openms_mssimulator: MSSimulator.xml annotate

annotate MSSimulator.xml @ 15:ad1ad0e62a92 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

author	galaxyp
date	Tue, 13 Oct 2020 18:51:30 +0000
parents	140b883daa61
children

rev	line source
0 ae8e96c8f9a4 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'?>
12 582f4ea310c5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5 galaxyp parents: 3 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 ae8e96c8f9a4 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 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	4 <tool id="MSSimulator" name="MSSimulator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
0 ae8e96c8f9a4 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>
ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	6 <macros>
ae8e96c8f9a4 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>
ae8e96c8f9a4 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>
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	9 <import>macros_autotest.xml</import>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	10 <import>macros_test.xml</import>
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	11 </macros>
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	12 <expand macro="requirements"/>
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	13 <expand macro="stdio"/>
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	15 @EXT_FOO@
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	16 #import re
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	17
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	18 ## Preprocessing
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	19 mkdir in &&
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	22 mkdir out &&
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	23 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	24 #if "out_pm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	25 mkdir out_pm &&
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	26 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	27 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	28 mkdir out_fm &&
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	29 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	30 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	31 mkdir out_cm &&
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	32 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	33 #if "out_lcm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	34 mkdir out_lcm &&
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	35 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	36 #if "out_cntm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	37 mkdir out_cntm &&
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	38 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	39 #if "out_id_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	40 mkdir out_id &&
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	41 #end if
ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	42
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	43 ## Main program call
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	44
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	45 set -o pipefail &&
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	46 @EXECUTABLE@ -write_ctd ./ &&
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	47 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	48 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	49 -in
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	50 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	51 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	52 -out
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	53 'out/output.${gxy2omsext("mzml")}'
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	54 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	55 #if "out_pm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	56 -out_pm
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	57 'out_pm/output.${gxy2omsext("mzml")}'
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	58 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	59 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	60 -out_fm
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	61 'out_fm/output.${gxy2omsext("featurexml")}'
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	62 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	63 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	64 -out_cm
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	65 'out_cm/output.${gxy2omsext("consensusxml")}'
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	66 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	67 #if "out_lcm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	68 -out_lcm
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	69 'out_lcm/output.${gxy2omsext("consensusxml")}'
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	70 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	71 #if "out_cntm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	72 -out_cntm
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	73 'out_cntm/output.${gxy2omsext("featurexml")}'
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	74 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	75 #if "out_id_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	76 -out_id
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	77 'out_id/output.${gxy2omsext("idxml")}'
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	78 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	79 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	80 \| tee '$stdout'
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	81 #end if
ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	82
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	83 ## Postprocessing
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	84 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	85 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	86 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	87 #if "out_pm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	88 && mv 'out_pm/output.${gxy2omsext("mzml")}' '$out_pm'
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	89 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	90 #if "out_fm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	91 && mv 'out_fm/output.${gxy2omsext("featurexml")}' '$out_fm'
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	92 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	93 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	94 && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	95 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	96 #if "out_lcm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	97 && mv 'out_lcm/output.${gxy2omsext("consensusxml")}' '$out_lcm'
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	98 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	99 #if "out_cntm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	100 && mv 'out_cntm/output.${gxy2omsext("featurexml")}' '$out_cntm'
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	101 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	102 #if "out_id_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	103 && mv 'out_id/output.${gxy2omsext("idxml")}' '$out_id'
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	104 #end if
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	105 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	106 && mv '@EXECUTABLE@.ctd' '$ctd_out'
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	107 #end if]]></command>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	108 <configfiles>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	109 <inputs name="args_json" data_style="paths"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	110 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	111 </configfiles>
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	112 <inputs>
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	113 <param name="in" argument="-in" type="data" format="fasta" multiple="true" optional="false" label="Input protein sequences" help=" select fasta data sets(s)"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	114 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	115 <section name="MSSim" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	116 <section name="Digestion" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	117 <param name="enzyme" argument="-algorithm:MSSim:Digestion:enzyme" type="select" optional="false" label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" help="">
15 ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	118 <option value="Trypsin/P">Trypsin/P</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	119 <option value="V8-DE">V8-DE</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	120 <option value="V8-E">V8-E</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	121 <option value="leukocyte elastase">leukocyte elastase</option>
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	122 <option value="Asp-N/B">Asp-N/B</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	123 <option value="Asp-N_ambic">Asp-N_ambic</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	124 <option value="Chymotrypsin">Chymotrypsin</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	125 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	126 <option value="CNBr">CNBr</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	127 <option value="Formic_acid">Formic_acid</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	128 <option value="Lys-C">Lys-C</option>
