morpheus: morpheus.xml annotate

annotate morpheus.xml @ 0:553f0336e43e draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty

author	galaxyp
date	Mon, 23 May 2016 09:51:47 -0400
parents
children	ecb9ec15083d

rev	line source
0 553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	1 <tool id="morpheus" name="Morpheus" version="2.255.0">
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>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	4 <xml name="modification_options">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	5 <option value="acetylation of protein N-terminus">acetylation of protein N-terminus</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	6 <option value="acetylation of lysine">acetylation of lysine</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	7 <option value="phosphorylation of S">phosphorylation of S</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	8 <option value="phosphorylation of T">phosphorylation of T</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	9 <option value="phosphorylation of Y">phosphorylation of Y</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	10 <option value="deamidation of N">deamidation of N</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	11 <option value="deamidation of Q">deamidation of Q</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	12 <option value="pyro-cmC">pyro-cmC</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	13 <option value="pyro-E">pyro-E</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	14 <option value="pyro-Q">pyro-Q</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	15 <option value="TMT zero on peptide N-terminus">TMT zero on peptide N-terminus</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	16 <option value="TMT zero on K">TMT zero on K</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	17 <option value="TMT zero on Y">TMT zero on Y</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	18 <option value="TMT duplex on peptide N-terminus">TMT duplex on peptide N-terminus</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	19 <option value="TMT duplex on K">TMT duplex on K</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	20 <option value="TMT duplex on Y">TMT duplex on Y</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	21 <option value="TMT sixplex/tenplex on peptide N-terminus">TMT sixplex/tenplex on peptide N-terminus</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	22 <option value="TMT sixplex/tenplex on K">TMT sixplex/tenplex on K</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	23 <option value="TMT sixplex/tenplex on Y">TMT sixplex/tenplex on Y</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	24 <option value="iTRAQ 4-plex on peptide N-terminus">iTRAQ 4-plex on peptide N-terminus</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	25 <option value="iTRAQ 4-plex on K">iTRAQ 4-plex on K</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	26 <option value="iTRAQ 4-plex on Y">iTRAQ 4-plex on Y</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	27 <option value="iTRAQ 8-plex on peptide N-terminus">iTRAQ 8-plex on peptide N-terminus</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	28 <option value="iTRAQ 8-plex on K">iTRAQ 8-plex on K</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	29 <option value="iTRAQ 8-plex on Y ">iTRAQ 8-plex on Y </option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	30 </xml>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	31 <xml name="variable_modification_options">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	32 <option value="oxidation of M" selected="true">oxidation of M</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	33 <option value="carbamidomethylation of C">carbamidomethylation of C</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	34 <expand macro="modification_options"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	35 </xml>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	36 <xml name="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	37 <option value="carbamidomethylation of C" selected="true">carbamidomethylation of C</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	38 <option value="oxidation of M">oxidation of M</option>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	39 <expand macro="modification_options"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	40 </xml>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	41 </macros>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	42
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	43 <requirements>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	44 <requirement version="4.0">mono</requirement>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	45 <requirement version="255">morpheus</requirement>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	46 </requirements>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	47
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	48 <stdio>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	49 <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	50 <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	51 source="both"
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	52 level="fatal"
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	53 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	54 </stdio>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	55
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	56 <command><![CDATA[
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	57 mkdir -p output_reports &&
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	58 cwd=`pwd`&&
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	59 #import re
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	60 #set $searchdb_name = $searchdb
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	61 #if isinstance($searchdb.datatype, $__app__.datatypes_registry.get_datatype_by_extension('uniprotxml').__class__):
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	62 #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	63 #else
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	64 #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	65 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	66 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	67 ## 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	68 #set $input_list = []
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	69 #for i,input in enumerate($inputs):
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	70 #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	71 #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	72 #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	73 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	74 #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	75 && 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	76 #end for
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	77 #set $input_names = ','.join($input_list)
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	78 && mono \${MORPHEUS_PATH}/morpheus_mzml_mono_cl.exe
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	79 -d="$input_names"
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	80 -db=$searchdb_name
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	81 #if isinstance($searchdb.datatype, $__app__.datatypes_registry.get_datatype_by_extension('uniprotxml').__class__):
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.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	83 $advanced.noup
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	84 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	85 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	86 ## fm vm fdr mvmi precmt precmtv precmtu
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	87 #if str($fdr) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	88 -fdr=$fdr
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	89 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	90 #if str($mvmi) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	91 -mvmi=$mvmi
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	92 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	93 #if str($precmtv) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	94 -precmtv=$precmtv
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	95 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	96 #if str($precmtu) != 'None':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	97 -precmtu=$precmtu
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	98 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	99 #if str( $advanced.adv_options_selector) == "set":
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	100 #if str($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	101 -precmt=$advanced.precmt
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	102 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	103 #if str($advanced.minprecz) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	104 -minprecz=$advanced.minprecz
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	105 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	106 #if str($advanced.maxprecz) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	107 -maxprecz=$advanced.maxprecz
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	108 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	109 #if str($advanced.at) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	110 -at=$advanced.at
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	111 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	112 #if str($advanced.rt) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	113 -rt=$advanced.rt
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	114 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	115 #if str($advanced.mp) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	116 -mp=$advanced.mp
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	117 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	118 #if str($advanced.mmc) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	119 -mmc=$advanced.mmc
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	120 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	121 #if str($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	122 -prodmt=$advanced.prodmt
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	123 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	124 #if str($advanced.prodmtv) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	125 -prodmtv=$advanced.prodmtv
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	126 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	127 #if str($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	128 -prodmtu=$advanced.prodmtu
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	129 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	130 #if str($advanced.minpmo) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	131 -minpmo=$advanced.minpmo
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	132 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	133 #if str($advanced.maxpmo) != '':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	134 -maxpmo=$advanced.maxpmo
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	135 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	136 #if str($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	137 -imb=$advanced.imb
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	138 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	139 #if str($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	140 -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	141 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	142 $advanced.acs $advanced.di $advanced.pmc $advanced.cmu $advanced.mmu
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	143 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	144 #if str($fm) != 'None':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	145 #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	146 -fm="$fmods"
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	147 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	148 #if str($vm) != 'None':
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	149 #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	150 -vm="$vmods"
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	151 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	152 -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	153 #set $out_list = 'log.txt summary.tsv aggregate.PSMs.tsv aggregate.unique_peptides.tsv aggregate.protein_groups.tsv aggregate.mzid *.pep.xml'
