursor:mz_isolation_window" type="float" optional="true" min="0.0" value="2.0" label="All peaks within a mass window (in Th) of a selected peak are also selected for fragmentation" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	340 <param name="exclude_overlapping_peaks" argument="-algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	341 <param name="charge_filter" argument="-algorithm:MSSim:RawTandemSignal:Precursor:charge_filter" type="text" optional="true" value="2 3" label="Charges considered for MS2 fragmentation" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	342 <expand macro="list_integer_valsan" name="charge_filter">
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	343 <validator type="expression" message="a space separated list of integer values in the range 1:5 is required"><![CDATA[len(value.split(' ')) == len([_ for _ in value.split(' ') if 1 <= int(_) <= 5])
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	344 ]]></validator>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	345 </expand>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	346 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	347 <section name="Exclusion" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	348 <param name="use_dynamic_exclusion" argument="-algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true dynamic exclusion is applied" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	349 <param name="exclusion_time" argument="-algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:exclusion_time" type="float" optional="true" min="0.0" value="100.0" label="The time (in seconds) a feature is excluded" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	350 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	351 <section name="ProteinBasedInclusion" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	352 <param name="max_list_size" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size" type="integer" optional="true" min="1" value="1000" label="The maximal number of precursors in the inclusion list" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	353 <section name="rt" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	354 <param name="min_rt" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt" type="float" optional="true" min="0.0" value="960.0" label="Minimal rt in seconds" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	355 <param name="max_rt" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt" type="float" optional="true" min="0.0" value="3840.0" label="Maximal rt in seconds" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	356 <param name="rt_step_size" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size" type="float" optional="true" min="1.0" value="30.0" label="rt step size in seconds" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	357 <param name="rt_window_size" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size" type="integer" optional="true" min="1" value="100" label="rt window size in seconds" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	358 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	359 <section name="thresholds" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	360 <param name="min_protein_id_probability" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="Minimal protein probability for a protein to be considered identified" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	361 <param name="min_pt_weight" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Minimal pt weight of a precurso" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	362 <param name="min_mz" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz" type="float" optional="true" min="0.0" value="500.0" label="Minimal mz to be considered in protein based LP formulation" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	363 <param name="max_mz" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz" type="float" optional="true" min="0.0" value="5000.0" label="Minimal mz to be considered in protein based LP formulation" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	364 <param name="use_peptide_rule" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use peptide rule instead of minimal protein id probability" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	365 <param name="min_peptide_ids" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids" type="integer" optional="true" min="1" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	366 <param name="min_peptide_probability" argument="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	367 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	368 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	369 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	370 <section name="MS_E" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	371 <param name="add_single_spectra" argument="-algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, the MS2 spectra for each peptide signal are included in the output (might be a lot)" help="They will have a meta value 'MSE_DebugSpectrum' attached, so they can be filtered out. Native MS_E spectra will have 'MSE_Spectrum' instead"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	372 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	373 <section name="TandemSim" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	374 <section name="Simple" title="" help="" expanded="false">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	375 <param name="isotope_model" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:isotope_model" type="select" optional="true" label="Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks" help="Note that adding isotopic peaks is very slow">
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	376 <option value="none" selected="true">none</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	377 <option value="coarse">coarse</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	378 <option value="fine">fine</option>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	379 <expand macro="list_string_san" name="isotope_model"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	380 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	381 <param name="max_isotope" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope" type="integer" optional="true" value="2" label="Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	382 <param name="max_isotope_probability" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope_probability" type="float" optional="true" value="0.05" label="Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	383 <param name="add_metainfo" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	384 <param name="add_losses" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	385 <param name="sort_by_position" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:sort_by_position" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Sort output by position" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	386 <param name="add_precursor_peaks" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds