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comparison mz_to_sqlite.xml @ 4:2a8a9f07782e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 1acf110c8836bf573d241a8fd33c842da369e76c"
author galaxyp
date Mon, 29 Jun 2020 21:05:40 +0000
parents c8bdcf574413
children 9a1ced29b130
comparison
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3:c8bdcf574413 4:2a8a9f07782e
1 <tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.2"> 1 <tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.4">
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="2.0.2">mztosqlite</requirement> 4 <requirement type="package" version="2.0.4">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 mz_to_sqlite -Xms1g -Xmx6g 11 mz_to_sqlite -Xms1g -Xmx6g
12 -numthreads "\${GALAXY_SLOTS:-4}" 12 -numthreads "\${GALAXY_SLOTS:-4}"
13 -dbname 'sqlite.db' 13 -dbname 'sqlite.db'
14 -mzid '$mzinput' 14 -mzid '$mzinput'
15 #if len($scanfiles) > 0: 15 #if len($scanfiles) > 0:
26 -fasta $dbFiles 26 -fasta $dbFiles
27 #end if 27 #end if
28 ]]> 28 ]]>
29 </command> 29 </command>
30 <inputs> 30 <inputs>
31 <param name="mzinput" type="data" format="mzid" label="Proteomics Identification files"/> 31 <param name="mzinput" type="data" format="mzid" label="Proteomics Identification files" />
32 <param name="scanfiles" type="data" format="mzml,mgf" multiple="true" optional="true" label="Proteomics Spectrum files"/> 32 <param name="scanfiles" type="data" format="mgf" multiple="true" optional="true" label="Proteomics Spectrum files" />
33 <param name="searchdbs" type="data" format="fasta,uniprotxml" multiple="true" optional="true" label="Proteomics Search Database Fasta" 33 <param name="searchdbs" type="data" format="fasta,uniprotxml" multiple="true" optional="true" label="Proteomics Search Database Fasta" help="These can provide sequences and length for proteins if not already present in the mzIdentML input" />
34 help="These can provide sequences and length for proteins if not already present in the mzIdentML input"/>
35 </inputs> 34 </inputs>
36 <outputs> 35 <outputs>
37 <data format="mz.sqlite" name="sqlite_db" label="${tool.name} on ${on_string}" from_work_dir="sqlite.db"/> 36 <data format="mz.sqlite" name="sqlite_db" label="${tool.name} on ${on_string}" from_work_dir="sqlite.db" />
38 </outputs> 37 </outputs>
39 <tests> 38 <tests>
40 <test> 39 <test>
41 <param name="mzinput" value="test_id.mzid" ftype="mzid"></param> 40 <param name="mzinput" value="test_id.mzid" ftype="mzid"></param>
42 <param name="scanfiles" value="test.mgf" ftype="mgf"></param> 41 <param name="scanfiles" value="test.mgf" ftype="mgf"></param>
43 <param name="searchdbs" value="test.fasta" ftype="fasta"></param> 42 <param name="searchdbs" value="test.fasta" ftype="fasta"></param>
44 <output name="sqlite_db" file="sqlite.db" /> 43 <output name="sqlite_db" file="sqlite.db" />
45 </test> 44 </test>
46 </tests> 45 </tests>
47 <help> 46 <help>
48 <![CDATA[ 47 <![CDATA[
49 ** mz_to_sqlite converts proteomics file formats to a SQLite database** 48 ** mz_to_sqlite converts proteomics file formats to a SQLite database**
50 49
51 ]]> 50 ]]>
52 </help> 51 </help>
53 <citations></citations> 52 <citations></citations>