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comparison mz_to_sqlite.xml @ 1:e34bdac5b157 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
author galaxyp
date Wed, 28 Mar 2018 09:33:18 -0400
parents ab33bd49de43
children 1320693cbf1e
comparison
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0:ab33bd49de43 1:e34bdac5b157
1 <tool id="mz_to_sqlite" name="mz to sqlite" version="1.2.0"> 1 <tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.0">
2 <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description> 2 <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2.0">mztosqlite</requirement> 4 <requirement type="package" version="2.0.0">mztosqlite</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" level="fatal" description="Error Running mz_to_sqlite" /> 7 <exit_code range="1:" level="fatal" description="Error Running mz_to_sqlite" />
8 </stdio> 8 </stdio>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 java -jar \$MZTOSQLITE_JAR_PATH -s $mzsqlite 11 mz_to_sqlite -Xms1g -Xmx6g
12 #if len($scanfiles) > 0: 12 -numthreads "\${GALAXY_SLOTS:-4}"
13 $scanfiles.__str__.replace(',',' ') 13 -dbname 'sqlite.db'
14 #end if 14 -mzid '$mzinput'
15 #if len($searchdbs) > 0: 15 #if len($scanfiles) > 0:
16 $searchdbs.__str__.replace(',',' ') 16 #set $files = " ".join(["'"+ a.strip() + "'" for a in str($scanfiles).split(',')])
17 #end if 17 -scanfiles $files
18 #if len($mzinputs) > 0: 18 #set $dfiles = [a for a in $scanfiles]
19 $mzinputs.__str__.replace(',',' ') 19 -scanFilesDisplayName
20 #end if 20 #for $f in $dfiles
21 '$f.display_name'
22 #end for
23 #end if
24 #if len($searchdbs) > 0:
25 #set $dbFiles = " ".join(["'"+ a.strip() + "'" for a in str($searchdbs).split(',')])
26 -fasta $dbFiles
27 #end if
21 ]]> 28 ]]>
22 </command> 29 </command>
23 <inputs> 30 <inputs>
24 <param name="mzinputs" type="data" format="mzid" multiple="true" optional="true" label="Proteomics Identification files"/> 31 <param name="mzinput" type="data" format="mzid" label="Proteomics Identification files"/>
25 <param name="scanfiles" type="data" format="mzml,mgf" multiple="true" optional="true" label="Proteomics Spectrum files"/> 32 <param name="scanfiles" type="data" format="mzml,mgf" multiple="true" optional="true" label="Proteomics Spectrum files"/>
26 <param name="searchdbs" type="data" format="fasta,uniprotxml" multiple="true" optional="true" label="Proteomics Search Database Fasta" 33 <param name="searchdbs" type="data" format="fasta,uniprotxml" multiple="true" optional="true" label="Proteomics Search Database Fasta"
27 help="These can provide sequences and length for proteins if not already present in the mzIdentML input"/> 34 help="These can provide sequences and length for proteins if not already present in the mzIdentML input"/>
28 </inputs> 35 </inputs>
29 <outputs> 36 <outputs>
30 <data format="mz.sqlite" name="mzsqlite" label="${tool.name} on ${on_string}"/> 37 <data format="mz.sqlite" name="sqlite_db" label="${tool.name} on ${on_string}" from_work_dir="sqlite.db"/>
31 </outputs> 38 </outputs>
32 <tests> 39 <tests>
33 <test> 40 <test>
34 </test> 41 </test>
35 </tests> 42 </tests>