comparison crossmap_bed.xml @ 4:1e24dd91db95 draft

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

3:b49e453e6f97

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

'${input}'

#if $merge_unmapped_entries:
    > '${output_combined}'
#else:
    '${output_valid}'
    && mv '${output_valid}.unmap' '${output_failed}'
#end if

    ]]></command>

        <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/>
    </inputs>

    <outputs>
        <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}">
            <filter>merge_unmapped_entries is False</filter>
        </data>
        <data name="output_failed" format="bed" label="${tool.name} (failed only) on ${on_string}">
            <filter>merge_unmapped_entries is False</filter>
        </data>

        <data name="output_combined" format="bed" label="${tool.name} on ${on_string}">
            <filter>merge_unmapped_entries is True</filter>

6. For standard BED format (12 columns). If any of the defined exon blocks
   cannot be uniquely mapped to target assembly, the whole entry will be
   skipped.
7. If input region cannot be consecutively mapped target assembly, it will be split.
8. \*.unmap file contains regions that cannot be unambiguously converted.

    ]]></help>

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

4:1e24dd91db95

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

'${input}'

#if $merge_unmapped_entries:
    > '${output_combined}'
#else:
    output
#end if

    ]]></command>

        <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/>
    </inputs>

    <outputs>
        <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}" from_work_dir="output">
            <filter>merge_unmapped_entries is False</filter>
        </data>
        <data name="output_failed" format="bed" label="${tool.name} (failed only) on ${on_string}" from_work_dir="output.unmap">
            <filter>merge_unmapped_entries is False</filter>
        </data>

        <data name="output_combined" format="bed" label="${tool.name} on ${on_string}">
            <filter>merge_unmapped_entries is True</filter>

6. For standard BED format (12 columns). If any of the defined exon blocks
   cannot be uniquely mapped to target assembly, the whole entry will be
   skipped.
7. If input region cannot be consecutively mapped target assembly, it will be split.
8. \*.unmap file contains regions that cannot be unambiguously converted.
    ]]></help>

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