comparison infer_experiment.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_infer_experiment" name="Infer Experiment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
    <description>speculates how RNA-seq were configured</description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>

    <expand macro="bio_tools"/>

    <expand macro="requirements" />

    <expand macro="stdio" />

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

    <command><![CDATA[
        @BAM_SAM_INPUTS@
        infer_experiment.py -i 'input.${extension}' -r '${refgene}'
            --sample-size ${sample_size}
            --mapq ${mapq}
            > '${output}'
            ]]>
    </command>

    <inputs>
        <expand macro="bam_param" />
        <expand macro="refgene_param" />
        <expand macro="sample_size_param" />
        <expand macro="mapq_param" />
    </inputs>

    <outputs>
        <data format="txt" name="output" label="${tool.name} on ${on_string}: RNA-seq experiment configuration" />
    </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"/>
            <output name="output" file="output.infer_experiment.txt"/>
        </test>
    </tests>

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

This program is used to speculate how RNA-seq sequencing were configured, especially how

@ABOUT@

]]>
    </help>

    <expand macro="citations" />

</tool>

63:27e16a30667a

<tool id="rseqc_infer_experiment" name="Infer Experiment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
    <description>speculates how RNA-seq were configured</description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <version_command><![CDATA[infer_experiment.py --version]]></version_command>
    <command><![CDATA[
        @BAM_SAM_INPUTS@
        infer_experiment.py -i 'input.${extension}' -r '${refgene}'
            --sample-size ${sample_size}
            --mapq ${mapq}
            > '${output}'
            ]]>
    </command>
    <inputs>
        <expand macro="bam_param"/>
        <expand macro="refgene_param"/>
        <expand macro="sample_size_param"/>
        <expand macro="mapq_param"/>
    </inputs>
    <outputs>
        <data format="txt" name="output" label="${tool.name} on ${on_string}: RNA-seq experiment configuration"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
            <output name="output" file="output.infer_experiment.txt"/>
        </test>
    </tests>
    <help><![CDATA[
infer_experiment.py
+++++++++++++++++++

This program is used to speculate how RNA-seq sequencing were configured, especially how

@ABOUT@

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