| Previous changeset 0:a24ca22b906e (2022-07-27) Next changeset 2:add230dddd52 (2022-09-26) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f |
|
modified:
arriba.xml macros.xml |
| b |
| diff -r a24ca22b906e -r 4f1efcc055d5 arriba.xml --- a/arriba.xml Wed Jul 27 11:24:44 2022 +0000 +++ b/arriba.xml Fri Sep 23 13:50:25 2022 +0000 |
| b |
| @@ -55,7 +55,7 @@ -c '$chimeric' #end if -a '$genome_assembly' - -g '$genome_annotation' + -g 'genome.gtf' #if $blacklist -b '$blacklist_file' #end if @@ -71,17 +71,17 @@ #if $tags -t '$tags_file' #end if - #if str($wgs.use_wgs) == "yes" - -d '$wgs.wgs' - #if str($wgs.max_genomic_breakpoint_distance) - -D $wgs.max_genomic_breakpoint_distance + #if str($wgs_cond.use_wgs) == "yes" + -d '$wgs_cond.wgs' + #if str($wg_cond.max_genomic_breakpoint_distance) + -D $wgs_cond.max_genomic_breakpoint_distance #end if #end if -o fusions.tsv -#if $output_fusions_discarded + #if $output_fusions_discarded -O fusions.discarded.tsv -#end if -## Arriba options + #end if + ## Arriba options #if $options.gtf_features -G '$options.gtf_features' #end if @@ -186,13 +186,13 @@ </param> <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion." help="This can be the known fusions if that input has a third column with a name"/> - <conditional name="wgs"> + <conditional name="wgs_cond"> <param name="use_wgs" type="select" label="Use whole-genome sequencing data"> <option value="no">no</option> <option value="yes">Yes</option> </param> <when value="yes"> - <param name="wgs" argument="-d" type="data" format="tabular" label="whole-genome sequencing structural variant data" + <param name="wgs" argument="-d" type="data" format="tabular,vcf" label="whole-genome sequencing structural variant data" help="These coordinates serve to increase sensitivity towards weakly expressed fusions and to eliminate fusions with low evidence."/> <param name="max_genomic_breakpoint_distance" argument="-D" type="integer" value="100000" min="0" label="Max genomic breakpoint distance" help="determines how far a genomic breakpoint may be away from a transcriptomic breakpoint to consider it as a related event."/> |
| b |
| diff -r a24ca22b906e -r 4f1efcc055d5 macros.xml --- a/macros.xml Wed Jul 27 11:24:44 2022 +0000 +++ b/macros.xml Fri Sep 23 13:50:25 2022 +0000 |
| [ |
| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.3.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">arriba</requirement> @@ -58,12 +58,7 @@ ]]></token> <token name="@GTF_SOURCE@"><![CDATA[ #if str($genome_gtf.gtf_source) == "history" - #if $genome_gtf.annotation.is_of_type('gtf.gz') - #set $genome_annotation = 'genome.gtf.gz' - #else - #set $genome_annotation = 'genome.gtf' - #end if - ln -sf '$genome_gtf.annotation' $genome_annotation && + ln -sf '$genome_gtf.annotation' genome.gtf && #end if ]]></token> @@ -300,7 +295,6 @@ #if str($visualization.options.pdfHeight) --pdfHeight=$visualization.options.pdfHeight #end if - # fontFamily #if $visualization.options.fontFamily --fontFamily=$visualization.options.fontFamily #end if |