morpheus: morpheus.xml annotate

annotate morpheus.xml @ 3:8295d959ca28 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 18:21:24 +0000
parents	e0104a9f20f0
children

rev	line source
3 8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	1 <tool id="morpheus" name="Morpheus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	2 <description>database search algorithm for high-resolution tandem mass spectra</description>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	3 <macros>
3 8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	4 <import>macros.xml</import>
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	5 </macros>
3 8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	6 <expand macro="edam_ontology"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	7 <expand macro="biotools"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	8 <expand macro="requirements"/>
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	9 <stdio>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	10 <exit_code range="1:" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	11 <regex match="System..*Exception"
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	12 source="both"
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	13 level="fatal"
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	14 description="Error encountered" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	15 </stdio>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	16
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	17 <command><![CDATA[
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	18 mkdir -p output_reports &&
1 ecb9ec15083d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 0 diff changeset	19 cwd=`pwd` &&
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	20 #import re
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	21 #set $searchdb_name = $searchdb
2 e0104a9f20f0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 93e02b037bfb37001de2bfb6fc731539c1902e80 galaxyp parents: 1 diff changeset	22 #if $searchdb.is_of_type('uniprotxml'):
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	23 #set $searchdb_name = 'searchdb.xml'
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	24 #else
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	25 #set $searchdb_name = 'searchdb.fasta'
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	26 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	27 ln -s $searchdb $searchdb_name
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	28 ## Need to link each input to a name in cwd, names must be unique
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	29 #set $input_list = []
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	30 #for i,input in enumerate($inputs):
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	31 #set $input_name = $re.sub('(?i)([.]?mzML)*$','.mzML',$re.sub('\W','_',$input.name))
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	32 #if $input_name in $input_list:
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	33 #set $input_name = str($i) + '_' + $input_name
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	34 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	35 #set $input_list = $input_list + [$input_name]
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	36 && ln -s $input $input_name
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	37 #end for
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	38 #set $input_names = ','.join($input_list)
1 ecb9ec15083d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 0 diff changeset	39 &&
ecb9ec15083d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 0 diff changeset	40
ecb9ec15083d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 0 diff changeset	41 mono `which morpheus`
ecb9ec15083d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 0 diff changeset	42 -d='$input_names'
ecb9ec15083d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 0 diff changeset	43 -db='$searchdb_name'
ecb9ec15083d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 0 diff changeset	44
2 e0104a9f20f0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 93e02b037bfb37001de2bfb6fc731539c1902e80 galaxyp parents: 1 diff changeset	45 #if $searchdb.is_of_type('uniprotxml'):
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	46 #if str( $advanced.adv_options_selector) == "set":
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	47 $advanced.noup
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	48 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	49 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	50 ## fm vm fdr mvmi precmt precmtv precmtu
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	51 #if str($fdr) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	52 -fdr=$fdr
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	53 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	54 #if str($mvmi) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	55 -mvmi=$mvmi
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	56 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	57 #if str($precmtv) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	58 -precmtv=$precmtv
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	59 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	60 #if str($precmtu) != 'None':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	61 -precmtu=$precmtu
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	62 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	63 #if str( $advanced.adv_options_selector) == "set":
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	64 #if str($advanced.precmt) != 'None':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	65 -precmt=$advanced.precmt
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	66 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	67 #if str($advanced.minprecz) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	68 -minprecz=$advanced.minprecz
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	69 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	70 #if str($advanced.maxprecz) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	71 -maxprecz=$advanced.maxprecz
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	72 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	73 #if str($advanced.at) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	74 -at=$advanced.at
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	75 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	76 #if str($advanced.rt) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	77 -rt=$advanced.rt
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	78 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	79 #if str($advanced.mp) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	80 -mp=$advanced.mp
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	81 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	82 #if str($advanced.mmc) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	83 -mmc=$advanced.mmc
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	84 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	85 #if str($advanced.prodmt) != 'None':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	86 -prodmt=$advanced.prodmt
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	87 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	88 #if str($advanced.prodmtv) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	89 -prodmtv=$advanced.prodmtv
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	90 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	91 #if str($advanced.prodmtu) != 'None':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	92 -prodmtu=$advanced.prodmtu
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	93 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	94 #if str($advanced.minpmo) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	95 -minpmo=$advanced.minpmo
