Mercurial > repos > galaxyp > mz_to_sqlite
changeset 0:946ce2e034a2
Uploaded
| author | galaxyp |
|---|---|
| date | Fri, 12 Jun 2015 17:28:09 -0400 |
| parents | |
| children | 77389cf7ff62 |
| files | mz_to_sqlite.xml repository_dependencies.xml tool_dependencies.xml |
| diffstat | 3 files changed, 52 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mz_to_sqlite.xml Fri Jun 12 17:28:09 2015 -0400 @@ -0,0 +1,42 @@ +<tool id="mz_to_sqlite" name="mz to sqlite" version="1.0.0"> + <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description> + <requirements> + <requirement type="package" version="1.0.0">mztosqlite</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Error Running mz_to_sqlite" /> + </stdio> + <command> +<![CDATA[ +java -jar \$MZTOSQLITE_JAR_PATH -s $mzsqlite +#if len($scanfiles) > 0: +$scanfiles.__str__.replace(',',' ') +#end if +#if len($searchdbs) > 0: +$searchdbs.__str__.replace(',',' ') +#end if +#if len($mzinputs) > 0: +$mzinputs.__str__.replace(',',' ') +#end if +]]> + </command> + <inputs> + <param name="mzinputs" type="data" format="mzid" multiple="true" optional="true" label="Proteomics Identification files"/> + <param name="scanfiles" type="data" format="mzml,mgf" multiple="true" optional="true" label="Proteomics Spectrum files"/> + <param name="searchdbs" type="data" format="fasta" multiple="true" optional="true" label="Proteomics Search Database Fasta" + help="These can provide sequences and length for proteins if not already present in the mzIdentML input"/> + </inputs> + <outputs> + <data format="sqlite" name="mzsqlite" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +<![CDATA[ +** mz_to_sqlite converts proteomics file formats to a SQLite database** + +]]> + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Fri Jun 12 17:28:09 2015 -0400 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Required proteomics dependencies."> + <repository changeset_revision="349af9298ff1" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> +</repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jun 12 17:28:09 2015 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="mztosqlite" version="1.0.0"> + <repository changeset_revision="6c82d072dbf4" name="package_mztosqlite_1_0_0" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>