peaks of the unfragmented precursor ion to the spectrum" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	387 <param name="add_all_precursor_charges" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds precursor peaks with all charges in the given range" help=""/>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	388 <param name="add_abundant_immonium_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add most abundant immonium ions (for Proline, Cystein, Iso/Leucine, Histidin, Phenylalanin, Tyrosine, Tryptophan)" help=""/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	389 <param name="add_first_prefix_ion" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true e.g. b1 ions are added" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	390 <param name="add_y_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Add peaks of y-ions to the spectrum" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	391 <param name="add_b_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Add peaks of b-ions to the spectrum" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	392 <param name="add_a_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of a-ions to the spectrum" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	393 <param name="add_c_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of c-ions to the spectrum" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	394 <param name="add_x_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of x-ions to the spectrum" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	395 <param name="add_z_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of z-ions to the spectrum" help=""/>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	396 <param name="y_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:y_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the y-ions" help=""/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	397 <param name="b_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:b_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the b-ions" help=""/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	398 <param name="a_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:a_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the a-ions" help=""/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	399 <param name="c_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:c_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the c-ions" help=""/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	400 <param name="x_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:x_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the x-ions" help=""/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	401 <param name="z_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:z_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the z-ions" help=""/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	402 <param name="relative_loss_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:relative_loss_intensity" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help=""/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	403 <param name="precursor_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the precursor peak" help=""/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	404 <param name="precursor_H2O_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the H2O loss peak of the precurso" help=""/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	405 <param name="precursor_NH3_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity" type="float" optional="true" min="0.0" value="1.0" label="Intensity of the NH3 loss peak of the precurso" help=""/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	406 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	407 <section name="SVM" title="" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	408 <param name="add_isotopes" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to 1 isotope peaks of the product ion peaks are added" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	409 <param name="max_isotope" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:max_isotope" type="integer" optional="true" value="2" label="Defines the maximal isotopic peak which is added, add_isotopes must be set to 1" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	410 <param name="add_metainfo" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_metainfo" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	411 <param name="add_first_prefix_ion" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_first_prefix_ion" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true e.g. b1 ions are added" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	412 <param name="hide_y_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of y-ions to the spectrum" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	413 <param name="hide_y2_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of y-ions to the spectrum" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	414 <param name="hide_b_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of b-ions to the spectrum" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	415 <param name="hide_b2_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of b-ions to the spectrum" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	416 <param name="hide_a_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of a-ions to the spectrum" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	417 <param name="hide_c_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of c-ions to the spectrum" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	418 <param name="hide_x_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of x-ions to the spectrum" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	419 <param name="hide_z_ions" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add peaks of z-ions to the spectrum" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	420 <param name="hide_losses" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	421 <param name="y_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:y_intensity" type="float" optional="true" value="1.0" label="Intensity of the y-ions" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	422 <param name="b_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:b_intensity" type="float" optional="true" value="1.0" label="Intensity of the b-ions" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	423 <param name="a_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:a_intensity" type="float" optional="true" value="1.0" label="Intensity of the a-ions" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	424 <param name="c_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:c_intensity" type="float" optional="true" value="1.0" label="Intensity of the c-ions" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	425 <param name="x_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:x_intensity" type="float" optional="true" value="1.0" label="Intensity of the x-ions" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	426 <param name="z_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:z_intensity" type="float" optional="true" value="1.0" label="Intensity of the z-ions" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	427 <param name="relative_loss_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity" type="float" optional="true" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	428 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	429 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	430 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	431 <section name="Global" title="" help="" expanded="false">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	432 <param name="ionization_type" argument="-algorithm:MSSim:Global:ionization_type" type="select" optional="true" label="Type of Ionization (MALDI or ESI)" help="">
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	433 <option value="MALDI">MALDI</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	434 <option value="ESI" selected="true">ESI</option>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	435 <expand macro="list_string_san" name="ionization_type"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	436 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	437 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	438 <section name="Labeling" title="" help="" expanded="false">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	439 <param name="type" argument="-algorithm:MSSim:Labeling:type" type="select" optional="true" label="Select the labeling type you want for your experiment" help="">
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	440 <option value="ICPL">ICPL</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	441 <option value="SILAC">SILAC</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	442 <option value="itraq">itraq</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	443 <option value="labelfree" selected="true">labelfree</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	444 <option value="o18">o18</option>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	445 <expand macro="list_string_san" name="type"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	446 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	447 <section name="ICPL" title="ICPL labeling on MS1 level of lysines and n-term (on protein or peptide level) with either two or three channels" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	448 <param name="ICPL_fixed_rtshift" argument="-algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift" type="float" optional="true" value="0.0" label="Fixed retention time shift between labeled pairs" help="If set to 0.0 only the retention times, computed by the RT model step are used"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	449 <param name="label_proteins" argument="-algorithm:MSSim:Labeling:ICPL:label_proteins" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables protein-labeling" help="(select 'false' if you only need peptide-labeling)"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	450 <param name="ICPL_light_channel_label" argument="-algorithm:MSSim:Labeling:ICPL:ICPL_light_channel_label" type="text" optional="true" value="UniMod:365" label="UniMod Id of the light channel ICPL label" help="">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	451 <expand macro="list_string_san" name="ICPL_light_channel_label"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	452 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	453 <param name="ICPL_medium_channel_label" argument="-algorithm:MSSim:Labeling:ICPL:ICPL_medium_channel_label" type="text" optional="true" value="UniMod:687" label="UniMod Id of the medium channel ICPL label" help="">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	454 <expand macro="list_string_san" name="ICPL_medium_channel_label"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	455 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	456 <param name="ICPL_heavy_channel_label" argument="-algorithm:MSSim:Labeling:ICPL:ICPL_heavy_channel_label" type="text" optional="true" value="UniMod:364" label="UniMod Id of the heavy channel ICPL label" help="">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	457 <expand macro="list_string_san" name="ICPL_heavy_channel_label"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	458 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	459 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	460 <section name="SILAC" title="SILAC labeling on MS1 level with up to 3 channels and custom modifications" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	461 <param name="fixed_rtshift" argument="-algorithm:MSSim:Labeling:SILAC:fixed_rtshift" type="float" optional="true" min="0.0" value="0.0001" label="Fixed retention time shift between labeled peptides" help="If set to 0.0 only the retention times computed by the RT model step are used"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	462 <section name="medium_channel" title="Modifications for the medium SILAC channel" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	463 <param name="modification_lysine" argument="-algorithm:MSSim:Labeling:SILAC:medium_channel:modification_lysine" type="text" optional="true" value="UniMod:481" label="Modification of Lysine in the medium SILAC channel" help="">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	464 <expand macro="list_string_san" name="modification_lysine"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	465 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	466 <param name="modification_arginine" argument="-algorithm:MSSim:Labeling:SILAC:medium_channel:modification_arginine" type="text" optional="true" value="UniMod:188" label="Modification of Arginine in the medium SILAC channel" help="">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	467 <expand macro="list_string_san" name="modification_arginine"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	468 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	469 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	470 <section name="heavy_channel" title="Modifications for the heavy SILAC channel" help="If you want to use only 2 channels, just leave the Labels as they are and provide only 2 input files" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	471 <param name="modification_lysine" argument="-algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_lysine" type="text" optional="true" value="UniMod:259" label="Modification of Lysine in the heavy SILAC channel" help="If left empty, two channelSILAC is assumed">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	472 <expand macro="list_string_san" name="modification_lysine"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	473 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	474 <param name="modification_arginine" argument="-algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine" type="text" optional="true" value="UniMod:267" label="Modification of Arginine in the heavy SILAC channel" help="If left empty, two-channel SILAC is assumed">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	475 <expand macro="list_string_san" name="modification_arginine"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	476 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	477 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	478 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	479 <section name="itraq" title="iTRAQ labeling on MS2 level with up to 4 (4plex) or 8 (8plex) channels" help="" expanded="false">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	480 <param name="iTRAQ" argument="-algorithm:MSSim:Labeling:itraq:iTRAQ" type="select" optional="true" label="4plex or 8plex iTRAQ?" help="">
