comparison chira_merge.xml @ 9:948f4bc1f030 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit a69b18084d0a9ade4e29869f8b0e2ce5fc4e0b73"

8:c836a05bd6a3

        #if str($annotation.choice) == "yes":
            -g '$annotation.gtf'
        #end if
        -so '$segment_overlap'
        -lt '$length_threshold'
        #if str($merge.mode) == "blockbuster":
            -bb
            -d '$merge.distance'
            -mc '$merge.min_cluster_height'
            -mb '$merge.min_block_height'
            -sc '$merge.scale'
        #else:
            -ao '$merge.alignment_overlap'
            -ls '$merge.min_locus_size'
        #end if
        #if str($reference.ref_type) == "split":
            -f1 '$reference.ref_fasta1'
            -f2 '$reference.ref_fasta2'

        </conditional>
        <param name="segment_overlap" type="float" value="0.7" label="Overlap fraction for merging mapped read positions to segments" min="0" max="1"
            help="Matching read positions with greater than this fraction overlap are merged into a segment"/>
        <param name="length_threshold" type="float" value="0.9" label="Minimum length of the alignments as a fraction of longest" min="0" max="1"
            help="Consider the alignments of a that read have at least longer than this value times the longest alignment for that read"/>
        <conditional name="merge">
            <param name="mode" type="select" label="Select the mode of merging">
                <option value="overlap">Overlap based</option>
                <option value="blockbuster">Gaussian based (blockbuster)</option>
            </param>
            <when value="overlap">
                <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments" min="0" max="1"
                    help="Minimum fraction of BED entries that must overlap inorder to merge"/>
                <param name="min_locus_size" type="integer" value="1" label="Minimum locus size"
                            help="Minimum number of alignments to be present to output the merged a locus"/>
            </when>
            <when value="blockbuster">
                <param name="distance" type="integer" value="30" label="Blockbuster parameter distance"

            <param name="alignments" value="alignments.bed" />
            <param name="choice" value="yes" />
            <param name="gtf" value="annotation.gtf" />
            <param name="mode" value="blockbuster" />
            <param name="min_block_height" value="1" />
            <param name="min_cluster_height" value="5" />
            <param name="ref_type" value="split"/>
            <param name="ref_fasta1" value="ref1.fasta"/>
            <param name="ref_fasta2" value="ref2.fasta"/>
            <output name="segments_bed" >
                <assert_contents>

9:948f4bc1f030

        #if str($annotation.choice) == "yes":
            -g '$annotation.gtf'
        #end if
        -so '$segment_overlap'
        -lt '$length_threshold'
        -ao '$alignment_overlap'
        #if str($merge.mode) == "blockbuster":
            -bb
            -d '$merge.distance'
            -mc '$merge.min_cluster_height'
            -mb '$merge.min_block_height'
            -sc '$merge.scale'
        #else:
            -ls '$merge.min_locus_size'
        #end if
        #if str($reference.ref_type) == "split":
            -f1 '$reference.ref_fasta1'
            -f2 '$reference.ref_fasta2'

        </conditional>
        <param name="segment_overlap" type="float" value="0.7" label="Overlap fraction for merging mapped read positions to segments" min="0" max="1"
            help="Matching read positions with greater than this fraction overlap are merged into a segment"/>
        <param name="length_threshold" type="float" value="0.9" label="Minimum length of the alignments as a fraction of longest" min="0" max="1"
            help="Consider the alignments of a that read have at least longer than this value times the longest alignment for that read"/>
        <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments/blocks" min="0" max="1"
            help="Minimum fraction of BED entries/blockbuster blocks that must overlap inorder to merge"/>
        <conditional name="merge">
            <param name="mode" type="select" label="Select the mode of merging">
                <option value="overlap">Overlap based</option>
                <option value="blockbuster">Gaussian based (blockbuster)</option>
            </param>
            <when value="overlap">
                <param name="min_locus_size" type="integer" value="1" label="Minimum locus size"
                            help="Minimum number of alignments to be present to output the merged a locus"/>
            </when>
            <when value="blockbuster">
                <param name="distance" type="integer" value="30" label="Blockbuster parameter distance"

            <param name="alignments" value="alignments.bed" />
            <param name="choice" value="yes" />
            <param name="gtf" value="annotation.gtf" />
            <param name="mode" value="blockbuster" />
            <param name="min_block_height" value="1" />
            <param name="min_cluster_height" value="0" />
            <param name="ref_type" value="split"/>
            <param name="ref_fasta1" value="ref1.fasta"/>
            <param name="ref_fasta2" value="ref2.fasta"/>
            <output name="segments_bed" >
                <assert_contents>