Mercurial > repos > galaxyp > mz_to_sqlite

annotate mz_to_sqlite.xml @ 5:9a1ced29b130 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 75b9f57bf0b41b2a0b1e1c9f73447a1125fc245e"
author galaxyp
date Wed, 08 Jul 2020 14:03:33 +0000
parents 2a8a9f07782e
children f52c286f7e0b
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9a1ced29b130 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 75b9f57bf0b41b2a0b1e1c9f73447a1125fc245e"
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1 <tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.4+galaxy1">
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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="2.0.4">mztosqlite</requirement>
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5 </requirements>
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2a8a9f07782e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 1acf110c8836bf573d241a8fd33c842da369e76c"
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Error Running mz_to_sqlite" />
2a8a9f07782e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 1acf110c8836bf573d241a8fd33c842da369e76c"
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8 </stdio>
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9 <command>
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10 <![CDATA[
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9a1ced29b130 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 75b9f57bf0b41b2a0b1e1c9f73447a1125fc245e"
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11 mz_to_sqlite
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12 -numthreads "\${GALAXY_SLOTS:-4}"
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13 -dbname 'sqlite.db'
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14 -mzid '$mzinput'
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15 #if len($scanfiles) > 0:
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16 #set $files = " ".join(["'"+ a.strip() + "'" for a in str($scanfiles).split(',')])
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17 -scanfiles $files
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18 #set $dfiles = [a for a in $scanfiles]
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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:
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25 #set $dbFiles = " ".join(["'"+ a.strip() + "'" for a in str($searchdbs).split(',')])
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26 -fasta $dbFiles
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27 #end if
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28 ]]>
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29 </command>
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30 <inputs>
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31 <param name="mzinput" type="data" format="mzid" label="Proteomics Identification files" />
2a8a9f07782e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 1acf110c8836bf573d241a8fd33c842da369e76c"
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32 <param name="scanfiles" type="data" format="mgf" multiple="true" optional="true" label="Proteomics Spectrum files" />
2a8a9f07782e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 1acf110c8836bf573d241a8fd33c842da369e76c"
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33 <param name="searchdbs" type="data" format="fasta,uniprotxml" multiple="true" optional="true" label="Proteomics Search Database Fasta" help="These can provide sequences and length for proteins if not already present in the mzIdentML input" />
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34 </inputs>
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35 <outputs>
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36 <data format="mz.sqlite" name="sqlite_db" label="${tool.name} on ${on_string}" from_work_dir="sqlite.db" />
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="mzinput" value="test_id.mzid" ftype="mzid"></param>
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41 <param name="scanfiles" value="test.mgf" ftype="mgf"></param>
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42 <param name="searchdbs" value="test.fasta" ftype="fasta"></param>
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43 <output name="sqlite_db" file="sqlite.db" />
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44 </test>
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45 </tests>
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46 <help>
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47 <![CDATA[
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48 ** mz_to_sqlite converts proteomics file formats to a SQLite database**
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49
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50 ]]>
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51 </help>
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52 <citations></citations>
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53 </tool>