comparison msgfplus.xml @ 4:58f9cf0de6d4 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b2712071afd2d74261bc3e3fc555355f5675a0d6
author galaxyp
date Wed, 23 Aug 2017 05:47:29 -0400
parents b4ccaf21855d
children ce4882b95b73
comparison
equal deleted inserted replaced
3:b4ccaf21855d 4:58f9cf0de6d4
1 <tool id="msgfplus" name="MS-GF+" version="0.1"> 1 <tool id="msgfplus" name="MS-GF+" version="0.2">
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="2016.10.26">msgf_plus</requirement> 6 <requirement type="package" version="2016.10.26">msgf_plus</requirement>
12 </stdio> 12 </stdio>
13 <command> 13 <command>
14 14
15 <![CDATA[ 15 <![CDATA[
16 #if $msgf_input.intype_selector == "single" 16 #if $msgf_input.intype_selector == "single"
17 #set $db_name = $msgf_input.d.display_name.replace(".fasta", "") + ".fasta" 17 #set $db_name = $msgf_input.d.element_identifier.replace(".fasta", "") + ".fasta"
18 #set $input_name = $msgf_input.s.display_name 18 #set $input_name = $msgf_input.s.element_identifier.replace(".mzML", "") + ".mzML"
19 ln -s '$msgf_input.s' '${input_name}' && 19 ln -s '$msgf_input.s' '${input_name}' &&
20 ln -s '$msgf_input.d' '${db_name}' && 20 ln -s '$msgf_input.d' '${db_name}' &&
21 #else if $msgf_input.intype_selector == "fractions" 21 #else if $msgf_input.intype_selector == "fractions"
22 #set $db_name = $msgf_input.db_spectra.reverse.display_name.replace(".fasta", "") + ".fasta" 22 #set $db_name = $msgf_input.db_spectra.reverse.element_identifier.replace(".fasta", "") + ".fasta"
23 #set $input_name = $msgf_input.db_spectra.forward.display_name 23 #set $input_name = $msgf_input.db_spectra.forward.element_identifier.replace(".mzML", "") + ".mzML"
24 ln -s '$msgf_input.db_spectra.forward' '${input_name}' && 24 ln -s '$msgf_input.db_spectra.forward' '${input_name}' &&
25 ln -s '$msgf_input.db_spectra.reverse' '${db_name}' && 25 ln -s '$msgf_input.db_spectra.reverse' '${db_name}' &&
26 #end if 26 #end if
27 #set $output_name = $input_name.replace(".mzML", "") + ".mzid" 27 #set $output_name = $input_name.replace(".mzML", ".mzid")
28 28
29 echo \\#Mods > Mods.txt && 29 echo \\#Mods > Mods.txt &&
30 #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications) 30 #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications)
31 #for $mod in $common_mods.split(",") 31 #for $mod in $common_mods.split(",")
32 echo '$mod.replace("_", ",")' >> Mods.txt && 32 echo '$mod.replace("_", ",")' >> Mods.txt &&
76 <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/> 76 <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/>
77 <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/> 77 <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/>
78 </when> 78 </when>
79 <when value="fractions"> 79 <when value="fractions">
80 <param name="db_spectra" type="data_collection" collection_type="paired" 80 <param name="db_spectra" type="data_collection" collection_type="paired"
81 label="Collection: Pairs of FASTA database (forward) and spectra (reverse)"/> 81 label="Collection: Pairs of spectra (forward) and FASTA database (reverse)"/>
82 </when> 82 </when>
83 </conditional> 83 </conditional>
84 <param name="tsvcheck" type="boolean" label="Output TSV as well?" /> 84 <param name="tsvcheck" type="boolean" label="Output TSV as well?" />
85 <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" /> 85 <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" />
86 <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/> 86 <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/>
267 <param name="ntt" value="1" /> 267 <param name="ntt" value="1" />
268 <param name="t" value="50" /> 268 <param name="t" value="50" />
269 <param name="precursor_ion_tol_units" value="ppm" /> 269 <param name="precursor_ion_tol_units" value="ppm" />
270 <param name="common_fixed_modifications" value="" /> 270 <param name="common_fixed_modifications" value="" />
271 <param name="common_variable_modifications" value="" /> 271 <param name="common_variable_modifications" value="" />
272 <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" /> 272 <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="100" />
273 </test> 273 </test>
274 <test> 274 <test>
275 <param name="msgf_input|intype_selector" value="single" /> 275 <param name="msgf_input|intype_selector" value="single" />
276 <param name="msgf_input|s" value="input/201208-378803.mzML" /> 276 <param name="msgf_input|s" value="input/201208-378803.mzML" />
277 <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" /> 277 <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" />