Mercurial > repos > jjohnson > arriba
diff arriba.xml @ 10:c58d1774c762 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
author | jjohnson |
---|---|
date | Fri, 11 Feb 2022 19:04:06 +0000 |
parents | 8c4c97fd0555 |
children | 8ed8af5836d1 |
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--- a/arriba.xml Wed Oct 13 18:45:16 2021 +0000 +++ b/arriba.xml Fri Feb 11 19:04:06 2022 +0000 @@ -161,6 +161,12 @@ #if $options.max_itd_length -l $options.max_itd_length #end if + #if $options.min_itd_allele_fraction + -z $options.min_itd_allele_fraction + #end if + #if $options.min_itd_supporting_reads + -Z $options.min_itd_supporting_reads + #end if $options.duplicate_marking $options.fill_discarded_columns $options.fill_the_gaps @@ -381,7 +387,7 @@ <param name="covered_fraction" argument="-C" type="float" value="" min="0." max="1.0" optional="true" label="Covered fraction"> <help>Ignore virally associated events if the virus is not fully expressed, i.e., less than the given fraction of the viral contig is transcribed. - Default: 0.150000 + Default: 0.050000 </help> </param> <param name="max_itd_length" argument="-l" type="integer" value="" min="1" optional="true" label="Maximum length of internal tandem duplications"> @@ -389,6 +395,14 @@ Default: 100 </help> </param> + <param name="min_itd_allele_fraction" argument="-z" type="float" value="" min="0." max="1.0" optional="true" label="Required fraction of supporting reads to report an internal tandem duplication"> + <help> Default: 0.070000 + </help> + </param> + <param name="min_itd_supporting_reads" argument="-Z" type="integer" value="" min="1" optional="true" label="Required number of supporting reads to report an internal tandem duplication"> + <help> Default: 10 + </help> + </param> <param name="duplicate_marking" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Use aligners duplicate marking"> <help>Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a preceding program using the BAM_FDUP flag. This makes sense when unique molecular @@ -442,8 +456,8 @@ </conditional> <conditional name="genome"> <param name="genome_source" value="history"/> - <param name="assembly" ftype="fasta" value="genome.fasta"/> - <param name="annotation" ftype="gtf" value="genome.gtf"/> + <param name="assembly" ftype="fasta" value="genome.fasta.gz"/> + <param name="annotation" ftype="gtf" value="genome.gtf.gz"/> </conditional> <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/> <conditional name="visualization"> @@ -465,8 +479,8 @@ </conditional> <conditional name="genome"> <param name="genome_source" value="history"/> - <param name="assembly" ftype="fasta" value="genome.fasta"/> - <param name="annotation" ftype="gtf" value="genome.gtf"/> + <param name="assembly" ftype="fasta" value="genome.fasta.gz"/> + <param name="annotation" ftype="gtf" value="genome.gtf.gz"/> </conditional> <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/> <conditional name="visualization">