comparison microsatbed.xml @ 11:c39202869825 draft

planemo upload for repository https://github.com/fubar2/microsatbed commit bfb57ff3a931bc3f3d3549707f7bcf1f561c84c6

10:43a8165cec3a

<tool id="microsatbedfubar" name="STR to bed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
    <description>Short Tandem Repeats to bed features from fasta</description>
    <macros>
        <token name="@TOOL_VERSION@">1.3.2</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PYTHON_VERSION@">3.12.3</token>

        <param name="tetramin" type="integer" min="2" value="2" label="Minimum repeats required for tetramers"/>
        <param name="pentamin" type="integer" min="2" value="2" label="Minimum repeats required for pentamers"/>
        <param name="hexamin" type="integer" min="2" value="2" label="Minimum repeats required for hexamers"/>
    </inputs>
    <outputs>
      <data name="bed" format="bed" label="STR">
        <change_format>
            <when input="mode_cond.outformat" value="gff" format="gff"/>
            <when input="mode_cond.outformat" value="csv" format="csv"/>
            <when input="mode_cond.outformat" value="tsv" format="tabular"/>
            <when input="mode_cond.mode" value="ALLBW" format="bigwig"/>

              </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="reference_genome">
                <param name="genome_type_select" value="indexed"/>
                <param name="reffa" value="hgtest"/>
            </conditional>
            <conditional name="mode_cond">
                <param name="mode" value="SPECIFICBW"/>
                <param name="specific" value="GC"/>
            </conditional>

11:c39202869825

<tool id="microsatbed" name="STR to bed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
    <description>Short Tandem Repeats to bed features from fasta</description>
    <macros>
        <token name="@TOOL_VERSION@">1.3.2</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PYTHON_VERSION@">3.12.3</token>

        <param name="tetramin" type="integer" min="2" value="2" label="Minimum repeats required for tetramers"/>
        <param name="pentamin" type="integer" min="2" value="2" label="Minimum repeats required for pentamers"/>
        <param name="hexamin" type="integer" min="2" value="2" label="Minimum repeats required for hexamers"/>
    </inputs>
    <outputs>
      <data name="bed" format="bed" label="STR on $reffa.element_identifier">
        <change_format>
            <when input="mode_cond.outformat" value="gff" format="gff"/>
            <when input="mode_cond.outformat" value="csv" format="csv"/>
            <when input="mode_cond.outformat" value="tsv" format="tabular"/>
            <when input="mode_cond.mode" value="ALLBW" format="bigwig"/>

              </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="reference_genome">
                <param name="genome_type_select" value="history"/>
                <param name="reffa" value="humsamp.fa"/>
            </conditional>
            <conditional name="mode_cond">
                <param name="mode" value="SPECIFICBW"/>
                <param name="specific" value="GC"/>
            </conditional>