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	96 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	97 #if str($advanced.maxpmo) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	98 -maxpmo=$advanced.maxpmo
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	99 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	100 #if str($advanced.imb) != 'None':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	101 -imb=$advanced.imb
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	102 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	103 #if str($advanced.ad) != 'None':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	104 -ad=$advanced.ad
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	105 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	106 $advanced.acs $advanced.di $advanced.pmc $advanced.cmu $advanced.mmu
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	107 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	108 #if str($fm) != 'None':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	109 #set $fmods = str($fm).replace(',',';')
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	110 -fm="$fmods"
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	111 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	112 #if str($vm) != 'None':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	113 #set $vmods = str($vm).replace(',',';')
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	114 -vm="$vmods"
3 8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	115 #end if
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	116 #if str($p) != 'None':
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	117 -p="$p"
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	118 #end if
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	119 -mt=\${GALAXY_SLOTS:-4}
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	120 #set $out_list = 'log.txt summary.tsv aggregate.PSMs.tsv aggregate.unique_peptides.tsv aggregate.protein_groups.tsv aggregate.mzid *.pep.xml'
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	121 #if len($input_list) == 1:
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	122 && ln -s *.log.txt log.txt
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	123 && ln -s *.mzid aggregate.mzid
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	124 && ln -s *.unique_peptides.tsv aggregate.unique_peptides.tsv
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	125 && ln -s *.protein_groups.tsv aggregate.protein_groups.tsv
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	126 && ln -s *.PSMs.tsv aggregate.PSMs.tsv
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	127 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	128 && ( basepath=`grep 'Proteome Database:' log.txt \| sed 's/Proteome Database: $.*$${$searchdb_name}/\1/'`;
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	129 for i in $out_list; do cat \$i \| sed "s#\${basepath}\##" > output_reports/\$i; done )
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	130 ]]></command>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	131 <inputs>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	132 <param name="inputs" type="data" format="mzml" multiple="true" label='Indexed mzML' />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	133 <param name="searchdb" type="data" format="fasta,uniprotxml" label="MS Protein Search Database: UniProt Xml or Fasta"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	134 <param name="fm" type="select" multiple="true" optional="true" label="Fixed Modifications">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	135 <expand macro="fixed_modification_options" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	136 </param>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	137 <param name="vm" type="select" multiple="true" optional="true" label="Variable Modifications">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	138 <expand macro="variable_modification_options" />
3 8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	139 </param>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	140 <param name="p" type="select" label="Proteases">
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	141 <expand macro="proteases_options"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	142 </param>
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty 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)" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	144 <param name="mvmi" type="integer" value="1024" optional="true" min="0" label="Maximum Variable Modification Isoforms Per Peptide" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	145 <param name="precmtv" type="float" value="10." optional="true" label="Precursor Mass Tolerance Value" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	146 <param name="precmtu" type="select" optional="true" label="Precursor Mass Tolerance Units">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	147 <option value="ppm" selected="true">ppm</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	148 <option value="Da">Daltons</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	149 </param>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	150 <conditional name="advanced">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	151 <param name="adv_options_selector" type="select" label="Set advanced options?" help="Provides additional controls">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	152 <option value="set">Set</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	153 <option value="do_not_set" selected="True">Do not set</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	154 </param>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	155 <when value="set">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	156 <param name="precmt" type="select" optional="true" label="Precursor Mass Type">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	157 <option value="Monoisotopic">Monoisotopic</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	158 <option value="Average">Average</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	159 </param>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty 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" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	161 <param name="minprecz" type="integer" value="2" optional="true" label="Minimum Unknown Precursor Charge State" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	162 <param name="maxprecz" type="integer" value="4" optional="true" label="Maximum Unknown Precursor Charge State" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	163 <param name="at" type="float" value="" optional="true" min="0.0" label="Absolute MS/MS Intensity Threshold" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	164 <param name="rt" type="float" value="" optional="true" min="0.0" label="Relative MS/MS Intensity Threshold" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: 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"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	166 <param name="acs" type="boolean" truevalue="-acs=True" falsevalue="-acs=False" checked="true" optional="true" label="Assign Charge States" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	167 <param name="di" type="boolean" truevalue="-di=True" falsevalue="-di=False" checked="false" optional="true" label="Deisotope" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	168 <param name="ad" type="select" optional="true" label="Create Target-Decoy Database On The Fly"
