comparison junction_annotation.xml @ 63:27e16a30667a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de

62:473382134e56

<tool id="rseqc_junction_annotation" name="Junction Annotation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
    <description>compares detected splice junctions to reference gene model</description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>

    <expand macro="bio_tools"/>

    <expand macro="requirements">
        <!--
            Required due to conda solver bug: https://github.com/conda/conda/issues/6269
            See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info
        -->
        <requirement type="package" version="4.2.2">r-base</requirement>
    </expand>

    <expand macro="stdio" />

    <version_command><![CDATA[junction_annotation.py --version]]></version_command>

    <command><![CDATA[
        @BAM_SAM_INPUTS@
        junction_annotation.py
            --input-file 'input.${extension}'
            --refgene '${refgene}'

            --min-intron ${min_intron}
            --mapq ${mapq}
        2> >(tee -a stats.txt >&2)
        ]]>
    </command>

    <inputs>
        <expand macro="bam_sam_param" />
        <expand macro="refgene_param" />
        <expand macro="min_intron_param" />
        <expand macro="mapq_param" />
        <expand macro="rscript_output_param" />
    </inputs>

    <outputs>
        <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string}: splice events (PDF)"/>
        <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string}: splice junction (PDF)" />
        <expand macro="xls_output_data" filename="output.junction.xls" label="${tool.name} on ${on_string}: splice junction (XLS)" />
        <expand macro="rscript_output_data" filename="output.junction_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
        <data format="txt" name="stats" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
            <param name="rscript_output" value="true" />
            <output name="outputxls" file="output.junction.xls" ftype="tabular"/>
            <output name="outputr" file="output.junction_plot_r" />
            <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size" />
            <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size" />
            <output name="stats" file="output.splice_junction.txt" ftype="txt" lines_diff="2" />
        </test>
    </tests>

    <help><![CDATA[
junction_annotation.py
++++++++++++++++++++++

For a given alignment file (-i) in BAM or SAM format and a reference gene model (-r) in BED

@ABOUT@

]]>
    </help>

    <expand macro="citations" />

</tool>

63:27e16a30667a

<tool id="rseqc_junction_annotation" name="Junction Annotation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
    <description>compares detected splice junctions to reference gene model</description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements">
        <!--
            Required due to conda solver bug: https://github.com/conda/conda/issues/6269
            See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info
        -->
        <requirement type="package" version="4.2.2">r-base</requirement>
    </expand>
    <expand macro="stdio"/>
    <version_command><![CDATA[junction_annotation.py --version]]></version_command>
    <command><![CDATA[
        @BAM_SAM_INPUTS@
        junction_annotation.py
            --input-file 'input.${extension}'
            --refgene '${refgene}'

            --min-intron ${min_intron}
            --mapq ${mapq}
        2> >(tee -a stats.txt >&2)
        ]]>
    </command>
    <inputs>
        <expand macro="bam_sam_param"/>
        <expand macro="refgene_param"/>
        <expand macro="min_intron_param"/>
        <expand macro="mapq_param"/>
        <expand macro="rscript_output_param"/>
    </inputs>
    <outputs>
        <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string}: splice events (PDF)"/>
        <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string}: splice junction (PDF)"/>
        <expand macro="xls_output_data" filename="output.junction.xls" label="${tool.name} on ${on_string}: splice junction (XLS)"/>
        <expand macro="rscript_output_data" filename="output.junction_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
        <data format="txt" name="stats" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats"/>
    </outputs>
    <tests>
        <test expect_num_outputs="5">
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
            <param name="rscript_output" value="true"/>
            <output name="outputxls" file="output.junction.xls" ftype="tabular"/>
            <output name="outputr" file="output.junction_plot_r"/>
            <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size"/>
            <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size"/>
            <output name="stats" file="output.splice_junction.txt" ftype="txt" lines_diff="2"/>
        </test>
    </tests>
    <help><![CDATA[
junction_annotation.py
++++++++++++++++++++++

For a given alignment file (-i) in BAM or SAM format and a reference gene model (-r) in BED

@ABOUT@

]]>
    </help>
    <expand macro="citations"/>
</tool>