Mercurial > repos > galaxyp > mz_to_sqlite
annotate mz_to_sqlite.xml @ 1:77389cf7ff62
Update mz_to_sqlite.xml to "mz.sqlite" and remove repository_dependencies.xml as proteomics datatypes are now in main.
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 05 Aug 2015 14:19:57 -0500 |
| parents | 946ce2e034a2 |
| children | 8df9fe030d68 |
| rev | line source |
|---|---|
| 0 | 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 $mzinputs.__str__.replace(',',' ') | |
| 20 #end if | |
| 21 ]]> | |
| 22 </command> | |
| 23 <inputs> | |
| 24 <param name="mzinputs" type="data" format="mzid" multiple="true" optional="true" label="Proteomics Identification files"/> | |
| 25 <param name="scanfiles" type="data" format="mzml,mgf" multiple="true" optional="true" label="Proteomics Spectrum files"/> | |
| 26 <param name="searchdbs" type="data" format="fasta" multiple="true" optional="true" label="Proteomics Search Database Fasta" | |
| 27 help="These can provide sequences and length for proteins if not already present in the mzIdentML input"/> | |
| 28 </inputs> | |
| 29 <outputs> | |
|
1
77389cf7ff62
Update mz_to_sqlite.xml to "mz.sqlite" and remove repository_dependencies.xml as proteomics datatypes are now in main.
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
30 <data format="mz.sqlite" name="mzsqlite" label="${tool.name} on ${on_string}"/> |
| 0 | 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> |