annotate expression_add_biomaterial.xml @ 0:11ec43bed5ea draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 869e5fd8535deca8325777efcd31c70a514b582a

<?xml version="1.0"?>
<tool id="expression_add_biomaterial" name="Create a biomaterial" version="@WRAPPER_VERSION@.0">
 <description>in Tripal</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <code file="tripal.py"/>
    <command detect_errors="aggressive"><![CDATA[
tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}"

&&

cp '${file_path}' "\${tmp_dir}/biomaterial_input"

&&

@AUTH@

tripaille expression add_biomaterial
'$organism_id'
"\${tmp_dir}/biomaterial_input"
'$file_path.extension'

&&

echo "Data loaded" > $results
]]></command>
    <inputs>
        <!-- arguments -->
        <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
        <param name="file_path" label="Biomaterial description sheet" argument="file_path" type="data" format="xml,tsv,csv" help="A file describing the biomaterial" />
    </inputs>
    <outputs>
        <data format="txt" name="results"/>
    </outputs>
    <help>
Add a new biomaterial to the database

@HELP@
    </help>
</tool>