Mercurial > repos > gga > tripal_analysis_load_interpro
view analysis_load_interpro.xml @ 2:a4901678ccfb draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
author | gga |
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date | Thu, 21 Jun 2018 08:48:49 -0400 |
parents | a19926451daa |
children | 9a4b816d8a86 |
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<?xml version="1.0"?> <tool id="analysis_load_interpro" profile="16.04" name="Load InterProScan results" version="@WRAPPER_VERSION@.1"> <description>into Tripal</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}" && cp '${input}' "\${tmp_dir}/interpro.xml" && @AUTH@ tripaille analysis load_interpro @ANALYSIS@ --interpro_parameters '${params}' ${parse_go} @MATCHING@ "\${tmp_dir}/interpro.xml" && echo "Data loaded" > $results ]]></command> <inputs> <param name="input" type="data" format="xml" label="InterProScan results" /> <param name="parse_go" type="boolean" checked="true" truevalue="--parse_go" falsevalue="" label="Load GO annotation to the database" /> <param name="params" type="text" label="InterProScan parameters used to produce the results" /> <expand macro="matching"/> <expand macro="analysis" /> <expand macro="wait_for"/> </inputs> <outputs> <data format="txt" name="results" label="Load InterProScan results into Tripal" /> </outputs> <tests> <test expect_failure="true" expect_exit_code="1"> <param name="input" value="interpro.xml" /> <param name="parse_go" value="true" /> <param name="params" value="--some --param" /> <param name="query_type" value="mRNA" /> <param name="query_uniquename" value="true" /> <section name="analysis"> <param name="name" value="Some analysis" /> <param name="program" value="interproscan" /> <param name="program_version" value="58.2" /> <param name="algorithm" value="interproscan" /> <param name="source" value="NCBI" /> <param name="source_version" value="1.0" /> <param name="source_uri" value="http://ncbi.com/somewhere" /> <param name="description" value="My cool new test analysis" /> <param name="date" value="2016-12-12" /> </section> <expand macro="test_result" /> </test> </tests> <help><![CDATA[ @HELP_OVERVIEW@ **Load InterProScan results** With this tool, you can load InterProScan results into the Tripal/Chado database. A corresponding analysis will be created, keep in mind that you cannot add multiple analysis with the same program, program version and source. The `tripal_analysis_interpro <http://github.com/tripal/tripal_analysis_interpro>`_ module must be installed and configured on the Tripal instance. @HELP@ ]]></help> <expand macro="citation"/> </tool>