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	481 <option value="4plex" selected="true">4plex</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	482 <option value="8plex">8plex</option>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	483 <expand macro="list_string_san" name="iTRAQ"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	484 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	485 <param name="reporter_mass_shift" argument="-algorithm:MSSim:Labeling:itraq:reporter_mass_shift" type="float" optional="true" min="0.0" max="0.5" value="0.1" label="Allowed shift (uniformly distributed - left to right) in Da from the expected position (of" help="e.g. 114.1, 115.1)"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	486 <param name="channel_active_4plex" argument="-algorithm:MSSim:Labeling:itraq:channel_active_4plex" type="text" optional="true" value="114:myReference" label="Four-plex only: Each channel that was used in the experiment and its description (114-117) in format <channel>:<name" help="e.g. "114:myref","115:liver" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	487 <expand macro="list_string_val" name="channel_active_4plex"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	488 <expand macro="list_string_san" name="channel_active_4plex"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	489 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	490 <param name="channel_active_8plex" argument="-algorithm:MSSim:Labeling:itraq:channel_active_8plex" type="text" optional="true" value="113:myReference" label="Eight-plex only: Each channel that was used in the experiment and its description (113-121) in format <channel>:<name" help="e.g. "113:myref","115:liver","118:lung" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	491 <expand macro="list_string_val" name="channel_active_8plex"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	492 <expand macro="list_string_san" name="channel_active_8plex"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	493 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	494 <param name="isotope_correction_values_4plex" argument="-algorithm:MSSim:Labeling:itraq:isotope_correction_values_4plex" type="text" optional="true" value="114:0.0/1.0/5.9/0.2 115:0.0/2.0/5.6/0.1 116:0.0/3.0/4.5/0.1 117:0.1/4.0/3.5/0.1" label="override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ;" help="e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	495 <expand macro="list_string_val" name="isotope_correction_values_4plex"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	496 <expand macro="list_string_san" name="isotope_correction_values_4plex"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	497 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	498 <param name="isotope_correction_values_8plex" argument="-algorithm:MSSim:Labeling:itraq:isotope_correction_values_8plex" type="text" optional="true" value="113:0.0/0.0/6.89/0.22 114:0.0/0.94/5.9/0.16 115:0.0/1.88/4.9/0.1 116:0.0/2.82/3.9/0.07 117:0.06/3.77/2.99/0.0 118:0.09/4.71/1.88/0.0 119:0.14/5.66/0.87/0.0 121:0.27/7.44/0.18/0.0" label="override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ;" help="e.g. '113:0/0.3/4/0' , '116:0.1/0.3/3/0.2' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	499 <expand macro="list_string_val" name="isotope_correction_values_8plex"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	500 <expand macro="list_string_san" name="isotope_correction_values_8plex"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	501 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	502 <param name="Y_contamination" argument="-algorithm:MSSim:Labeling:itraq:Y_contamination" type="float" optional="true" min="0.0" max="1.0" value="0.3" label="Efficiency of labeling tyrosine ('Y') residues" help="0=off, 1=full labeling"/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	503 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	504 <section name="o18" title="18O labeling on MS1 level with 2 channels, requiring trypsin digestion" help="" expanded="false">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	505 <param name="labeling_efficiency" argument="-algorithm:MSSim:Labeling:o18:labeling_efficiency" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Describes the distribution of the labeled peptide over the different states (unlabeled, mono- and di-labeled)" help=""/>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	506 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	507 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	508 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	509 <section name="RandomNumberGenerators" title="Parameters for generating the random aspects" help="(e.g. noise) in the simulated data. The generation is separated into two parts, the technical part, like noise in the raw signal, and the biological part, like systematic deviations in the predicted retention times" expanded="false">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	510 <param name="biological" argument="-algorithm:RandomNumberGenerators:biological" type="select" optional="true" label="Controls the 'biological' randomness of the generated data" help="(e.g. systematic effects like deviations in RT). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same)">
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	511 <option value="reproducible">reproducible</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	512 <option value="random" selected="true">random</option>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	513 <expand macro="list_string_san" name="biological"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	514 </param>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	515 <param name="technical" argument="-algorithm:RandomNumberGenerators:technical" type="select" optional="true" label="Controls the 'technical' randomness of the generated data" help="(e.g. noise in the raw signal). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same)">
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	516 <option value="reproducible">reproducible</option>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	517 <option value="random" selected="true">random</option>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	518 <expand macro="list_string_san" name="technical"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	519 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	520 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	521 </section>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	522 <expand macro="adv_opts_macro">