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	154 #if len($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	155 && 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	156 && 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	157 && 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	158 && 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	159 && 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	160 #end if
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	161 && ( 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	162 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	163 ]]></command>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	164 <inputs>
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="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	166 <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	167 <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	168 <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	169 </param>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	170 <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	171 <expand macro="variable_modification_options" />
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="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	174 <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	175 <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	176 <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	177 <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	178 <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	179 </param>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	180 <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	181 <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	182 <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	183 <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	184 </param>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	185 <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	186 <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	187 <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	188 <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	189 </param>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	190 <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	191 <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	192 <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	193 <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	194 <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	195 <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	196 <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	197 <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	198 <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	199 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	200 <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	201 <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	202 </param>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	203 <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	204 <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	205 <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	206 <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	207 <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	208 <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	209 <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	210 </param>
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="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	212 <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	213 <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	214 <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	215 </param>
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="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	217 <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	218 <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	219 <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	220 </param>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	221 <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	222 <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	223 </when>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	224 <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	225 </conditional>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	226 </inputs>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	227 <outputs>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	228 <data name="log" format="txt" label="${tool.name} on ${on_string}: log.txt" from_work_dir="output_reports/log.txt" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	229 <data name="summary" format="txt" label="${tool.name} on ${on_string}: summary.tsv" from_work_dir="output_reports/summary.tsv" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	230 <data name="output_psms" format="tabular" label="${tool.name} on ${on_string}: PSMs.tsv" from_work_dir="output_reports/aggregate.PSMs.tsv" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	231 <data name="output_unique_peptides" format="tabular" label="${tool.name} on ${on_string}: unique_peptides.tsv" from_work_dir="output_reports/aggregate.unique_peptides.tsv" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	232 <data name="output_protein_groups" format="tabular" label="${tool.name} on ${on_string}: protein_groups.tsv" from_work_dir="output_reports/aggregate.protein_groups.tsv" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	233 <data name="aggregate_mzid" format="mzid" label="${tool.name} on ${on_string}: aggregate.mzid" from_work_dir="output_reports/aggregate.mzid" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	234 <collection name="morpheus_pep_xmls" type="list" label="${tool.name} on ${on_string} pep.xml">
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	235 <discover_datasets pattern="(?P<name>.*\.pep.xml)" ext="pepxml" visible="False" directory="output_reports" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	236 </collection>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	237 </outputs>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	238 <tests>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	239 <test>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	240 <param name="input" value="test_input.mzML" ftype="mzml"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	241 <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	242 <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	243 <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	244 <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	245 <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	246 <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	247 <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	248 <assert_contents>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	249 <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	250 <not_has_text text="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	251 <not_has_text text="(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	252 </assert_contents>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	253 </output>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	254 </test>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	255 <test>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	256 <param name="input" value="test_input.mzML" ftype="mzml"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	257 <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	258 <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	259 <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	260 <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	261 <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	262 <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	263 <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	264 <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	265 <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	266 <assert_contents>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	267 <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	268 <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	269 </assert_contents>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	270 </output>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	271 </test>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	272 <test>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	273 <param name="input" value="test_input.mzML" ftype="mzml"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	274 <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	275 <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	276 <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	277 <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	278 <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	279 <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	280 <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	281 <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	282 <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	283 <assert_contents>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	284 <has_text text="R.KRSLFDS(UniProt: Phosphoserine)AFSSR.A" />
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	285 <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	286 </assert_contents>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	287 </output>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	288 </test>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	289 <test>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	290 <param name="input" value="test_input.mzML" ftype="mzml"/>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	291 <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	292 <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	293 <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	294 <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	295 <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	296 <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	297 <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	298 <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	299 <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	300 <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	301 <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	302 <assert_contents>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	303 <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	304 <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	305 </assert_contents>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	306 </output>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	307 </test>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	308
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	309 </tests>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	310 <help><![CDATA[
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	311 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	312
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	313 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	314
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	315 INPUTS
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	316
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	317 - 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	318 - 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	319
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	320 OUTPUTS
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 - summary.tsv
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	323 - 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	324 - 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	325 - 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	326 - 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	327 - 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	328
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	329 .. _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	330
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	331 ]]></help>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	332 <citations>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	333 <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	334 </citations>
553f0336e43e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 2cfe229337e1cea060d77b49df588237dfbd1ce0-dirty galaxyp parents: diff changeset	335 </tool>

Mercurial > repos > galaxyp > morpheus

annotate morpheus.xml @ 0:553f0336e43e draft