comparison crossmap_wig.xml @ 4:454886ffaa41 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622

3:792bd038a59c

<tool id="crossmap_wig" name="CrossMap Wig" version="@WRAPPER_VERSION@-0">
    <description>Convert genome coordinates or annotation files between genome assemblies</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    <expand macro="version_command"/>
    <command><![CDATA[
CrossMap.py wig
'${chain_source.input_chain}'
'${input}'
'${output}'

&& mv '${output}.bw' '${output}'
&& mv '${output}.sorted.bgr' '${output2}'
    ]]></command>

    <inputs>
        <param name="input" type="data" format="wig" label="Wiggle file"/>

        <expand macro="chain" />
    </inputs>

    <outputs>
        <data name="output" format="wig" label="${tool.name} on ${on_string}" />
        <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" />
    </outputs>

    <tests>
    <!-- WIG - Doesn't understand fixedStep -->
        <test>

the input, the output will always in bedGraph format. bedGraph format is
similar to wiggle format and can be converted into BigWig format using UCSC
wigToBigWig tool. We export files in bedGraph because it is usually much
smaller than file in wiggle format, and more importantly, CrossMap
internally transforms wiggle into bedGraph to increase running speed.

    ]]></help>

    <citations>
        <citation type="doi">10.1093/bioinformatics/btt730</citation>
    </citations>

4:454886ffaa41

<tool id="crossmap_wig" name="CrossMap Wig" version="@WRAPPER_VERSION@">
    <description>Convert genome coordinates or annotation files between genome assemblies</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    <expand macro="version_command"/>
    <command><![CDATA[
CrossMap.py wig
'${chain_source.input_chain}'
'${input}'
output
    ]]></command>

    <inputs>
        <param name="input" type="data" format="wig" label="Wiggle file"/>

        <expand macro="chain" />
    </inputs>

    <outputs>
        <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw" />
        <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" from_work_dir="output.sorted.bgr" />
    </outputs>

    <tests>
    <!-- WIG - Doesn't understand fixedStep -->
        <test>

the input, the output will always in bedGraph format. bedGraph format is
similar to wiggle format and can be converted into BigWig format using UCSC
wigToBigWig tool. We export files in bedGraph because it is usually much
smaller than file in wiggle format, and more importantly, CrossMap
internally transforms wiggle into bedGraph to increase running speed.
    ]]></help>

    <citations>
        <citation type="doi">10.1093/bioinformatics/btt730</citation>
    </citations>