morpheus: morpheus.xml annotate

annotate morpheus.xml @ 7:cf9a994e0447 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1

author	galaxyp
date	Mon, 15 Jul 2024 18:21:18 +0000
parents	01a572a3a716
children

rev	line source
7 cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	1 <tool id="morpheus" name="Morpheus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	2 <description>database search algorithm for high-resolution tandem mass spectra</description>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	3 <macros>
7 cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	4 <import>macros.xml</import>
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	5 </macros>
7 cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	6 <expand macro="edam_ontology"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	7 <expand macro="biotools"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	8 <expand macro="requirements"/>
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	9 <stdio>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	10 <exit_code range="1:" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	11 <regex match="System..*Exception"
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	12 source="both"
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	13 level="fatal"
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	14 description="Error encountered" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	15 </stdio>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	16
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	17 <command><![CDATA[
5 f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	18 mkdir -p output_reports &&
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	19 cwd=`pwd` &&
4 a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	20 #import re
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	21 #set $searchdb_name = $searchdb
6 01a572a3a716 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 93e02b037bfb37001de2bfb6fc731539c1902e80 galaxyp parents: 5 diff changeset	22 #if $searchdb.is_of_type('uniprotxml'):
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	23 #set $searchdb_name = 'searchdb.xml'
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	24 #else
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	25 #set $searchdb_name = 'searchdb.fasta'
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	26 #end if
4 a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	27 ln -s $searchdb $searchdb_name
a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	28 ## Need to link each input to a name in cwd, names must be unique
a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	29 #set $input_list = []
a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	30 #for i,input in enumerate($inputs):
a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	31 #set $input_name = $re.sub('(?i)([.]?mzML)*$','.mzML',$re.sub('\W','_',$input.name))
a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	32 #if $input_name in $input_list:
a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	33 #set $input_name = str($i) + '_' + $input_name
a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	34 #end if
a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	35 #set $input_list = $input_list + [$input_name]
a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	36 && ln -s $input $input_name
a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	37 #end for
a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	38 #set $input_names = ','.join($input_list)
5 f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	39 &&
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	40
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	41 mono `which morpheus`
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	42 -d='$input_names'
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	43 -db='$searchdb_name'
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	44
6 01a572a3a716 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 93e02b037bfb37001de2bfb6fc731539c1902e80 galaxyp parents: 5 diff changeset	45 #if $searchdb.is_of_type('uniprotxml'):
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	46 #if str( $advanced.adv_options_selector) == "set":
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	47 $advanced.noup
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	48 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	49 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	50 ## fm vm fdr mvmi precmt precmtv precmtu
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	51 #if str($fdr) != '':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	52 -fdr=$fdr
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	53 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	54 #if str($mvmi) != '':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	55 -mvmi=$mvmi
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	56 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	57 #if str($precmtv) != '':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	58 -precmtv=$precmtv
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	59 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	60 #if str($precmtu) != 'None':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	61 -precmtu=$precmtu
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	62 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	63 #if str( $advanced.adv_options_selector) == "set":
3 12c5c3a50d4b Uploaded galaxyp parents: 2 diff changeset	64 #if str($advanced.precmt) != 'None':
12c5c3a50d4b Uploaded galaxyp parents: 2 diff changeset	65 -precmt=$advanced.precmt
12c5c3a50d4b Uploaded galaxyp parents: 2 diff changeset	66 #end if
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	67 #if str($advanced.minprecz) != '':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	68 -minprecz=$advanced.minprecz
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	69 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	70 #if str($advanced.maxprecz) != '':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	71 -maxprecz=$advanced.maxprecz
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	72 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	73 #if str($advanced.at) != '':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	74 -at=$advanced.at
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	75 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	76 #if str($advanced.rt) != '':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	77 -rt=$advanced.rt
