comparison samtools_phase.xml @ 4:1e5880498f52 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 0f75269223c0821c6c82acf98fde947d0f816f2b"

3:b5c3b1856370

<tool id="samtools_phase" name="Call and phase" version="2.0.1">
    <description>heterozygous SNPs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>

        <data format="bam" from_work_dir="phase_wrapper.1.bam" name="phase1" label="${tool.name} on ${on_string}: Phase-1 reads" />
        <data format="bam" from_work_dir="phase_wrapper.chimera.bam" name="chimera" label="${tool.name} on ${on_string}: Chimeric reads" />
    </outputs>
    <tests>
        <test>
            <param name="option_sets" value="default" /> 
            <param name="input_bam" value="samtools_phase_in_1.bam" /> 
            <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt" />
            <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" />
            <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" />
            <output name="chimera" file="empty_file.bam" ftype="bam" />
        </test>
        <test>
            <param name="input_bam" value="samtools_phase_in_2.bam" /> 
            <param name="option_sets" value="advanced" /> 
            <param name="option_set|block_length" value="13" />
            <param name="option_set|min_het" value="37" />
            <param name="option_set|min_bq" value="13" />
            <param name="option_set|read_depth" value="256" />
            <param name="option_set|ignore_chimeras" value="false" />
            <param name="option_set|drop_ambiguous" value="true" />
            <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt" />
            <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" />
            <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" />
            <output name="chimera" file="samtools_phase_out_2_chimera.bam" />
        </test>
        <test>
            <param name="input_bam" value="samtools_phase_in_2.bam" /> 
            <param name="option_sets" value="advanced" /> 
            <param name="option_set|block_length" value="13" />
            <param name="option_set|min_het" value="37" />
            <param name="option_set|min_bq" value="13" />
            <param name="option_set|read_depth" value="256" />
            <param name="option_set|ignore_chimeras" value="true" />
            <param name="option_set|drop_ambiguous" value="false" />
            <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt" />
            <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" />
            <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" />
            <output name="chimera" file="empty_file.bam"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

4:1e5880498f52

<tool id="samtools_phase" name="Samtools phase" version="2.0.2" profile="@PROFILE@">
    <description>call and phase heterozygous SNPs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>

        <data format="bam" from_work_dir="phase_wrapper.1.bam" name="phase1" label="${tool.name} on ${on_string}: Phase-1 reads" />
        <data format="bam" from_work_dir="phase_wrapper.chimera.bam" name="chimera" label="${tool.name} on ${on_string}: Chimeric reads" />
    </outputs>
    <tests>
        <test>
            <param name="option_sets" value="default" />
            <param name="input_bam" value="samtools_phase_in_1.bam" />
            <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt" />
            <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" lines_diff="4" />
            <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" lines_diff="4" />
            <output name="chimera" file="empty_file_1.bam" ftype="bam" lines_diff="4" />
        </test>
        <test>
            <param name="input_bam" value="samtools_phase_in_2.bam" />
            <param name="option_sets" value="advanced" />
            <param name="option_set|block_length" value="13" />
            <param name="option_set|min_het" value="37" />
            <param name="option_set|min_bq" value="13" />
            <param name="option_set|read_depth" value="256" />
            <param name="option_set|ignore_chimeras" value="false" />
            <param name="option_set|drop_ambiguous" value="true" />
            <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt" />
            <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" lines_diff="4" />
            <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" lines_diff="4" />
            <output name="chimera" file="samtools_phase_out_2_chimera.bam" ftype="bam" lines_diff="4" />
        </test>
        <test>
            <param name="input_bam" value="samtools_phase_in_2.bam" />
            <param name="option_sets" value="advanced" />
            <param name="option_set|block_length" value="13" />
            <param name="option_set|min_het" value="37" />
            <param name="option_set|min_bq" value="13" />
            <param name="option_set|read_depth" value="256" />
            <param name="option_set|ignore_chimeras" value="true" />
            <param name="option_set|drop_ambiguous" value="false" />
            <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt" />
            <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" lines_diff="4" />
            <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" lines_diff="4" />
            <output name="chimera" file="empty_file_3.bam" ftype="bam" lines_diff="4" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**