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	523 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	524 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	525 <expand macro="list_string_san" name="test"/>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	526 </param>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	527 </expand>
11 04228172e123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	528 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
04228172e123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	529 <option value="out_FLAG">out (output: simulated MS raw (profile) data)</option>
04228172e123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	530 <option value="out_pm_FLAG">out_pm (output: ground-truth picked (centroided) MS data)</option>
04228172e123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	531 <option value="out_fm_FLAG">out_fm (output: ground-truth features)</option>
04228172e123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	532 <option value="out_cm_FLAG">out_cm (output: ground-truth features, grouping ESI charge variants of each parent peptide)</option>
04228172e123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	533 <option value="out_lcm_FLAG">out_lcm (output: ground-truth features, grouping labeled variants)</option>
04228172e123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	534 <option value="out_cntm_FLAG">out_cntm (output: ground-truth features caused by contaminants)</option>
04228172e123 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	535 <option value="out_id_FLAG">out_id (output: ground-truth MS2 peptide identifications)</option>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	536 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	537 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	538 </inputs>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	539 <outputs>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	540 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	541 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	542 </data>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	543 <data name="out_pm" label="${tool.name} on ${on_string}: out_pm" format="mzml">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	544 <filter>OPTIONAL_OUTPUTS is not None and "out_pm_FLAG" in OPTIONAL_OUTPUTS</filter>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	545 </data>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	546 <data name="out_fm" label="${tool.name} on ${on_string}: out_fm" format="featurexml">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	547 <filter>OPTIONAL_OUTPUTS is not None and "out_fm_FLAG" in OPTIONAL_OUTPUTS</filter>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	548 </data>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	549 <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	550 <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	551 </data>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	552 <data name="out_lcm" label="${tool.name} on ${on_string}: out_lcm" format="consensusxml">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	553 <filter>OPTIONAL_OUTPUTS is not None and "out_lcm_FLAG" in OPTIONAL_OUTPUTS</filter>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	554 </data>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	555 <data name="out_cntm" label="${tool.name} on ${on_string}: out_cntm" format="featurexml">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	556 <filter>OPTIONAL_OUTPUTS is not None and "out_cntm_FLAG" in OPTIONAL_OUTPUTS</filter>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	557 </data>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	558 <data name="out_id" label="${tool.name} on ${on_string}: out_id" format="idxml">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	559 <filter>OPTIONAL_OUTPUTS is not None and "out_id_FLAG" in OPTIONAL_OUTPUTS</filter>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	560 </data>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	561 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	562 <filter>OPTIONAL_OUTPUTS is None</filter>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	563 </data>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	564 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	565 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	566 </data>
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	567 </outputs>
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	568 <tests><test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	569 <param name="adv_opts\|test" value="true"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	570 <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	571 <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	572 <output name="out" ftype="mzml" value="MSsimulator.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	573 <param name="algorithm\|RandomNumberGenerators\|biological" value="reproducible"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	574 <param name="algorithm\|RandomNumberGenerators\|technical" value="reproducible"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	575 </test>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	576 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter generate MALDI output for use in the test for DeMeanderize -->
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	577 <param name="adv_opts\|test" value="true"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	578 <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	579 <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	580 <output name="out" ftype="mzml" value="MSsimulator_MALDI.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	581 <param name="algorithm\|RandomNumberGenerators\|biological" value="reproducible"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	582 <param name="algorithm\|RandomNumberGenerators\|technical" value="reproducible"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	583 <param name="algorithm\|MSSim\|Global\|ionization_type" value="MALDI"/>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	584 </test>
9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	585 </tests>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	586 <help><![CDATA[A highly configurable simulator for mass spectrometry experiments.
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	587
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	588
13 9e6a371d539b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	589 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MSSimulator.html]]></help>
9 98bb49e7b5ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	590 <expand macro="references"/>
0 7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	591 </tool>

Mercurial > repos > galaxyp > openms_mssimulator

annotate MSSimulator.xml @ 13:9e6a371d539b draft default tip