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comparison mz_to_sqlite.xml @ 0:946ce2e034a2

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author galaxyp
date Fri, 12 Jun 2015 17:28:09 -0400
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children 77389cf7ff62
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1 <tool id="mz_to_sqlite" name="mz to sqlite" version="1.0.0">
2 <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description>
3 <requirements>
4 <requirement type="package" version="1.0.0">mztosqlite</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" level="fatal" description="Error Running mz_to_sqlite" />
8 </stdio>
9 <command>
10 <![CDATA[
11 java -jar \$MZTOSQLITE_JAR_PATH -s $mzsqlite
12 #if len($scanfiles) > 0:
13 $scanfiles.__str__.replace(',',' ')
14 #end if
15 #if len($searchdbs) > 0:
16 $searchdbs.__str__.replace(',',' ')
17 #end if
18 #if len($mzinputs) > 0:
19 $mzinputs.__str__.replace(',',' ')
20 #end if
21 ]]>
22 </command>
23 <inputs>
24 <param name="mzinputs" type="data" format="mzid" multiple="true" optional="true" label="Proteomics Identification files"/>
25 <param name="scanfiles" type="data" format="mzml,mgf" multiple="true" optional="true" label="Proteomics Spectrum files"/>
26 <param name="searchdbs" type="data" format="fasta" multiple="true" optional="true" label="Proteomics Search Database Fasta"
27 help="These can provide sequences and length for proteins if not already present in the mzIdentML input"/>
28 </inputs>
29 <outputs>
30 <data format="sqlite" name="mzsqlite" label="${tool.name} on ${on_string}"/>
31 </outputs>
32 <tests>
33 <test>
34 </test>
35 </tests>
36 <help>
37 <![CDATA[
38 ** mz_to_sqlite converts proteomics file formats to a SQLite database**
39
40 ]]>
41 </help>
42 </tool>