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annotate mz_to_sqlite.xml @ 3:c8bdcf574413 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit ae0093d9f1576f38aee83b2ed5e7f70c901d5864
author galaxyp
date Mon, 11 Feb 2019 17:30:12 -0500
parents 8df9fe030d68
children 2a8a9f07782e
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c8bdcf574413 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit ae0093d9f1576f38aee83b2ed5e7f70c901d5864
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1 <tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.2">
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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="2.0.2">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 mz_to_sqlite -Xms1g -Xmx6g
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12 -numthreads "\${GALAXY_SLOTS:-4}"
c8bdcf574413 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit ae0093d9f1576f38aee83b2ed5e7f70c901d5864
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13 -dbname 'sqlite.db'
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14 -mzid '$mzinput'
c8bdcf574413 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit ae0093d9f1576f38aee83b2ed5e7f70c901d5864
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15 #if len($scanfiles) > 0:
c8bdcf574413 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit ae0093d9f1576f38aee83b2ed5e7f70c901d5864
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16 #set $files = " ".join(["'"+ a.strip() + "'" for a in str($scanfiles).split(',')])
c8bdcf574413 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit ae0093d9f1576f38aee83b2ed5e7f70c901d5864
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17 -scanfiles $files
c8bdcf574413 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit ae0093d9f1576f38aee83b2ed5e7f70c901d5864
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18 #set $dfiles = [a for a in $scanfiles]
c8bdcf574413 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit ae0093d9f1576f38aee83b2ed5e7f70c901d5864
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19 -scanFilesDisplayName
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20 #for $f in $dfiles
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21 '$f.display_name'
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22 #end for
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23 #end if
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24 #if len($searchdbs) > 0:
c8bdcf574413 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit ae0093d9f1576f38aee83b2ed5e7f70c901d5864
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25 #set $dbFiles = " ".join(["'"+ a.strip() + "'" for a in str($searchdbs).split(',')])
c8bdcf574413 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit ae0093d9f1576f38aee83b2ed5e7f70c901d5864
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26 -fasta $dbFiles
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27 #end if
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28 ]]>
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29 </command>
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30 <inputs>
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31 <param name="mzinput" type="data" format="mzid" label="Proteomics Identification files"/>
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32 <param name="scanfiles" type="data" format="mzml,mgf" multiple="true" optional="true" label="Proteomics Spectrum files"/>
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33 <param name="searchdbs" type="data" format="fasta,uniprotxml" multiple="true" optional="true" label="Proteomics Search Database Fasta"
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34 help="These can provide sequences and length for proteins if not already present in the mzIdentML input"/>
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35 </inputs>
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36 <outputs>
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37 <data format="mz.sqlite" name="sqlite_db" label="${tool.name} on ${on_string}" from_work_dir="sqlite.db"/>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="mzinput" value="test_id.mzid" ftype="mzid"></param>
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42 <param name="scanfiles" value="test.mgf" ftype="mgf"></param>
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43 <param name="searchdbs" value="test.fasta" ftype="fasta"></param>
c8bdcf574413 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit ae0093d9f1576f38aee83b2ed5e7f70c901d5864
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44 <output name="sqlite_db" file="sqlite.db" />
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45 </test>
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46 </tests>
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47 <help>
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48 <![CDATA[
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49 ** mz_to_sqlite converts proteomics file formats to a SQLite database**
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50
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51 ]]>
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52 </help>
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53 <citations></citations>
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54 </tool>