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comparison msgfplus.xml @ 8:47408c5b1517 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit a030bdf85b5d74b7c1a16926322e47154b120fea
author galaxyp
date Wed, 13 Sep 2017 15:57:15 -0400
parents 51fd56b09e64
children b45ced785e01
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7:51fd56b09e64 8:47408c5b1517
1 <tool id="msgfplus" name="MS-GF+" version="0.2"> 1 <tool id="msgfplus" name="MS-GF+" version="0.3">
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>
18 #set $input_name = $msgf_input.s.element_identifier.replace(".mzML", "") + ".mzML" 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.element_identifier.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.element_identifier.replace(".mzML", "") + ".mzML" 23 #set $input_name = $msgf_input.db_spectra.name.replace(".mzML", "") + ".mzML"
24 ln -s '$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