comparison samtools_idxstats.xml @ 3:20fea18b2830 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4

2:e726bb429392

<tool id="samtools_idxstats" name="IdxStats" version="2.0.1">
    <description>reports stats of the BAM index file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        ln -f -s '${input.metadata.bam_index}' '${input}.bai' &&

        samtools idxstats '${input}' > '${output}'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bam" label="BAM file" />
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="phiX.bam" ftype="bam" />
            <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[

3:20fea18b2830

<tool id="samtools_idxstats" name="Samtools idxstats" version="2.0.2">
    <description>reports stats of the BAM index file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        @PREPARE_IDX@
        samtools idxstats infile > '${output}'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bam,cram" label="BAM file" />
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <!-- test from https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl#L2556 -->
        <test>
            <param name="input" value="test_input_1_a.bam" ftype="bam" />
            <output name="output" file="test_input_1_a.bam.expected" compare="diff" ftype="tabular" />
        </test>
        <!-- test from original tool -->
	<test>
            <param name="input" value="phiX.bam" ftype="bam" />
            <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[