annotate analysis_add_analysis.xml @ 11:a2efb5aff729 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d

<?xml version="1.0"?>
<tool id="analysis_add_analysis" name="Chado analysis add" version="@WRAPPER_VERSION@.2">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
@START_PSQL@ &&

chakin analysis add_analysis
'$name'
'$program'
'$programversion'
'$sourcename'

#if $algorithm:
  --algorithm '$algorithm'
#end if
#if $sourceversion:
  --sourceversion '$sourceversion'
#end if
#if $sourceuri:
  --sourceuri '$sourceuri'
#end if
#if $description:
  --description '$description'
#end if
#if $date_executed:
  --date_executed '$date_executed'
#end if

| jq -S . > '$results'

@ZIP_PSQL@
    ]]></command>
    <inputs>
    <expand macro="psql_target"/>
    <!-- arguments -->
    <param name="name" label="Name" argument="name" type="text" help="analysis name" />
    <param name="program" label="Program" argument="program" type="text" help="analysis program" />
    <param name="programversion" label="Programversion" argument="programversion" type="text" help="analysis programversion" />
    <param name="sourcename" label="Sourcename" argument="sourcename" type="text" help="analysis sourcename" />

    <!-- options -->
    <param name="algorithm" label="Algorithm" argument="--algorithm" type="text" help="analysis algorithm" optional="True" />
    <param name="sourceversion" label="Sourceversion" argument="--sourceversion" type="text" help="analysis sourceversion" optional="True" />
    <param name="sourceuri" label="Sourceuri" argument="--sourceuri" type="text" help="analysis sourceuri" optional="True" />
    <param name="description" label="Description" argument="--description" type="text" help="analysis description" optional="True" />
    <param name="date_executed" label="Date Executed" argument="--date_executed" type="text" optional="True" help="analysis date_executed (yyyy-mm-dd)">
        <validator type="regex" message="Date in YYYY-MM-DD format">^[0-9]{4}-[0-9]{2}-[0-9]{2}$</validator>
    </param>

    </inputs>
    <outputs>
        <data format="json" name="results" label="Chado analysis add: ${name}"/>
        <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} '${name}' on ${on_string}">
          <filter>psql_target['method'] == "pgtools"</filter>
        </data>
    </outputs>
    <help>
Create an analysis

@HELP@
    </help>
</tool>