15 ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	129 <option value="proline endopeptidase">proline endopeptidase</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	130 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	131 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	132 <option value="2-iodobenzoate">2-iodobenzoate</option>
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	133 <option value="iodosobenzoate">iodosobenzoate</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	134 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	135 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	136 <option value="Glu-C+P">Glu-C+P</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	137 <option value="PepsinA + P">PepsinA + P</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	138 <option value="cyanogen-bromide">cyanogen-bromide</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	139 <option value="Clostripain/P">Clostripain/P</option>
15 ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	140 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	141 <option value="Arg-C">Arg-C</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	142 <option value="Arg-C/P">Arg-C/P</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	143 <option value="Asp-N">Asp-N</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	144 <option value="no cleavage">no cleavage</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	145 <option value="unspecific cleavage">unspecific cleavage</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	146 <option value="Lys-N">Lys-N</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	147 <option value="Lys-C/P">Lys-C/P</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	148 <option value="PepsinA">PepsinA</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	149 <option value="TrypChymo">TrypChymo</option>
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	150 <option value="Trypsin" selected="true">Trypsin</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	151 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	152 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	153 <param name="model" argument="-algorithm:MSSim:Digestion:model" display="radio" type="select" optional="false" label="The cleavage model to use for digestion" help="'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	154 <option value="trained">trained</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	155 <option value="naive" selected="true">naive</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	156 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	157 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	158 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	159 <section name="model_trained" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	160 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	161 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	162 <section name="model_naive" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	163 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	164 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	165 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	166 <section name="RT" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	167 <param name="rt_column" argument="-algorithm:MSSim:RT:rt_column" display="radio" type="select" optional="false" label="Modelling of an RT or CE column" help="">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	168 <option value="none">none</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	169 <option value="HPLC" selected="true">HPLC</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	170 <option value="CE">CE</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	171 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	172 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	173 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	174 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	175 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	176 <section name="scan_window" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	177 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	178 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	179 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	180 <section name="variation" title="Random component that simulates technical/biological variation" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	181 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	182 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	183 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	184 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	185 <section name="column_condition" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	186 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	187 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	188 <section name="profile_shape" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	189 <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">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	190 <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]"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	191 <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)"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	192 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	193 <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">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	194 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	195 <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)"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	196 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	197 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	198 <section name="HPLC" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	199 <param name="model_file" argument="-algorithm:MSSim:RT:HPLC:model_file" type="text" optional="true" value="examples/simulation/RTPredict.model" label="SVM model for retention time prediction" help="">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	200 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	201 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	202 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	203 <section name="CE" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	204 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	205 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	206 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	207 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	208 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	209 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	210 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	211 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	212 <section name="Detectability" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	213 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	214 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	215 <param name="dt_model_file" argument="-algorithm:MSSim:Detectability:dt_model_file" type="text" optional="true" value="examples/simulation/DTPredict.model" label="SVM model for peptide detectability prediction" help="">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	216 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	217 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	218 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	219 <section name="Ionization" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	220 <section name="esi" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	221 <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">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	222 <option value="Ala">Ala</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	223 <option value="Cys">Cys</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	224 <option value="Asp">Asp</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	225 <option value="Glu">Glu</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	226 <option value="Phe">Phe</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	227 <option value="Gly">Gly</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	228 <option value="His" selected="true">His</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	229 <option value="Ile">Ile</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	230 <option value="Lys" selected="true">Lys</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	231 <option value="Leu">Leu</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	232 <option value="Met">Met</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	233 <option value="Asn">Asn</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	234 <option value="Pro">Pro</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	235 <option value="Gln">Gln</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	236 <option value="Arg" selected="true">Arg</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	237 <option value="Sec">Sec</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	238 <option value="Ser">Ser</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	239 <option value="Thr">Thr</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	240 <option value="Val">Val</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	241 <option value="Trp">Trp</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	242 <option value="Tyr">Tyr</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	243 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	