Mercurial > repos > galaxyp > mz_to_sqlite

annotate mz_to_sqlite.xml @ 6:705821bf30d2 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 03090c9f45e9be50ed4c5e4df6419d0e8525c52d
author galaxyp
date Tue, 12 Mar 2024 11:46:44 +0000
parents 8190f6083c0d
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8190f6083c0d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 24561502a9bed97f351af6a0438aa82414a351ab"
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1 <tool id="mz_to_sqlite" name="mz to sqlite" version="2.1.1+galaxy0">
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2 <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description>
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3 <xrefs>
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4 <xref type="bio.tools">mztosqlite</xref>
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5 </xrefs>
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6 <requirements>
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7 <requirement type="package" version="2.1.1">mztosqlite</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" level="fatal" description="Error Running mz_to_sqlite" />
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11 </stdio>
0
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12 <command>
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13 <![CDATA[
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f5c632894818 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 75b9f57bf0b41b2a0b1e1c9f73447a1125fc245e"
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14 mz_to_sqlite
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15 -numthreads "\${GALAXY_SLOTS:-4}"
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16 -dbname 'sqlite.db'
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17 -mzid '$mzinput'
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18 #if len($scanfiles) > 0:
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19 #set $files = " ".join(["'"+ a.strip() + "'" for a in str($scanfiles).split(',')])
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20 -scanfiles $files
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21 #set $dfiles = [a for a in $scanfiles]
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22 -scanFilesDisplayName
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23 #for $f in $dfiles
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24 '$f.display_name'
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25 #end for
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26 #end if
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27 #if len($searchdbs) > 0:
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28 #set $dbFiles = " ".join(["'"+ a.strip() + "'" for a in str($searchdbs).split(',')])
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29 -fasta $dbFiles
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30 #end if
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31 ]]>
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32 </command>
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33 <inputs>
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34 <param name="mzinput" type="data" format="mzid" label="Proteomics Identification files" />
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35 <param name="scanfiles" type="data" format="mgf" multiple="true" optional="true" label="Proteomics Spectrum files" />
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36 <param name="searchdbs" type="data" format="fasta,uniprotxml" multiple="true" optional="true" label="Proteomics Search Database Fasta" help="These can provide sequences and length for proteins if not already present in the mzIdentML input" />
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37 </inputs>
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38 <outputs>
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39 <data format="mz.sqlite" name="sqlite_db" label="${tool.name} on ${on_string}" from_work_dir="sqlite.db" />
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40 </outputs>
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41 <tests>
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42 <test>
2
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43 <param name="mzinput" value="test_id.mzid" ftype="mzid"></param>
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44 <param name="scanfiles" value="test.mgf" ftype="mgf"></param>
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45 <param name="searchdbs" value="test.fasta" ftype="fasta"></param>
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46 <output name="sqlite_db" file="sqlite.db" />
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47 </test>
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48 </tests>
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49 <help>
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50 <![CDATA[
0
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51 ** mz_to_sqlite converts proteomics file formats to a SQLite database**
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52
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53 ]]>
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54 </help>
6
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55 <citations>
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56 <citation type="bibtex">
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57 @misc{
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58 mzToSQLite,
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59 author = {GalaxyP},
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60 year = {2021},
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61 title = {mzToSQLite},
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62 publisher = {GitHub},
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63 journal = {GitHub repository},
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64 url = {https://github.com/galaxyproteomics/mzToSQLite},
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65 }
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66 </citation>
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67 </citations>
0
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68 </tool>