comparison chira_quantify.xml @ 8:e40017f9cff1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"

7:a1694947910f

    <inputs>
        <param format="bed" name="segments" type="data" label="BED file of aligned segments"/>
        <param format="tabular" name="merged" type="data" label="Tabular file of merged alignments"/>
        <param name="crl_share" type="float" value="0.7" label="CRL locus fraction" min="0" max="1"
            help="Minimum fraction of reads of a locus that must overlap with all CRL loci inorder to merge itinto that CRL."/>
        <param name="min_locus_size" type="integer" value="5" label="Minimum locus size" min="1"
            help="Minimum number of reads a locus should have in order to participate in CRL creation.
                 Always set this value relative to your sequencing depth. Setting this to lower leads
                 CRLs of random multimappings Also consider setting the --crl_share option
                 along with this"/>
       <param name="em_threshold" type="float" value="1" label="EM threshold"

    <tests>
        <test expect_num_outputs="1">
            <param name="segments" value="segments.bed"/>
            <param name="merged" value="merged.bed"/>
            <output name="loci" file="loci.counts"/>
        </test>
    </tests>

    <help>

8:e40017f9cff1

    <inputs>
        <param format="bed" name="segments" type="data" label="BED file of aligned segments"/>
        <param format="tabular" name="merged" type="data" label="Tabular file of merged alignments"/>
        <param name="crl_share" type="float" value="0.7" label="CRL locus fraction" min="0" max="1"
            help="Minimum fraction of reads of a locus that must overlap with all CRL loci inorder to merge itinto that CRL."/>
        <param name="min_locus_size" type="integer" value="10" label="Minimum locus size" min="1"
            help="Minimum number of reads a locus should have in order to participate in CRL creation.
                 Always set this value relative to your sequencing depth. Setting this to lower leads
                 CRLs of random multimappings Also consider setting the --crl_share option
                 along with this"/>
       <param name="em_threshold" type="float" value="1" label="EM threshold"

    <tests>
        <test expect_num_outputs="1">
            <param name="segments" value="segments.bed"/>
            <param name="merged" value="merged.bed"/>
            <param name="min_locus_size" value="5"/>
            <output name="loci" file="loci.counts"/>
        </test>
    </tests>

    <help>