244 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	245 <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)">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	246 <expand macro="list_string_val"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	247 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	248 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	249 <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+'"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	250 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	251 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	252 <section name="maldi" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	253 <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)">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	254 <expand macro="list_float_valsan"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	255 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	256 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	257 <section name="mz" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	258 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	259 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	260 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	261 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	262 <section name="RawSignal" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	263 <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)"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	264 <param name="peak_shape" argument="-algorithm:MSSim:RawSignal:peak_shape" display="radio" type="select" optional="false" 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="">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	265 <option value="Gaussian" selected="true">Gaussian</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	266 <option value="Lorentzian">Lorentzian</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	267 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	268 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	269 <section name="resolution" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	270 <param name="value" argument="-algorithm:MSSim:RawSignal:resolution:value" type="integer" optional="true" value="50000" label="Instrument resolution at 400 Th" help=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	271 <param name="type" argument="-algorithm:MSSim:RawSignal:resolution:type" display="radio" type="select" optional="false" 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">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	272 <option value="constant">constant</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	273 <option value="linear" selected="true">linear</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	274 <option value="sqrt">sqrt</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	275 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	276 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	277 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	278 <section name="baseline" title="Baseline modeling for MALDI ionization" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	279 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	280 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	281 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	282 <section name="mz" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	283 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	284 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	285 <section name="contaminants" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	286 <param name="file" argument="-algorithm:MSSim:RawSignal:contaminants:file" type="text" optional="true" value="examples/simulation/contaminants.csv" label="Contaminants file with sum formula and absolute RT interval" help="See 'OpenMS/examples/simulation/contaminants.txt' for details">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	287 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	288 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	289 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	290 <section name="variation" title="Random components that simulate biological and technical variations of the simulated data" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	291 <section name="mz" title="Shifts in mass to charge dimension of the simulated signals" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	292 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	293 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	294 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	295 <section name="intensity" title="Variations in intensity to model randomness in feature intensity" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	296 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	297 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	298 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	299 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	300 <section name="noise" title="Parameters modeling noise in mass spectrometry measurements" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	301 <section name="shot" title="Parameters of Poisson and Exponential for shot noise modeling (set :rate OR :mean = 0 to disable)" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	302 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	303 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	304 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	305 <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">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	306 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	307 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	308 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	309 <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">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	310 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	311 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	312 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	313 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	314 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	315 <section name="RawTandemSignal" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	316 <param name="status" argument="-algorithm:MSSim:RawTandemSignal:status" display="radio" type="select" optional="false" label="Create Tandem-MS scans?" help="">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	317 <option value="disabled" selected="true">disabled</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	318 <option value="precursor">precursor</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	319 <option value="MS^E">MS^E</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	320 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	321 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	322 <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 . "/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	323 <param name="svm_model_set_file" argument="-algorithm:MSSim:RawTandemSignal:svm_model_set_file" type="text" optional="true" value="examples/simulation/SvmModelSet.model" label="File containing the filenames of SVM Models for different charge variants" help="">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	324 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	325 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	326 <section name="Precursor" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	327 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	328 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	329 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	330 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	331 <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)">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	332 <expand macro="list_integer_valsan">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	333 <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])
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	334 ]]></validator>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	335 </expand>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	336 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	337 <section name="Exclusion" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	338 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	339 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	340 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	341 <section name="ProteinBasedInclusion" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	342 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	343 <section name="rt" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	344 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	345 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	346 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	347 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	348 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	349 <section name="thresholds" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	350 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	351 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	352 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	353 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	354 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	355 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	356 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	357 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	358 