comparison alleyoop.xml @ 6:141f65f7c7c8 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0502309b17c070efd9c8ab28e538279055835a45"

5:8b62f89924a7

<tool id="alleyoop" name="Alleyoop" version="@TOOL_VERSION@">
    <description>- post-processing and QC of Slamdunk analyses</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

            <param name="variants" ftype="vcf" value="reads1_snp.vcf,reads2_snp.vcf" />
            <param name="l" value="100" />
            <param name="mq" value="27" />
            <param name="bams" value="True" />
            <output_collection name="outputTCReads" count="2">
                <element name="reads1" ftype="bam" file="reads1_TCReads.bam" />
            </output_collection>
            <output_collection name="outputbkgdReads" count="2">
                <element name="reads1" ftype="bam" file="reads1_backgroundReads.bam" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
SLAMseq

6:141f65f7c7c8

<tool id="alleyoop" name="Alleyoop" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>- post-processing and QC of Slamdunk analyses</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

            <param name="variants" ftype="vcf" value="reads1_snp.vcf,reads2_snp.vcf" />
            <param name="l" value="100" />
            <param name="mq" value="27" />
            <param name="bams" value="True" />
            <output_collection name="outputTCReads" count="2">
                <element name="reads1" ftype="bam" file="reads1_TCReads.bam" lines_diff="8"/>
            </output_collection>
            <output_collection name="outputbkgdReads" count="2">
                <element name="reads1" ftype="bam" file="reads1_backgroundReads.bam" lines_diff="8"/><!-- allow for diff in RG and PG lines -->
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
SLAMseq