comparison chira_quantify.xml @ 10:e0f08a05b24c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 51f68a6d51d9e87f8e54021ce760b1506a3589b8"

9:96ed25eb39f0

        <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"
              help="The maximum difference of transcripts expression between two consecutive iterations of EM algorithm to converge."/>
       <param name="crl" type="boolean" truevalue="-crl" falsevalue="" checked="true"
              label="Create CRLs" help="Create CRLs and qunatify them or use the loci further without creating the CRLs" />
    </inputs>
    <outputs>

    </outputs>

    <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>

10:e0f08a05b24c

        <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="0.1" label="EM threshold"
              help="The maximum difference of transcripts expression between two consecutive iterations of EM algorithm to converge."/>
       <param name="crl" type="boolean" truevalue="-crl" falsevalue="" checked="true"
              label="Create CRLs" help="Create CRLs and qunatify them or use the loci further without creating the CRLs" />
    </inputs>
    <outputs>

    </outputs>

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