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	78 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	79 #if str($advanced.mp) != '':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	80 -mp=$advanced.mp
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	81 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	82 #if str($advanced.mmc) != '':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	83 -mmc=$advanced.mmc
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	84 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	85 #if str($advanced.prodmt) != 'None':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	86 -prodmt=$advanced.prodmt
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	87 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	88 #if str($advanced.prodmtv) != '':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	89 -prodmtv=$advanced.prodmtv
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	90 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	91 #if str($advanced.prodmtu) != 'None':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	92 -prodmtu=$advanced.prodmtu
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	93 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	94 #if str($advanced.minpmo) != '':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	95 -minpmo=$advanced.minpmo
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	96 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	97 #if str($advanced.maxpmo) != '':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	98 -maxpmo=$advanced.maxpmo
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	99 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	100 #if str($advanced.imb) != 'None':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	101 -imb=$advanced.imb
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	102 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	103 #if str($advanced.ad) != 'None':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	104 -ad=$advanced.ad
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	105 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	106 $advanced.acs $advanced.di $advanced.pmc $advanced.cmu $advanced.mmu
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	107 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	108 #if str($fm) != 'None':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	109 #set $fmods = str($fm).replace(',',';')
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	110 -fm="$fmods"
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	111 #end if
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	112 #if str($vm) != 'None':
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	113 #set $vmods = str($vm).replace(',',';')
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	114 -vm="$vmods"
7 cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	115 #end if
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	116 #if str($p) != 'None':
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	117 -p="$p"
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	118 #end if
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	119 -mt=\${GALAXY_SLOTS:-4}
5 f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	120 #set $out_list = 'log.txt summary.tsv aggregate.PSMs.tsv aggregate.unique_peptides.tsv aggregate.protein_groups.tsv aggregate.mzid *.pep.xml'
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	121 #if len($input_list) == 1:
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	122 && ln -s *.log.txt log.txt
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	123 && ln -s *.mzid aggregate.mzid
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	124 && ln -s *.unique_peptides.tsv aggregate.unique_peptides.tsv
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	125 && ln -s *.protein_groups.tsv aggregate.protein_groups.tsv
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	126 && ln -s *.PSMs.tsv aggregate.PSMs.tsv
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	127 #end if
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	128 && ( basepath=`grep 'Proteome Database:' log.txt \| sed 's/Proteome Database: $.*$${$searchdb_name}/\1/'`;
4 a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	129 for i in $out_list; do cat \$i \| sed "s#\${basepath}\##" > output_reports/\$i; done )
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	130 ]]></command>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	131 <inputs>
4 a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	132 <param name="inputs" type="data" format="mzml" multiple="true" label='Indexed mzML' />
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	133 <param name="searchdb" type="data" format="fasta,uniprotxml" label="MS Protein Search Database: UniProt Xml or Fasta"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	134 <param name="fm" type="select" multiple="true" optional="true" label="Fixed Modifications">
3 12c5c3a50d4b Uploaded galaxyp parents: 2 diff changeset	135 <expand macro="fixed_modification_options" />
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	136 </param>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	137 <param name="vm" type="select" multiple="true" optional="true" label="Variable Modifications">
3 12c5c3a50d4b Uploaded galaxyp parents: 2 diff changeset	138 <expand macro="variable_modification_options" />
7 cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	139 </param>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	140 <param name="p" type="select" label="Proteases">
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	141 <expand macro="proteases_options"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	142 </param>
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	143 <param name="fdr" type="float" value="1" optional="true" min="0.0" max="100.0" label="FDR (Maximum False Discovery Rate percent)" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	144 <param name="mvmi" type="integer" value="1024" optional="true" min="0" label="Maximum Variable Modification Isoforms Per Peptide" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	145 <param name="precmtv" type="float" value="10." optional="true" label="Precursor Mass Tolerance Value" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	146 <param name="precmtu" type="select" optional="true" label="Precursor Mass Tolerance Units">
