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comparison msgfplus.xml @ 9:a26f5807eb85 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 75603eb19ef066d891fd906d7dd4b06f5498ca68
author galaxyp
date Mon, 04 Dec 2017 08:57:35 -0500
parents 09e0ae6f661b
children
comparison
equal deleted inserted replaced
8:09e0ae6f661b 9:a26f5807eb85
1 <tool id="msgfplus" name="MS-GF+" version="0.4"> 1 <tool id="msgfplus" name="MS-GF+" version="0.5">
2 <description> 2 <description>
3 Identifies peptides in tandem mass spectra using the MS-GF+ search engine. 3 Identifies peptides in tandem mass spectra using the MS-GF+ search engine.
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="2017.07.21">msgf_plus</requirement> 6 <requirement type="package" version="2017.07.21">msgf_plus</requirement>
54 -maxLength $advanced.maxLength 54 -maxLength $advanced.maxLength
55 -minCharge $advanced.minCharge 55 -minCharge $advanced.minCharge
56 -maxCharge $advanced.maxCharge 56 -maxCharge $advanced.maxCharge
57 -n $advanced.n 57 -n $advanced.n
58 -addFeatures $advanced.addFeatures 58 -addFeatures $advanced.addFeatures
59 #if $tsvcheck 59 #if $tsv == 'targets' or $tsv == 'decoys'
60 && 60 &&
61 msgf_plus 61 msgf_plus
62 edu.ucsd.msjava.ui.MzIDToTsv 62 edu.ucsd.msjava.ui.MzIDToTsv
63 -i '$output_name' 63 -i '$output_name'
64 -o output.tsv 64 -o output.tsv
65 #if $tsv == 'decoys'
66 -showDecoy 1
67 #end if
65 #end if 68 #end if
66 && 69 &&
67 mv '$output_name' output 70 mv '$output_name' output
68 ]]> 71 ]]>
69 </command> 72 </command>
80 <when value="fractions"> 83 <when value="fractions">
81 <param name="db_spectra" type="data_collection" collection_type="paired" 84 <param name="db_spectra" type="data_collection" collection_type="paired"
82 label="Collection: Pairs of spectra (forward) and FASTA database (reverse)"/> 85 label="Collection: Pairs of spectra (forward) and FASTA database (reverse)"/>
83 </when> 86 </when>
84 </conditional> 87 </conditional>
85 <param name="tsvcheck" type="boolean" label="Output TSV as well?" /> 88 <param name="tsv" type="select" label="Output TSV as well?">
89 <option value="targets">Only target PSMs</option>
90 <option value="decoys">Both target and decoy PSMs</option>
91 </param>
86 <param argument="-tda" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Search with on-the-fly decoy database?" help="MSGF+ uses XXX_ as an accession prefix to indicate a decoy hit" /> 92 <param argument="-tda" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Search with on-the-fly decoy database?" help="MSGF+ uses XXX_ as an accession prefix to indicate a decoy hit" />
87 <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/> 93 <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/>
88 <param name="precursor_ion_tol_units" type="select" label="Precursor mass tolerance units" help="Daltons are common for low-res instruments, ppm for high-res instruments"> 94 <param name="precursor_ion_tol_units" type="select" label="Precursor mass tolerance units" help="Daltons are common for low-res instruments, ppm for high-res instruments">
89 <option value="ppm" selected="true">Parts per million (ppm)</option> 95 <option value="ppm" selected="true">Parts per million (ppm)</option>
90 <option value="Da">Daltons</option> 96 <option value="Da">Daltons</option>
244 </test> 250 </test>
245 <test> 251 <test>
246 <param name="msgf_input|intype_selector" value="single" /> 252 <param name="msgf_input|intype_selector" value="single" />
247 <param name="msgf_input|s" value="input/201208-378803.mzML" /> 253 <param name="msgf_input|s" value="input/201208-378803.mzML" />
248 <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" /> 254 <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" />
249 <param name="tsvcheck" value="true" /> 255 <param name="tsv" value="decoys" />
250 <param name="tda" value="1" /> 256 <param name="tda" value="1" />
251 <param name="ntt" value="1" /> 257 <param name="ntt" value="1" />
252 <param name="t" value="50" /> 258 <param name="t" value="50" />
253 <param name="precursor_ion_tol_units" value="ppm" /> 259 <param name="precursor_ion_tol_units" value="ppm" />
254 <param name="common_fixed_modifications" value="" /> 260 <param name="common_fixed_modifications" value="" />