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	359 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	360 <section name="MS_E" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	361 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	362 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	363 <section name="TandemSim" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	364 <section name="Simple" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	365 <param name="isotope_model" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:isotope_model" display="radio" type="select" optional="false" 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">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	366 <option value="none" selected="true">none</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	367 <option value="coarse">coarse</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	368 <option value="fine">fine</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	369 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	370 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	371 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	372 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	373 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	374 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	375 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	376 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	377 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	378 <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" help=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	379 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	380 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	381 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	382 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	383 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	384 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	385 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	386 <param name="y_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:y_intensity" type="float" optional="true" value="1.0" label="Intensity of the y-ions" help=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	387 <param name="b_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:b_intensity" type="float" optional="true" value="1.0" label="Intensity of the b-ions" help=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	388 <param name="a_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:a_intensity" type="float" optional="true" value="1.0" label="Intensity of the a-ions" help=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	389 <param name="c_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:c_intensity" type="float" optional="true" value="1.0" label="Intensity of the c-ions" help=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	390 <param name="x_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:x_intensity" type="float" optional="true" value="1.0" label="Intensity of the x-ions" help=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	391 <param name="z_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:z_intensity" type="float" optional="true" value="1.0" label="Intensity of the z-ions" help=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	392 <param name="relative_loss_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:relative_loss_intensity" type="float" optional="true" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	393 <param name="precursor_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_intensity" type="float" optional="true" value="1.0" label="Intensity of the precursor peak" help=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	394 <param name="precursor_H2O_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity" type="float" optional="true" value="1.0" label="Intensity of the H2O loss peak of the precurso" help=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	395 <param name="precursor_NH3_intensity" argument="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity" type="float" optional="true" value="1.0" label="Intensity of the NH3 loss peak of the precurso" help=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	396 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	397 <section name="SVM" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	398 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	399 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	400 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	401 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	402 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	403 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	404 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	405 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	406 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	407 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	408 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	409 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	410 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	411 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	412 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	413 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	414 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	415 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	416 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	417 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	418 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	419 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	420 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	421 <section name="Global" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	422 <param name="ionization_type" argument="-algorithm:MSSim:Global:ionization_type" display="radio" type="select" optional="false" label="Type of Ionization (MALDI or ESI)" help="">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	423 <option value="MALDI">MALDI</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	424 <option value="ESI" selected="true">ESI</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	425 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	426 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	427 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	428 <section name="Labeling" title="" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	429 <param name="type" argument="-algorithm:MSSim:Labeling:type" type="select" optional="false" label="Select the labeling type you want for your experiment" help="">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	430 <option value="ICPL">ICPL</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	431 <option value="SILAC">SILAC</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	432 <option value="itraq">itraq</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	433 <option value="labelfree" selected="true">labelfree</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	434 <option value="o18">o18</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	435 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	436 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	437 <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">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	438 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	439 <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)"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	440 <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="">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	441 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	442 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	443 <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="">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	444 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	445 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	446 <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="">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	447 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	448 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	449 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	450 <section name="SILAC" title="SILAC labeling on MS1 level with up to 3 channels and custom modifications" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	451 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	452 <section name="medium_channel" title="Modifications for the medium SILAC channel" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	453 <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="">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	454 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	455 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	456 <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="">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	457 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	458 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	459 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	460 <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">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	461 <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">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	462 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	463 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	464 <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">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	465 