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	169 help="Set to No if Search Database ia a fasta that already includes decoys.">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	170 <option value="True" selected="true">Yes</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	171 <option value="False">No</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	172 </param>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	173 <param name="mmc" type="integer" value="2" optional="true" min="0" max="20" label="Maximum Missed Cleavages" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty 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" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	175 <param name="minpmo" type="integer" value="" optional="true" label="Minimum Precursor Monoisotopic Peak Correction" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	176 <param name="maxpmo" type="integer" value="" optional="true" label="Maximum Precursor Monoisotopic Peak Correction" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	177 <param name="prodmt" type="select" optional="true" label="Product Mass Type">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	178 <option value="Monoisotopic">Monoisotopic</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	179 <option value="Average">Average</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	180 </param>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	181 <param name="prodmtv" type="float" value="" optional="true" label="Product Mass Tolerance Value" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	182 <param name="prodmtu" type="select" optional="true" label="Product Mass Tolerance Units">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	183 <option value="Da">Daltons</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	184 <option value="ppm">ppm</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	185 </param>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	186 <param name="imb" type="select" optional="true" label="Initiator Methionine Behavior">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	187 <option value="Variable">Variable</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	188 <option value="Retain">Retain</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	189 <option value="Cleave">Cleave</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	190 </param>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: 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" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	192 <param name="mmu" type="boolean" truevalue="-mmu=True" falsevalue="-mmu=False" checked="false" optional="true" label="Minimize Memory Usage" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	193 </when>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	194 <when value="do_not_set"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	195 </conditional>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	196 </inputs>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	197 <outputs>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	198 <data name="log" format="txt" label="${tool.name} on ${on_string}: log.txt" from_work_dir="output_reports/log.txt" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	199 <data name="summary" format="txt" label="${tool.name} on ${on_string}: summary.tsv" from_work_dir="output_reports/summary.tsv" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	200 <data name="output_psms" format="tabular" label="${tool.name} on ${on_string}: PSMs.tsv" from_work_dir="output_reports/aggregate.PSMs.tsv" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	201 <data name="output_unique_peptides" format="tabular" label="${tool.name} on ${on_string}: unique_peptides.tsv" from_work_dir="output_reports/aggregate.unique_peptides.tsv" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	202 <data name="output_protein_groups" format="tabular" label="${tool.name} on ${on_string}: protein_groups.tsv" from_work_dir="output_reports/aggregate.protein_groups.tsv" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	203 <data name="aggregate_mzid" format="mzid" label="${tool.name} on ${on_string}: aggregate.mzid" from_work_dir="output_reports/aggregate.mzid" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	204 <collection name="morpheus_pep_xmls" type="list" label="${tool.name} on ${on_string} pep.xml">
1 ecb9ec15083d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 0 diff changeset	205 <discover_datasets pattern="(?P<name>.*\.pep.xml)" ext="pepxml" visible="false" directory="output_reports" />
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	206 </collection>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	207 </outputs>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	208 <tests>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	209 <test>
1 ecb9ec15083d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 0 diff changeset	210 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	211 <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	212 <param name="fdr" value="1"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	213 <param name="mvmi" value="1024"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	214 <param name="precmt" value="Monoisotopic"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	215 <param name="precmtu" value="Da"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	216 <param name="precmtv" value="2.5"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	217 <output name="output_psms">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	218 <assert_contents>
1 ecb9ec15083d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 0 diff changeset	219 <not_has_text text="K.TTGSSSSSSSK.K" />
ecb9ec15083d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 0 diff changeset	220 <has_text text="carbamidomethylation of C" />
ecb9ec15083d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 0 diff changeset	221 <has_text text="(oxidation of M)" />
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	222 </assert_contents>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	223 </output>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	224 </test>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	225 <test>
1 ecb9ec15083d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 0 diff changeset	226 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	227 <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	228 <param name="fdr" value="1"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	229 <param name="mvmi" value="1024"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	230 <param name="precmt" value="Monoisotopic"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	231 <param name="precmtu" value="Da"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	232 <param name="precmtv" value="2.5"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	233 <param name="fm" value="carbamidomethylation of C"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	234 <param name="vm" value="oxidation of M"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	235 <output name="output_psms">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	236 <assert_contents>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	237 <has_text text="K.VETYM(oxidation of M)ETK.I" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	238 <not_has_text text="K.TTGSSSSSSSK.K" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	239 </assert_contents>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	240 </output>
3 8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	241 </test>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	242 <test>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	243 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	244 <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	245 <param name="fdr" value="1"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	246 <param name="mvmi" value="1024"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	247 <param name="precmt" value="Monoisotopic"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	248 <param name="precmtu" value="Da"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	249 <param name="precmtv" value="2.5"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	250 <param name="fm" value="carbamidomethylation of C"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	251 <param name="vm" value="oxidation of M"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	252 <param name="p" value="trypsin" />
