Mercurial > repos > galaxyp > mz_to_sqlite
diff mz_to_sqlite.xml @ 3:728d459bafe8 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 1acf110c8836bf573d241a8fd33c842da369e76c"
| author | galaxyp |
|---|---|
| date | Mon, 29 Jun 2020 17:06:00 -0400 |
| parents | 1320693cbf1e |
| children | f5c632894818 |
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--- a/mz_to_sqlite.xml Mon Feb 11 17:30:46 2019 -0500 +++ b/mz_to_sqlite.xml Mon Jun 29 17:06:00 2020 -0400 @@ -1,13 +1,13 @@ -<tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.2"> +<tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.4"> <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description> <requirements> - <requirement type="package" version="2.0.2">mztosqlite</requirement> + <requirement type="package" version="2.0.4">mztosqlite</requirement> </requirements> - <stdio> - <exit_code range="1:" level="fatal" description="Error Running mz_to_sqlite" /> - </stdio> + <stdio> + <exit_code range="1:" level="fatal" description="Error Running mz_to_sqlite" /> + </stdio> <command> -<![CDATA[ + <![CDATA[ mz_to_sqlite -Xms1g -Xmx6g -numthreads "\${GALAXY_SLOTS:-4}" -dbname 'sqlite.db' @@ -28,13 +28,12 @@ ]]> </command> <inputs> - <param name="mzinput" type="data" format="mzid" label="Proteomics Identification files"/> - <param name="scanfiles" type="data" format="mzml,mgf" multiple="true" optional="true" label="Proteomics Spectrum files"/> - <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"/> + <param name="mzinput" type="data" format="mzid" label="Proteomics Identification files" /> + <param name="scanfiles" type="data" format="mgf" multiple="true" optional="true" label="Proteomics Spectrum files" /> + <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" /> </inputs> <outputs> - <data format="mz.sqlite" name="sqlite_db" label="${tool.name} on ${on_string}" from_work_dir="sqlite.db"/> + <data format="mz.sqlite" name="sqlite_db" label="${tool.name} on ${on_string}" from_work_dir="sqlite.db" /> </outputs> <tests> <test> @@ -45,7 +44,7 @@ </test> </tests> <help> -<![CDATA[ + <![CDATA[ ** mz_to_sqlite converts proteomics file formats to a SQLite database** ]]>