comparison parse.xml @ 9:d3a7b17714c1 draft

planemo upload for repository https://github.com/open2c/pairtools commit 13aa776596c927adff29d936740ac80f0e37375d

8:44cb74c154bc

            --max-inter-align-gap '$max_inter_algn_gap'
            --nproc-in \${GALAXY_SLOTS:-4}
            --nproc-out \${GALAXY_SLOTS:-4}
    ]]></command>
    <inputs>
        <param name="sam_path" type="data" format="sam,bam" label="Input SAM/BAM file" help="Input SAM or BAM file with paired-end sequence alignments of Hi-C molecules."/>    
        <param name="chroms_path" argument="-c" type="data" format="tabular" label="Input a chromosome order file" help="Chromosome order used to flip interchromosomal mates. Any scaffolds not listed will be ordered lexicographically."/>
        <param name="assembly_name" type="text" value="" label="Input a name of genome assembly" help="Name of genome assembly (e.g. hg19, mm10) to store in the pairs header"></param>
        <param argument="--min-mapq" type="integer" value="40" min="0" label="Minimal MAPQ" help="Minimal MAPQ score to consider a read as uniquely mapped."/>
        <param argument="--max-molecule-size" type="integer" min="0" value="750" label="Input the maximal size of a Hi-C molecule" help="The maximal size of a Hi-C molecule; used to rescue single ligations(from molecules with three alignments) and to rescue complex ligations."></param>
        <param argument="--drop-readid" type="boolean" truevalue="--drop-readid" falsevalue="" checked="False" label="Do not add read ids to the output"></param>

    <help><![CDATA[
        **Pairtools parse**

        Detects ligation events in the aligned sequences of DNA molecules formed in Hi-C experiments and reports them in the .pairs/.pairsam format.
        
        sam_path : an input .sam/.bam file with paired-end sequence alignments of Hi-C molecules. 
              
    ]]></help>
    <expand macro="citations"/>
    <expand macro="creator"/>
</tool>

9:d3a7b17714c1

            --max-inter-align-gap '$max_inter_algn_gap'
            --nproc-in \${GALAXY_SLOTS:-4}
            --nproc-out \${GALAXY_SLOTS:-4}
    ]]></command>
    <inputs>
        <param name="sam_path" type="data" format="sam,qname_input_sorted.bam,qname_sorted.bam" label="Input SAM/BAM file" help="Input SAM or BAM (unsorted/name-sorted) file with paired-end sequence alignments of Hi-C molecules."/>
        <param name="chroms_path" argument="-c" type="data" format="tabular" label="Input a chromosome order file" help="Chromosome order used to flip interchromosomal mates. Any scaffolds not listed will be ordered lexicographically."/>
        <param name="assembly_name" type="text" value="" label="Input a name of genome assembly" help="Name of genome assembly (e.g. hg19, mm10) to store in the pairs header"></param>
        <param argument="--min-mapq" type="integer" value="40" min="0" label="Minimal MAPQ" help="Minimal MAPQ score to consider a read as uniquely mapped."/>
        <param argument="--max-molecule-size" type="integer" min="0" value="750" label="Input the maximal size of a Hi-C molecule" help="The maximal size of a Hi-C molecule; used to rescue single ligations(from molecules with three alignments) and to rescue complex ligations."></param>
        <param argument="--drop-readid" type="boolean" truevalue="--drop-readid" falsevalue="" checked="False" label="Do not add read ids to the output"></param>

    <help><![CDATA[
        **Pairtools parse**

        Detects ligation events in the aligned sequences of DNA molecules formed in Hi-C experiments and reports them in the .pairs/.pairsam format.
        
        sam_path : an input .sam/.bam (unsorted/name-sorted) file with paired-end sequence alignments of Hi-C molecules. 
              
    ]]></help>
    <expand macro="citations"/>
    <expand macro="creator"/>
</tool>