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	466 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	467 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	468 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	469 <section name="itraq" title="iTRAQ labeling on MS2 level with up to 4 (4plex) or 8 (8plex) channels" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	470 <param name="iTRAQ" argument="-algorithm:MSSim:Labeling:itraq:iTRAQ" display="radio" type="select" optional="false" label="4plex or 8plex iTRAQ?" help="">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	471 <option value="4plex" selected="true">4plex</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	472 <option value="8plex">8plex</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	473 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	474 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	475 <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)"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	476 <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)">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	477 <expand macro="list_string_val"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	478 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	479 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	480 <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)">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	481 <expand macro="list_string_val"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	482 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	483 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	484 <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)">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	485 <expand macro="list_string_val"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	486 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	487 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	488 <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)">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	489 <expand macro="list_string_val"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	490 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	491 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	492 <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"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	493 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	494 <section name="o18" title="18O labeling on MS1 level with 2 channels, requiring trypsin digestion" help="" expanded="false">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	495 <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=""/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	496 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	497 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	498 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	499 <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">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	500 <param name="biological" argument="-algorithm:RandomNumberGenerators:biological" display="radio" type="select" optional="false" 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)">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	501 <option value="reproducible">reproducible</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	502 <option value="random" selected="true">random</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	503 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	504 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	505 <param name="technical" argument="-algorithm:RandomNumberGenerators:technical" display="radio" type="select" optional="false" 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)">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	506 <option value="reproducible">reproducible</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	507 <option value="random" selected="true">random</option>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	508 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	509 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	510 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	511 </section>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	512 <expand macro="adv_opts_macro">
15 ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	513 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	514 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	515 <expand macro="list_string_san"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	516 </param>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	517 </expand>
15 ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	518 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	519 <option value="out_FLAG">out (output: simulated MS raw (profile) data)</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	520 <option value="out_pm_FLAG">out_pm (output: ground-truth picked (centroided) MS data)</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	521 <option value="out_fm_FLAG">out_fm (output: ground-truth features)</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	522 <option value="out_cm_FLAG">out_cm (output: ground-truth features, grouping ESI charge variants of each parent peptide)</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	523 <option value="out_lcm_FLAG">out_lcm (output: ground-truth features, grouping labeled variants)</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	524 <option value="out_cntm_FLAG">out_cntm (output: ground-truth features caused by contaminants)</option>
ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	525 <option value="out_id_FLAG">out_id (output: ground-truth MS2 peptide identifications)</option>
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	526 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	527 </param>
ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	528 </inputs>
ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	529 <outputs>
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	530 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	531 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	532 </data>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	533 <data name="out_pm" label="${tool.name} on ${on_string}: out_pm" format="mzml">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	534 <filter>OPTIONAL_OUTPUTS is not None and "out_pm_FLAG" in OPTIONAL_OUTPUTS</filter>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	535 </data>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	536 <data name="out_fm" label="${tool.name} on ${on_string}: out_fm" format="featurexml">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	537 <filter>OPTIONAL_OUTPUTS is not None and "out_fm_FLAG" in OPTIONAL_OUTPUTS</filter>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	538 </data>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	539 <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	540 <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	541 </data>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	542 <data name="out_lcm" label="${tool.name} on ${on_string}: out_lcm" format="consensusxml">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	543 <filter>OPTIONAL_OUTPUTS is not None and "out_lcm_FLAG" in OPTIONAL_OUTPUTS</filter>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	544 </data>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	545 <data name="out_cntm" label="${tool.name} on ${on_string}: out_cntm" format="featurexml">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	546 <filter>OPTIONAL_OUTPUTS is not None and "out_cntm_FLAG" in OPTIONAL_OUTPUTS</filter>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	547 </data>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	548 <data name="out_id" label="${tool.name} on ${on_string}: out_id" format="idxml">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	549 <filter>OPTIONAL_OUTPUTS is not None and "out_id_FLAG" in OPTIONAL_OUTPUTS</filter>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	550 </data>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	551 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	552 <filter>OPTIONAL_OUTPUTS is None</filter>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	553 </data>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	554 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	555 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	556 </data>
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	557 </outputs>
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	558 <tests>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	559 <expand macro="autotest_MSSimulator"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	560 <expand macro="manutest_MSSimulator"/>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	561 </tests>
140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	562 <help><![CDATA[A highly configurable simulator for mass spectrometry experiments.
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	563
ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	564
15 ad1ad0e62a92 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 13 diff changeset	565 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MSSimulator.html]]></help>
13 140b883daa61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9" galaxyp parents: 12 diff changeset	566 <expand macro="references"/>
0 ae8e96c8f9a4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	567 </tool>

Mercurial > repos > galaxyp > openms_mssimulator

annotate MSSimulator.xml @ 15:ad1ad0e62a92 draft