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	147 <option value="ppm" selected="true">ppm</option>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	148 <option value="Da">Daltons</option>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	149 </param>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	150 <conditional name="advanced">
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	151 <param name="adv_options_selector" type="select" label="Set advanced options?" help="Provides additional controls">
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	152 <option value="set">Set</option>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	153 <option value="do_not_set" selected="True">Do not set</option>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	154 </param>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	155 <when value="set">
3 12c5c3a50d4b Uploaded galaxyp parents: 2 diff changeset	156 <param name="precmt" type="select" optional="true" label="Precursor Mass Type">
12c5c3a50d4b Uploaded galaxyp parents: 2 diff changeset	157 <option value="Monoisotopic">Monoisotopic</option>
12c5c3a50d4b Uploaded galaxyp parents: 2 diff changeset	158 <option value="Average">Average</option>
12c5c3a50d4b Uploaded galaxyp parents: 2 diff changeset	159 </param>
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	160 <param name="noup" type="boolean" truevalue="" falsevalue="-noup=True" checked="True" label="Use G-PTM with Uniprot Proteome Search Databases" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	161 <param name="minprecz" type="integer" value="2" optional="true" label="Minimum Unknown Precursor Charge State" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	162 <param name="maxprecz" type="integer" value="4" optional="true" label="Maximum Unknown Precursor Charge State" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	163 <param name="at" type="float" value="" optional="true" min="0.0" label="Absolute MS/MS Intensity Threshold" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	164 <param name="rt" type="float" value="" optional="true" min="0.0" label="Relative MS/MS Intensity Threshold" />
3 12c5c3a50d4b Uploaded galaxyp parents: 2 diff changeset	165 <param name="mp" type="integer" value="400" optional="true" min="-1" label="Maximum Number of MS/MS Peaks" help="to disable set to: -1"/>
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	166 <param name="acs" type="boolean" truevalue="-acs=True" falsevalue="-acs=False" checked="true" optional="true" label="Assign Charge States" />
3 12c5c3a50d4b Uploaded galaxyp parents: 2 diff changeset	167 <param name="di" type="boolean" truevalue="-di=True" falsevalue="-di=False" checked="false" optional="true" label="Deisotope" />
12c5c3a50d4b Uploaded galaxyp parents: 2 diff changeset	168 <param name="ad" type="select" optional="true" label="Create Target-Decoy Database On The Fly"
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	169 help="Set to No if Search Database ia a fasta that already includes decoys.">
3 12c5c3a50d4b Uploaded galaxyp parents: 2 diff changeset	170 <option value="True" selected="true">Yes</option>
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	171 <option value="False">No</option>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	172 </param>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	173 <param name="mmc" type="integer" value="2" optional="true" min="0" max="20" label="Maximum Missed Cleavages" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	174 <param name="pmc" type="boolean" truevalue="-pmc=True" falsevalue="-pmc=False" checked="false" optional="true" label="Precursor Monoisotopic Peak Correction" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	175 <param name="minpmo" type="integer" value="" optional="true" label="Minimum Precursor Monoisotopic Peak Correction" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	176 <param name="maxpmo" type="integer" value="" optional="true" label="Maximum Precursor Monoisotopic Peak Correction" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	177 <param name="prodmt" type="select" optional="true" label="Product Mass Type">
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	178 <option value="Monoisotopic">Monoisotopic</option>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	179 <option value="Average">Average</option>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	180 </param>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	181 <param name="prodmtv" type="float" value="" optional="true" label="Product Mass Tolerance Value" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	182 <param name="prodmtu" type="select" optional="true" label="Product Mass Tolerance Units">
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	183 <option value="Da">Daltons</option>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	184 <option value="ppm">ppm</option>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	185 </param>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	186 <param name="imb" type="select" optional="true" label="Initiator Methionine Behavior">
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	187 <option value="Variable">Variable</option>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	188 <option value="Retain">Retain</option>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	189 <option value="Cleave">Cleave</option>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	190 </param>
3 12c5c3a50d4b Uploaded galaxyp parents: 2 diff changeset	191 <param name="cmu" type="boolean" truevalue="-cmu=True" falsevalue="-cmu=False" checked="false" optional="true" label="Consider Modified Forms as Unique Peptides" />
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	192 <param name="mmu" type="boolean" truevalue="-mmu=True" falsevalue="-mmu=False" checked="false" optional="true" label="Minimize Memory Usage" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	193 </when>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	194 <when value="do_not_set"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	195 </conditional>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	196 </inputs>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	197 <outputs>
5 f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	198 <data name="log" format="txt" label="${tool.name} on ${on_string}: log.txt" from_work_dir="output_reports/log.txt" />
