comparison lofreq_alnqual.xml @ 6:791f73caa0c8 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2

5:09d6e4693887

<tool id="lofreq_alnqual" name="Add LoFreq alignment quality scores" version="@TOOL_VERSION@+galaxy0" profile="18.01">
    <description>to aligned read SAM/BAM records</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

    <tests>
        <test>
            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
            <param name="ref_selector" value="history" />
            <param name="ref" ftype="fasta" value="pBR322.fa" />
            <output name="output" file="alnqual-out1.bam" />
        </test>
        <test>
            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
            <param name="ref_selector" value="history" />
            <param name="ref" ftype="fasta" value="pBR322.fa" />
            <conditional name="alnqual_choice">
                <param name="alnquals_to_use" value="-B" />
            </conditional>
            <output name="output" file="alnqual-out2.bam" />
        </test>
        <test>
            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
            <param name="ref_selector" value="history" />
            <param name="ref" ftype="fasta" value="pBR322.fa" />
            <conditional name="alnqual_choice">
                <param name="alnquals_to_use" value="-A" />
            </conditional>
            <output name="output" file="alnqual-out3.bam" />
        </test>
        <test>
            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
            <param name="ref_selector" value="history" />
            <param name="ref" ftype="fasta" value="pBR322.fa" />
            <conditional name="alnqual_choice">
                <param name="extended_baq" value="false" />
            </conditional>
            <output name="output" file="alnqual-out4.bam" />
        </test>
        <test>
            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
            <param name="ref_selector" value="history" />
            <param name="ref" ftype="fasta" value="pBR322.fa" />
            <param name="recompute" value="true" />
            <output name="output" file="alnqual-out5.bam" />
        </test>
    </tests>
    <help><![CDATA[
lofreq alnqual: add base- and indel-alignment qualities (BAQ, IDAQ) to
aligned read records

6:791f73caa0c8

<tool id="lofreq_alnqual" name="Add LoFreq alignment quality scores" version="@TOOL_VERSION@+galaxy1" profile="18.01">
    <description>to aligned read SAM/BAM records</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

    <tests>
        <test>
            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
            <param name="ref_selector" value="history" />
            <param name="ref" ftype="fasta" value="pBR322.fa" />
            <output name="output" file="alnqual-out1.bam" ftype="bam" />
        </test>
        <test>
            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
            <param name="ref_selector" value="history" />
            <param name="ref" ftype="fasta" value="pBR322.fa" />
            <conditional name="alnqual_choice">
                <param name="alnquals_to_use" value="-B" />
            </conditional>
            <output name="output" file="alnqual-out2.bam" ftype="bam" />
        </test>
        <test>
            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
            <param name="ref_selector" value="history" />
            <param name="ref" ftype="fasta" value="pBR322.fa" />
            <conditional name="alnqual_choice">
                <param name="alnquals_to_use" value="-A" />
            </conditional>
            <output name="output" file="alnqual-out3.bam" ftype="bam" />
        </test>
        <test>
            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
            <param name="ref_selector" value="history" />
            <param name="ref" ftype="fasta" value="pBR322.fa" />
            <conditional name="alnqual_choice">
                <param name="extended_baq" value="false" />
            </conditional>
            <output name="output" file="alnqual-out4.bam" ftype="bam" />
        </test>
        <test>
            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
            <param name="ref_selector" value="history" />
            <param name="ref" ftype="fasta" value="pBR322.fa" />
            <param name="recompute" value="true" />
            <output name="output" file="alnqual-out5.bam" ftype="bam" />
        </test>
    </tests>
    <help><![CDATA[
lofreq alnqual: add base- and indel-alignment qualities (BAQ, IDAQ) to
aligned read records