| Previous changeset 0:ab33bd49de43 (2016-06-17) Next changeset 2:1320693cbf1e (2019-02-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e |
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modified:
mz_to_sqlite.xml |
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removed:
tool_dependencies.xml |
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| diff -r ab33bd49de43 -r e34bdac5b157 mz_to_sqlite.xml --- a/mz_to_sqlite.xml Fri Jun 17 15:13:02 2016 -0400 +++ b/mz_to_sqlite.xml Wed Mar 28 09:33:18 2018 -0400 |
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| @@ -1,33 +1,40 @@ -<tool id="mz_to_sqlite" name="mz to sqlite" version="1.2.0"> +<tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.0"> <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description> <requirements> - <requirement type="package" version="1.2.0">mztosqlite</requirement> + <requirement type="package" version="2.0.0">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: -$mzinputs.__str__.replace(',',' ') -#end if +mz_to_sqlite -Xms1g -Xmx6g + -numthreads "\${GALAXY_SLOTS:-4}" + -dbname 'sqlite.db' + -mzid '$mzinput' + #if len($scanfiles) > 0: + #set $files = " ".join(["'"+ a.strip() + "'" for a in str($scanfiles).split(',')]) + -scanfiles $files + #set $dfiles = [a for a in $scanfiles] + -scanFilesDisplayName + #for $f in $dfiles + '$f.display_name' + #end for + #end if + #if len($searchdbs) > 0: + #set $dbFiles = " ".join(["'"+ a.strip() + "'" for a in str($searchdbs).split(',')]) + -fasta $dbFiles + #end if ]]> </command> <inputs> - <param name="mzinputs" type="data" format="mzid" multiple="true" optional="true" label="Proteomics Identification files"/> + <param name="mzinput" type="data" format="mzid" label="Proteomics Identification files"/> <param name="scanfiles" type="data" format="mzml,mgf" multiple="true" optional="true" label="Proteomics Spectrum files"/> <param name="searchdbs" type="data" format="fasta,uniprotxml" multiple="true" optional="true" label="Proteomics Search Database Fasta" help="These can provide sequences and length for proteins if not already present in the mzIdentML input"/> </inputs> <outputs> - <data format="mz.sqlite" name="mzsqlite" label="${tool.name} on ${on_string}"/> + <data format="mz.sqlite" name="sqlite_db" label="${tool.name} on ${on_string}" from_work_dir="sqlite.db"/> </outputs> <tests> <test> |
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| diff -r ab33bd49de43 -r e34bdac5b157 tool_dependencies.xml --- a/tool_dependencies.xml Fri Jun 17 15:13:02 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="mztosqlite" version="1.2.0"> - <repository changeset_revision="c6fd2675f552" name="package_mztosqlite_1_2_0" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |