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