comparison macros.xml @ 3:3242dbeea69c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 00d6705a08a9d9cc9093846b730c4dec247cf5e7

2:b4b6b660293a

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.0.4</token>
    <token name="@PROFILE@">20.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.9">samtools</requirement>
            <requirement type="package" version="@TOOL_VERSION@">irissv</requirement>
        </requirements>
    </xml>
    <xml name="version_command">
        <version_command>iris</version_command>

              url = {https://github.com/mkirsche/Iris},
              urldate = {2021-01-13}
            }</citation>
        </citations>
    </xml>

    <!--
        command
    -->

    <token name="@REF_FASTA@"><![CDATA[
        #if $reference_source.reference_source_selector == 'history':
            #set reference = $reference_source.ref_file
            #set ext = $reference.ext
        #else:

            gunzip -c '$reference' > reference &&
        #else:
            ln -sf '$reference' reference &&
        #end if
    ]]></token>

    <xml name="reference">
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
                <option value="cached">Use a built-in genome</option>
                <option value="history">Use a genome from history</option>

        </conditional>
    </xml>
    <!--
        Help
    -->

    <token name="@WID@"><![CDATA[
*irissv*, or Implement for Refining Insertion Sequences is a tool which corrects the sequences of structural variant calls (currently only insertions). It uses FalconSense to obtain consensus sequences of the reads surrounding each variant and aligns these sequences back to the reference at the insertion site, resulting in an insertion which takes into account the aggregate information of all supporting reads.
    ]]></token>
    <token name="@REFERENCES@"><![CDATA[
More information is available in the `github <https://github.com/mkirsche/Iris>`_.

3:3242dbeea69c

<macros>
    <token name="@TOOL_VERSION@">1.0.5</token>
    <token name="@PROFILE@">20.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.19.2">samtools</requirement>
            <requirement type="package" version="@TOOL_VERSION@">irissv</requirement>
        </requirements>
    </xml>
    <xml name="version_command">
        <version_command>iris</version_command>

              url = {https://github.com/mkirsche/Iris},
              urldate = {2021-01-13}
            }</citation>
        </citations>
    </xml>
    <!--
        command
    -->
    <token name="@REF_FASTA@"><![CDATA[
        #if $reference_source.reference_source_selector == 'history':
            #set reference = $reference_source.ref_file
            #set ext = $reference.ext
        #else:

            gunzip -c '$reference' > reference &&
        #else:
            ln -sf '$reference' reference &&
        #end if
    ]]></token>
    <xml name="reference">
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
                <option value="cached">Use a built-in genome</option>
                <option value="history">Use a genome from history</option>

        </conditional>
    </xml>
    <!--
        Help
    -->
    <token name="@WID@"><![CDATA[
*irissv*, or Implement for Refining Insertion Sequences is a tool which corrects the sequences of structural variant calls (currently only insertions). It uses FalconSense to obtain consensus sequences of the reads surrounding each variant and aligns these sequences back to the reference at the insertion site, resulting in an insertion which takes into account the aggregate information of all supporting reads.
    ]]></token>
    <token name="@REFERENCES@"><![CDATA[
More information is available in the `github <https://github.com/mkirsche/Iris>`_.