4 a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	199 <data name="summary" format="txt" label="${tool.name} on ${on_string}: summary.tsv" from_work_dir="output_reports/summary.tsv" />
5 f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	200 <data name="output_psms" format="tabular" label="${tool.name} on ${on_string}: PSMs.tsv" from_work_dir="output_reports/aggregate.PSMs.tsv" />
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	201 <data name="output_unique_peptides" format="tabular" label="${tool.name} on ${on_string}: unique_peptides.tsv" from_work_dir="output_reports/aggregate.unique_peptides.tsv" />
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	202 <data name="output_protein_groups" format="tabular" label="${tool.name} on ${on_string}: protein_groups.tsv" from_work_dir="output_reports/aggregate.protein_groups.tsv" />
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	203 <data name="aggregate_mzid" format="mzid" label="${tool.name} on ${on_string}: aggregate.mzid" from_work_dir="output_reports/aggregate.mzid" />
4 a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	204 <collection name="morpheus_pep_xmls" type="list" label="${tool.name} on ${on_string} pep.xml">
5 f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	205 <discover_datasets pattern="(?P<name>.*\.pep.xml)" ext="pepxml" visible="false" directory="output_reports" />
4 a7c58067f5ee Uploaded galaxyp parents: 3 diff changeset	206 </collection>
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	207 </outputs>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	208 <tests>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	209 <test>
5 f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	210 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	211 <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	212 <param name="fdr" value="1"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	213 <param name="mvmi" value="1024"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	214 <param name="precmt" value="Monoisotopic"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	215 <param name="precmtu" value="Da"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	216 <param name="precmtv" value="2.5"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	217 <output name="output_psms">
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	218 <assert_contents>
5 f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	219 <not_has_text text="K.TTGSSSSSSSK.K" />
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	220 <has_text text="carbamidomethylation of C" />
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	221 <has_text text="(oxidation of M)" />
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	222 </assert_contents>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	223 </output>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	224 </test>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	225 <test>
5 f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	226 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	227 <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	228 <param name="fdr" value="1"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	229 <param name="mvmi" value="1024"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	230 <param name="precmt" value="Monoisotopic"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	231 <param name="precmtu" value="Da"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	232 <param name="precmtv" value="2.5"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	233 <param name="fm" value="carbamidomethylation of C"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	234 <param name="vm" value="oxidation of M"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	235 <output name="output_psms">
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	236 <assert_contents>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	237 <has_text text="K.VETYM(oxidation of M)ETK.I" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	238 <not_has_text text="K.TTGSSSSSSSK.K" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	239 </assert_contents>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	240 </output>
7 cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	241 </test>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	242 <test>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	243 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	244 <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	245 <param name="fdr" value="1"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	246 <param name="mvmi" value="1024"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	247 <param name="precmt" value="Monoisotopic"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	248 <param name="precmtu" value="Da"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	249 <param name="precmtv" value="2.5"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	250 <param name="fm" value="carbamidomethylation of C"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	251 <param name="vm" value="oxidation of M"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	252 <param name="p" value="trypsin" />
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	253 <output name="output_psms">
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	254 <assert_contents>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	255 <has_text text="K.DGM(oxidation of M)KAYAQNVQQR.E" />
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	256 <not_has_text text="K.TTGSSSSSSSK.K" />
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	257 </assert_contents>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	258 </output>
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	259 </test>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	260 <test>
5 f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	261 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	262 <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	263 <param name="fdr" value="1"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	264 <param name="mvmi" value="1024"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	265 <param name="precmt" value="Monoisotopic"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	266 <param name="precmtu" value="Da"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	267 <param name="precmtv" value="2.5"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	268 <param name="fm" value="carbamidomethylation of C"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	269 <param name="vm" value="oxidation of M"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	270 <output name="output_psms">
