comparison samtools_phase.xml @ 3:b5c3b1856370 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6

2:6166013090c0

                <param name="block_length" argument="-k" type="integer" value="13" label="Maximum length for local phasing" />
                <param name="min_het" argument="-q" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" />
                <param name="min_bq" argument="-Q" type="integer" value="13" label="Minimum base quality to be used in het calling" />
                <param name="read_depth" argument="-D" type="integer" value="256" label="Read depth" />
                <param name="ignore_chimeras" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" />
                <param name="drop_ambiguous" argument="-A" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="phase_sets" />
        <data format="bam" from_work_dir="phase_wrapper.0.bam" name="phase0" label="${tool.name} on ${on_string}: Phase-0 reads" />
        <data format="bam" from_work_dir="phase_wrapper.1.bam" name="phase1" label="${tool.name} on ${on_string}: Phase-1 reads" />
        <data format="bam" from_work_dir="phase_wrapper.chimeras.bam" name="chimera" label="${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" compare="contains" />
        </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|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="empty_file.bam" compare="contains" />
        </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|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" compare="contains" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

3:b5c3b1856370

                <param name="block_length" argument="-k" type="integer" value="13" label="Maximum length for local phasing" />
                <param name="min_het" argument="-q" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" />
                <param name="min_bq" argument="-Q" type="integer" value="13" label="Minimum base quality to be used in het calling" />
                <param name="read_depth" argument="-D" type="integer" value="256" label="Read depth" />
                <param name="ignore_chimeras" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" />
                <param name="drop_ambiguous" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Drop reads with ambiguous phase" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="phase_sets" />
        <data format="bam" from_work_dir="phase_wrapper.0.bam" name="phase0" label="${tool.name} on ${on_string}: Phase-0 reads" />
        <data format="bam" from_work_dir="phase_wrapper.1.bam" name="phase1" label="${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|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|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**