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

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

--- a/arriba.xml	Tue Apr 26 20:35:35 2022 +0000
+++ b/arriba.xml	Mon Jun 13 12:09:32 2022 +0000
@@ -13,6 +13,10 @@
     <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'
@@ -20,7 +24,12 @@
     #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 $known_fusions_file = 'known_fusions.tsv.gz'
@@ -106,8 +115,9 @@
     -g '$genome_annotation'
     #if $blacklist
         -b '$blacklist_file'
-    #else
-        -f 'blacklist'
+    #end if
+    #if $filters
+        -f '$filters'
     #end if
     #if $protein_domains
         -p '$protein_domains'
@@ -317,6 +327,46 @@
                       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
@@ -560,6 +610,7 @@
                 <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"/>