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comparison arriba.xml @ 1:4f1efcc055d5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f
author iuc
date Fri, 23 Sep 2022 13:50:25 +0000
parents a24ca22b906e
children add230dddd52
comparison
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0:a24ca22b906e 1:4f1efcc055d5
53 -x '$input' 53 -x '$input'
54 #if $chimeric 54 #if $chimeric
55 -c '$chimeric' 55 -c '$chimeric'
56 #end if 56 #end if
57 -a '$genome_assembly' 57 -a '$genome_assembly'
58 -g '$genome_annotation' 58 -g 'genome.gtf'
59 #if $blacklist 59 #if $blacklist
60 -b '$blacklist_file' 60 -b '$blacklist_file'
61 #end if 61 #end if
62 #if $filters 62 #if $filters
63 -f '$filters' 63 -f '$filters'
69 -k '$known_fusions_file' 69 -k '$known_fusions_file'
70 #end if 70 #end if
71 #if $tags 71 #if $tags
72 -t '$tags_file' 72 -t '$tags_file'
73 #end if 73 #end if
74 #if str($wgs.use_wgs) == "yes" 74 #if str($wgs_cond.use_wgs) == "yes"
75 -d '$wgs.wgs' 75 -d '$wgs_cond.wgs'
76 #if str($wgs.max_genomic_breakpoint_distance) 76 #if str($wg_cond.max_genomic_breakpoint_distance)
77 -D $wgs.max_genomic_breakpoint_distance 77 -D $wgs_cond.max_genomic_breakpoint_distance
78 #end if 78 #end if
79 #end if 79 #end if
80 -o fusions.tsv 80 -o fusions.tsv
81 #if $output_fusions_discarded 81 #if $output_fusions_discarded
82 -O fusions.discarded.tsv 82 -O fusions.discarded.tsv
83 #end if 83 #end if
84 ## Arriba options 84 ## Arriba options
85 #if $options.gtf_features 85 #if $options.gtf_features
86 -G '$options.gtf_features' 86 -G '$options.gtf_features'
87 #end if 87 #end if
88 #if $options.strandedness 88 #if $options.strandedness
89 -s $options.strandedness 89 -s $options.strandedness
184 <param name="known_fusions" argument="-k" type="data" format="tabular,tabular.gz" optional="true" label="File containing known fusions"> 184 <param name="known_fusions" argument="-k" type="data" format="tabular,tabular.gz" optional="true" label="File containing known fusions">
185 <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help> 185 <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help>
186 </param> 186 </param>
187 <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion." 187 <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion."
188 help="This can be the known fusions if that input has a third column with a name"/> 188 help="This can be the known fusions if that input has a third column with a name"/>
189 <conditional name="wgs"> 189 <conditional name="wgs_cond">
190 <param name="use_wgs" type="select" label="Use whole-genome sequencing data"> 190 <param name="use_wgs" type="select" label="Use whole-genome sequencing data">
191 <option value="no">no</option> 191 <option value="no">no</option>
192 <option value="yes">Yes</option> 192 <option value="yes">Yes</option>
193 </param> 193 </param>
194 <when value="yes"> 194 <when value="yes">
195 <param name="wgs" argument="-d" type="data" format="tabular" label="whole-genome sequencing structural variant data" 195 <param name="wgs" argument="-d" type="data" format="tabular,vcf" label="whole-genome sequencing structural variant data"
196 help="These coordinates serve to increase sensitivity towards weakly expressed fusions and to eliminate fusions with low evidence."/> 196 help="These coordinates serve to increase sensitivity towards weakly expressed fusions and to eliminate fusions with low evidence."/>
197 <param name="max_genomic_breakpoint_distance" argument="-D" type="integer" value="100000" min="0" label="Max genomic breakpoint distance" 197 <param name="max_genomic_breakpoint_distance" argument="-D" type="integer" value="100000" min="0" label="Max genomic breakpoint distance"
198 help="determines how far a genomic breakpoint may be away from a transcriptomic breakpoint to consider it as a related event."/> 198 help="determines how far a genomic breakpoint may be away from a transcriptomic breakpoint to consider it as a related event."/>
199 </when> 199 </when>
200 <when value="no"/> 200 <when value="no"/>