comparison arriba.xml @ 13:1d459aaa5765 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"

12:73fd7703a743

    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
@GENOME_SOURCE@
#if $blacklist
    #if $blacklist.is_of_type('tabular.gz')
        #set $blacklist_file = 'blacklist.tsv.gz'
        ln -sf '$blacklist'  $blacklist_file &&
    #else
        #set $blacklist_file = $blacklist
    #end if
#end if
#if $known_fusions
    #if $known_fusions.is_of_type('tabular.gz')
        #set $known_fusions_file = 'known_fusions.tsv.gz'
        ln -sf '$known_fusions'  $known_fusions_file &&
    #else

#end if
    -a '$genome_assembly'
    -g '$genome_annotation'
    #if $blacklist
        -b '$blacklist_file'
    #else
        -f 'blacklist'
    #end if
    #if $protein_domains
        -p '$protein_domains'
    #end if
    #if $known_fusions

                <help>Comma-/space-separated list of viral contigs. 
                      Asterisks (*) are treated as wild-cards.
                      Default: AC_* NC_*
                </help>
            </param>
            <param name="max_evalue" argument="-E" type="float" value="" optional="true" label="Max e-value threahold">
                <help>Arriba estimates the number of fusions with a given number of supporting
                      reads which one would expect to see by random chance. If the expected number
                      of fusions (e-value) is higher than this threshold, the fusion is
                      discarded by the 'relative_support' filter. Note: Increasing this

            <conditional name="genome">
                <param name="genome_source" value="cached"/>
                <param name="arriba_ref" value="GRCh38+ENSEMBL93"/>
            </conditional>
            <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
            <conditional name="visualization">
                <param name="do_viz" value="no"/>
                <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
            </conditional>
            <output name="fusions_tsv">

13:1d459aaa5765

    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
@GENOME_SOURCE@
#set $filter_list = []
#if $options.filters
    #set $filter_list = $options.filters.split(',')
#end if
#if $blacklist
    #if $blacklist.is_of_type('tabular.gz')
        #set $blacklist_file = 'blacklist.tsv.gz'
        ln -sf '$blacklist'  $blacklist_file &&
    #else
        #set $blacklist_file = $blacklist
    #end if
#else
    #if 'blacklist' not in $filter_list
        #silent $filter_list.append('blacklist')
    #end if
#end if
#set $filters = ','.join($filter_list) 
#if $known_fusions
    #if $known_fusions.is_of_type('tabular.gz')
        #set $known_fusions_file = 'known_fusions.tsv.gz'
        ln -sf '$known_fusions'  $known_fusions_file &&
    #else

#end if
    -a '$genome_assembly'
    -g '$genome_annotation'
    #if $blacklist
        -b '$blacklist_file'
    #end if
    #if $filters
        -f '$filters'
    #end if
    #if $protein_domains
        -p '$protein_domains'
    #end if
    #if $known_fusions

                <help>Comma-/space-separated list of viral contigs. 
                      Asterisks (*) are treated as wild-cards.
                      Default: AC_* NC_*
                </help>
            </param>
            <param name="filters" argument="-f" type="select" optional="true" multiple="true" label="Diable filters">
                <help>By default all filters are enabled.</help>
                <option value="top_expressed_viral_contigs">top_expressed_viral_contigs</option>
                <option value="viral_contigs">viral_contigs</option>
                <option value="low_coverage_viral_contigs">low_coverage_viral_contigs</option>
                <option value="uninteresting_contigs">uninteresting_contigs</option>
                <option value="no_genomic_support">no_genomic_support</option>
                <option value="short_anchor">short_anchor</option>
                <option value="select_best">select_best</option>
                <option value="many_spliced">many_spliced</option>
                <option value="long_gap">long_gap</option>
                <option value="merge_adjacent">merge_adjacent</option>
                <option value="hairpin">hairpin</option>
                <option value="small_insert_size">small_insert_size</option>
                <option value="same_gene">same_gene</option>
                <option value="genomic_support">genomic_support</option>
                <option value="read_through">read_through</option>
                <option value="no_coverage">no_coverage</option>
                <option value="mismatches">mismatches</option>
                <option value="homopolymer">homopolymer</option>
                <option value="low_entropy">low_entropy</option>
                <option value="multimappers">multimappers</option>
                <option value="inconsistently_clipped">inconsistently_clipped</option>
                <option value="duplicates">duplicates</option>
                <option value="homologs">homologs</option>
                <option value="blacklist">blacklist</option>
                <option value="mismappers">mismappers</option>
                <option value="spliced">spliced</option>
                <option value="relative_support">relative_support</option>
                <option value="min_support">min_support</option>
                <option value="known_fusions">known_fusions</option>
                <option value="end_to_end">end_to_end</option>
                <option value="non_coding_neighbors">non_coding_neighbors</option>
                <option value="isoforms">isoforms</option>
                <option value="intronic">intronic</option>
                <option value="in_vitro">in_vitro</option>
                <option value="intragenic_exonic">intragenic_exonic</option>
                <option value="internal_tandem_duplication">internal_tandem_duplication</option>
            </param>
    
            <param name="max_evalue" argument="-E" type="float" value="" optional="true" label="Max e-value threahold">
                <help>Arriba estimates the number of fusions with a given number of supporting
                      reads which one would expect to see by random chance. If the expected number
                      of fusions (e-value) is higher than this threshold, the fusion is
                      discarded by the 'relative_support' filter. Note: Increasing this

            <conditional name="genome">
                <param name="genome_source" value="cached"/>
                <param name="arriba_ref" value="GRCh38+ENSEMBL93"/>
            </conditional>
            <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
            <param name="output_fusions_vcf" value="false"/>
            <conditional name="visualization">
                <param name="do_viz" value="no"/>
                <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
            </conditional>
            <output name="fusions_tsv">