comparison biopython-convert.xml @ 5:1c71c770bfd4 draft default tip

planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit cae3bd2f937dee563791707ffb4aab8fe5b7e13b

4:a5cb5e374399

<tool id="biopython-convert" name="BioPython SeqIO Converter" version="1.0" profile="16.04">
    <description>Interconvert between the various sequence file formats that BioPython supports</description>
    <edam_topics>
        <edam_topic>topic_0091</edam_topic>
    </edam_topics>
    <edam_operations>

        <edam_operation>operation_3359</edam_operation>
        <edam_operation>operation_0224</edam_operation>
        <edam_operation>operation_3695</edam_operation>
    </edam_operations>
    <requirements>
        <requirement type="package" version="1.0.4">biopython.convert</requirement>
    </requirements>
    <version_command><![CDATA[ biopython.convert -v ]]></version_command>
    <command detect_errors="aggressive"><![CDATA[
        #if $bioperl
            #set $script = 'python ' + $__tool_directory__ + '/bioperl_compat.py'

            <option value="sff">sff</option>
            <option value="stockholm">stockholm</option>
            <option value="tab">tab</option>
            <option value="qual">qual</option>
            <option value="gff3">gff3</option>
        </param>
        <param name="split" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Split each record into a different file" />
        <param name="info" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Output record information while converting" />
        <param name="query" type="text" label="Query records, keeping only what matches path" help="Provide a JMESPath selecting records to keep. The root is the list of records. The path must return a list of records.">
            <sanitizer>

                <when input="output_type" value="sff" format="sff" />
                <when input="output_type" value="stockholm" format="stockholm" />
                <when input="output_type" value="tab" format="tabular" />
                <when input="output_type" value="qual" format="qual" />
                <when input="output_type" value="gff3" format="gff3" />
            </change_format>
        </data>
        <collection name="split_output" type="list" label="Output split per record from ${tool.name} on ${on_string}">
            <filter>split</filter>
            <discover_datasets pattern=".*" directory="output" format="$output_type" />

5:1c71c770bfd4

<tool id="biopython-convert" name="BioPython SeqIO Converter" version="1.1" profile="16.04">
    <description>Interconvert between the various sequence file formats that BioPython supports</description>
    <edam_topics>
        <edam_topic>topic_0091</edam_topic>
    </edam_topics>
    <edam_operations>

        <edam_operation>operation_3359</edam_operation>
        <edam_operation>operation_0224</edam_operation>
        <edam_operation>operation_3695</edam_operation>
    </edam_operations>
    <requirements>
        <requirement type="package" version="1.3.3">biopython.convert</requirement>
    </requirements>
    <version_command><![CDATA[ biopython.convert -v ]]></version_command>
    <command detect_errors="aggressive"><![CDATA[
        #if $bioperl
            #set $script = 'python ' + $__tool_directory__ + '/bioperl_compat.py'

            <option value="sff">sff</option>
            <option value="stockholm">stockholm</option>
            <option value="tab">tab</option>
            <option value="qual">qual</option>
            <option value="gff3">gff3</option>
            <option value="yaml">yaml</option>
            <option value="json">json</option>
            <option value="text">text</option>
        </param>
        <param name="split" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Split each record into a different file" />
        <param name="info" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Output record information while converting" />
        <param name="query" type="text" label="Query records, keeping only what matches path" help="Provide a JMESPath selecting records to keep. The root is the list of records. The path must return a list of records.">
            <sanitizer>

                <when input="output_type" value="sff" format="sff" />
                <when input="output_type" value="stockholm" format="stockholm" />
                <when input="output_type" value="tab" format="tabular" />
                <when input="output_type" value="qual" format="qual" />
                <when input="output_type" value="gff3" format="gff3" />
                <when input="output_type" value="yaml" format="yaml" />
                <when input="output_type" value="json" format="json" />
                <when input="output_type" value="text" format="txt" />
            </change_format>
        </data>
        <collection name="split_output" type="list" label="Output split per record from ${tool.name} on ${on_string}">
            <filter>split</filter>
            <discover_datasets pattern=".*" directory="output" format="$output_type" />