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	271 <assert_contents>
7 cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	272 <has_text text="K.RSPSGNISTNSMR.P" />
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	273 <not_has_text text="K.KYFLENKIGTDR.R" />
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	274 </assert_contents>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	275 </output>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	276 </test>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	277 <test>
5 f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	278 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	279 <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	280 <param name="fdr" value="1"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	281 <param name="mvmi" value="1024"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	282 <param name="precmt" value="Monoisotopic"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	283 <param name="precmtu" value="Da"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	284 <param name="precmtv" value="2.5"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	285 <param name="fm" value="carbamidomethylation of C"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	286 <param name="vm" value="oxidation of M"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	287 <param name="adv_options_selector" value="set"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	288 <param name="prodmtv" value=".01"/>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	289 <output name="output_psms">
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	290 <assert_contents>
5 f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	291 <has_text text="K.KTLKSDGVAGLYR.G" />
f0202024f80b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 4 diff changeset	292 <not_has_text text="K.RSPSGNISTNSMR.P" />
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	293 </assert_contents>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	294 </output>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	295 </test>
7 cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	296 <test>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	297 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	298 <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	299 <param name="fdr" value="1"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	300 <param name="mvmi" value="1024"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	301 <param name="precmt" value="Monoisotopic"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	302 <param name="precmtu" value="Da"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	303 <param name="precmtv" value="2.5"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	304 <param name="fm" value="carbamidomethylation of C"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	305 <param name="vm" value="oxidation of M"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	306 <param name="p" value="trypsin"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	307 <param name="adv_options_selector" value="set"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	308 <param name="prodmtv" value=".01"/>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	309 <output name="output_psms">
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	310 <assert_contents>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	311 <has_text text="K.KTLKSDGVAGLYR.G" />
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	312 <not_has_text text="K.KYFLENKIGTDR.R" />
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	313 </assert_contents>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	314 </output>
cf9a994e0447 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 6 diff changeset	315 </test>
0 ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	316 </tests>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	317 <help><![CDATA[
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	318 Morpheus_ is a database search algorithm for high-resolution tandem mass spectra.
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	319
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	320 When a Uniprot Proteome XML file is used for the search database, Morpheus will include all known modifications from the proteome in searching for peptide spectral matches. To fetch Uniprot Proteome XML files see: http://www.uniprot.org/help/retrieve_sets
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	321
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	322 INPUTS
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	323
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	324 - spectral data file in mzML format
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	325 - protein search database, either a fasta file or a uniprot proteome xml file
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	326
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	327 OUTPUTS
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	328
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	329 - summary.tsv
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	330 - input.log.txt
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	331 - input.PSMs.tsv
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	332 - input.unique_peptides.tsv
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	333 - input.protein_groups.tsv
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	334 - input.pep.xml
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	335
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	336 .. _Morpheus: http://morpheus-ms.sourceforge.net/
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	337
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	338 ]]></help>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	339 <citations>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	340 <citation type="doi">10.1021/pr301024c</citation>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	341 </citations>
ac0a6f10d8b1 Uploaded galaxyp parents: diff changeset	342 </tool>

Mercurial > repos > galaxyp > morpheus

annotate morpheus.xml @ 7:cf9a994e0447 draft default tip