comparison ribotaper_part2_create_metaplots.xml @ 1:56ffbec351b3 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 07674fe3507909d11d7431e3b8c48afcfb1f4b5e"

0:bade631353d2

<tool id="ribotaper_create_metaplots" name="ribotaper part 2: metagene analysis for P-sites definition" version="0.1.0">
    <requirements>
            <requirement type="package" version="1.3.1a">ribotaper</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>

    <command><![CDATA[
        create_metaplots.bash
            "$ribo_bam"
            "$start_stops_FAR"
            "metagene"

        &&

        find "metaplots"
            "-name"
            "metagene*.pdf"
            | sort | xargs gs
            "-dAutoRotatePages=/None"
            "-dBATCH"
            "-dNOPAUSE"
            "-q"
            "-sDEVICE=pdfwrite"
            "-sOutputFile=merged_metagene.pdf"

    ]]></command>
    <inputs>
        <param name="ribo_bam" type="data" format="bam" label="ribo_bam" help="Ribo-seq alignment file in BAM format."/>
        <param name="start_stops_FAR" type="data" format="bed" label="start_stops_FAR" help="Please run 'ribotaper part 1' to generate the table."/>
    </inputs>
    <outputs>
        <data name="output1" format="pdf" from_work_dir="merged_metagene.pdf" label="Metagene analysis results for P-sites definition (figures)"/>
        <data name="output2" format="tabular" from_work_dir="metagene" label="Metagene analysis results for P-sites definition (table)"/>
    </outputs>
    <tests>
        <test>
            <param name="ribo_bam" value="test_ribo.bam" ftype="bam"/>
            <param name="start_stops_FAR" value="annotation_path/start_stops_FAR.bed"  ftype="bed"/>
            <output name="output2" file="metagene"/>
        </test>
    </tests>

From the output, user shall determine the appropriate
read lengths and cutoffs which are required
for running ``ribotaper part 3``, ribosome profiling.

]]></help>
    <citations>
        <citation type="doi">10.1038/nmeth.3688</citation>
    </citations>
</tool>

1:56ffbec351b3

<tool id="ribotaper_create_metaplots" name="ribotaper part 2: metagene analysis for P-sites definition" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile='20.01'>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='bio_tools'/>
    <expand macro='requirements'/>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        create_metaplots.bash
            "$ribo_bam"
            "$start_stops_FAR"
            "metagene"
        &&
        find "metaplots"
            "-name"
            "metagene*.pdf"
            | sort | xargs gs
            "-dAutoRotatePages=/None"
            "-dBATCH"
            "-dNOPAUSE"
            "-q"
            "-sDEVICE=pdfwrite"
            "-sOutputFile=merged_metagene.pdf"
    ]]></command>
    <inputs>
        <param name="ribo_bam" type="data" format="bam" label="Ribo-seq alignment file" help="Ribo-seq alignment file in BAM format."/>
        <param name="start_stops_FAR" type="data" format="bed" label="Start_stops FAR" help="Please run 'ribotaper part 1' to generate the table."/>
    </inputs>
    <outputs>
        <data name="output1" format="pdf" from_work_dir="merged_metagene.pdf" label="${tool.name} on ${on_string}: Metagene analysis results for P-sites definition (figures)"/>
        <data name="output2" format="tabular" from_work_dir="metagene" label="${tool.name} on ${on_string}: Metagene analysis results for P-sites definition (table)"/>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="ribo_bam" value="test_ribo.bam" ftype="bam"/>
            <param name="start_stops_FAR" value="annotation_path/start_stops_FAR.bed"  ftype="bed"/>
            <output name="output2" file="metagene"/>
        </test>
    </tests>

From the output, user shall determine the appropriate
read lengths and cutoffs which are required
for running ``ribotaper part 3``, ribosome profiling.

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