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	253 <output name="output_psms">
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	254 <assert_contents>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	255 <has_text text="K.DGM(oxidation of M)KAYAQNVQQR.E" />
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	256 <not_has_text text="K.TTGSSSSSSSK.K" />
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	257 </assert_contents>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	258 </output>
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	259 </test>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	260 <test>
1 ecb9ec15083d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 0 diff changeset	261 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	262 <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	263 <param name="fdr" value="1"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	264 <param name="mvmi" value="1024"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	265 <param name="precmt" value="Monoisotopic"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	266 <param name="precmtu" value="Da"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	267 <param name="precmtv" value="2.5"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	268 <param name="fm" value="carbamidomethylation of C"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	269 <param name="vm" value="oxidation of M"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	270 <output name="output_psms">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	271 <assert_contents>
3 8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	272 <has_text text="K.RSPSGNISTNSMR.P" />
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	273 <not_has_text text="K.KYFLENKIGTDR.R" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	274 </assert_contents>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	275 </output>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	276 </test>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	277 <test>
1 ecb9ec15083d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit fbd807a9986aaff2a119a70d9c9df97290b80999 galaxyp parents: 0 diff changeset	278 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	279 <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	280 <param name="fdr" value="1"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	281 <param name="mvmi" value="1024"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	282 <param name="precmt" value="Monoisotopic"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	283 <param name="precmtu" value="Da"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	284 <param name="precmtv" value="2.5"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	285 <param name="fm" value="carbamidomethylation of C"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	286 <param name="vm" value="oxidation of M"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	287 <param name="adv_options_selector" value="set"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	288 <param name="prodmtv" value=".01"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	289 <output name="output_psms">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	290 <assert_contents>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	291 <has_text text="K.KTLKSDGVAGLYR.G" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	292 <not_has_text text="K.RSPSGNISTNSMR.P" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	293 </assert_contents>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	294 </output>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	295 </test>
3 8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	296 <test>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	297 <param name="inputs" value="test_input.mzML" ftype="mzml"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	298 <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	299 <param name="fdr" value="1"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	300 <param name="mvmi" value="1024"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	301 <param name="precmt" value="Monoisotopic"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	302 <param name="precmtu" value="Da"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	303 <param name="precmtv" value="2.5"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	304 <param name="fm" value="carbamidomethylation of C"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	305 <param name="vm" value="oxidation of M"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	306 <param name="p" value="trypsin"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	307 <param name="adv_options_selector" value="set"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	308 <param name="prodmtv" value=".01"/>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	309 <output name="output_psms">
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	310 <assert_contents>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	311 <has_text text="K.KTLKSDGVAGLYR.G" />
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	312 <not_has_text text="K.KYFLENKIGTDR.R" />
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	313 </assert_contents>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	314 </output>
8295d959ca28 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1 galaxyp parents: 2 diff changeset	315 </test>
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	316 </tests>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	317 <help><![CDATA[
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	318 Morpheus_ is a database search algorithm for high-resolution tandem mass spectra.
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	319
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty 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
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	321
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	322 INPUTS
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	323
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	324 - spectral data file in mzML format
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	325 - protein search database, either a fasta file or a uniprot proteome xml file
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	326
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	327 OUTPUTS
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	328
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	329 - summary.tsv
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	330 - input.log.txt
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	331 - input.PSMs.tsv
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	332 - input.unique_peptides.tsv
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	333 - input.protein_groups.tsv
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	334 - input.pep.xml
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	335
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	336 .. _Morpheus: http://morpheus-ms.sourceforge.net/
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	337
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	338 ]]></help>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	339 <citations>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	340 <citation type="doi">10.1021/pr301024c</citation>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	341 </citations>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	342 </tool>

Mercurial > repos > galaxyp > morpheus

annotate morpheus.xml @ 3:8295d959ca28 draft default tip