annotate pretext_graph.xml @ 1:eca7d3a0c5f2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 50ddb7e5275f15196246e25f85f79d2ece455e53

<tool id="pretext_graph" name="Pretextgraph"  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>Embed bedgraph formatted data inside a Pretext contact map.</description>
    <macros>
        <token name="@TOOL_VERSION@">0.0.6</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">pretextgraph</requirement>
        <requirement type="package" version="377"> ucsc-bigwigtobedgraph</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        cp '$pretext' input.pretext &&
        #if $input.is_of_type("bedgraph"):
            cat '$input' | 
        #else if $input.is_of_type("bigwig"):
            ln -s '$input' input.bigwig &&
            bigWigToBedGraph input.bigwig /dev/stdout |
        #end if
        PretextGraph -i input.pretext
        #if $name:
            -n '$name'
        #end if
        -o output.pretext
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bigwig,bedgraph" label="Input bigwig or bedgraph file"/>
        <param name="pretext" type="data" format="pretext" label="Pretext file" help="Sequence names in the Pretext file must match sequence names in the bedgraph data; although relative sort order is unimportant."/>
        <param name="name" type="text" label="Label for the graph" optional="true"/>
    </inputs>
    <outputs>
        <data name="graph_out" format="pretext" from_work_dir="output.pretext" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <!-- BIGWIG TEST -->
        <test expect_num_outputs="1">
            <param name="input" value="input_graph.bw" ftype="bigwig"/>
            <param name="pretext" value="input_graph.pretext" ftype="pretext"/>
            <param name="name" value="testing"/>
            <output name="graph_out" file="output_4.pretext"/>
        </test>
            <!-- BEDGRAPH TEST -->
            <test expect_num_outputs="1">
                <param name="input" value="input_graph.bgr" ftype="bedgraph"/>
                <param name="pretext" value="input_graph.pretext" ftype="pretext"/>
                <param name="name" value="testing_2"/>
                <output name="graph_out" file="output_5.pretext"/>
            </test>
    </tests>
    <help><![CDATA[
        Adds additional data onto existing pretextmap files.
        Input Pretext file acts as a foundation for additional data to be added onto. 
        Sequence names in the Pretext file must match sequence names in the bedgraph data; although relative sort order is unimportant.
        The chosen name acts as a lable on the graph.
    ]]></help>
        <citations>
            <citation type="bibtex">
                @misc{Harry_et_al,
                Author={Harry, E},
                title={Paired REad TEXTure Graph: Embeds bedgraph data into Pretext contact maps.},
                url = {https://github.com/wtsi-hpag/PretextGraph},}
            </citation>
        </citations>
</tool>