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comparison arriba.xml @ 3:f6b8b38636a4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit cd9d5f90669555dc06b2467043c01846cd8c4078
author iuc
date Tue, 06 Dec 2022 10:38:51 +0000
parents add230dddd52
children 01ccd366690d
comparison
equal deleted inserted replaced
2:add230dddd52 3:f6b8b38636a4
152 -Z $options.min_itd_supporting_reads 152 -Z $options.min_itd_supporting_reads
153 #end if 153 #end if
154 $options.duplicate_marking 154 $options.duplicate_marking
155 $options.fill_discarded_columns 155 $options.fill_discarded_columns
156 $options.fill_the_gaps 156 $options.fill_the_gaps
157 #if str($visualization.do_viz) == "yes" 157 #if $output_fusion_bams or str($visualization.do_viz) == "yes"
158 && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input' > Aligned.sortedByCoord.out.bam 158 && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input' > Aligned.sortedByCoord.out.bam
159 && samtools index Aligned.sortedByCoord.out.bam 159 && samtools index Aligned.sortedByCoord.out.bam
160 #end if 160 #end if
161 #if $output_fusions_vcf 161 #if $output_fusions_vcf
162 && convert_fusions_to_vcf.sh '$genome_assembly' fusions.tsv fusions.vcf 162 && convert_fusions_to_vcf.sh '$genome_assembly' fusions.tsv fusions.vcf
439 </data> 439 </data>
440 <collection name="fusion_bams" type="list" label="${tool.name} on ${on_string}: Fusion Alignments"> 440 <collection name="fusion_bams" type="list" label="${tool.name} on ${on_string}: Fusion Alignments">
441 <discover_datasets pattern="(?P&lt;name&gt;fusion_\d+\.bam)$" format="bam" directory="fusion_bams" visible="false"/> 441 <discover_datasets pattern="(?P&lt;name&gt;fusion_\d+\.bam)$" format="bam" directory="fusion_bams" visible="false"/>
442 <filter>output_fusion_bams == True</filter> 442 <filter>output_fusion_bams == True</filter>
443 </collection> 443 </collection>
444 <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
445 <filter>input_params['input_source'] == "use_fastq"</filter>
446 </data>
447 <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf"> 444 <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf">
448 <filter>visualization['do_viz'] == "yes"</filter> 445 <filter>visualization['do_viz'] == "yes"</filter>
449 </data> 446 </data>
450 </outputs> 447 </outputs>
451 <tests> 448 <tests>
452 <!-- Test 1 - From exisitng BAM --> 449 <!-- Test 1 - From exisitng BAM -->
453 <test> 450 <test expect_num_outputs="3">
454 <param name="input" ftype="sam" value="Aligned.out.sam"/> 451 <param name="input" ftype="sam" value="Aligned.out.sam"/>
455 <conditional name="genome"> 452 <conditional name="genome">
456 <param name="genome_source" value="history"/> 453 <param name="genome_source" value="history"/>
457 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/> 454 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
458 </conditional> 455 </conditional>
470 <has_text_matching expression="BCR\tABL1"/> 467 <has_text_matching expression="BCR\tABL1"/>
471 </assert_contents> 468 </assert_contents>
472 </output> 469 </output>
473 </test> 470 </test>
474 <!-- Test 2 - From exisitng BAM with protein_domains and visualization --> 471 <!-- Test 2 - From exisitng BAM with protein_domains and visualization -->
475 <test> 472 <test expect_num_outputs="4">
476 <param name="input" ftype="sam" value="Aligned.out.sam"/> 473 <param name="input" ftype="sam" value="Aligned.out.sam"/>
477 <conditional name="genome"> 474 <conditional name="genome">
478 <param name="genome_source" value="history"/> 475 <param name="genome_source" value="history"/>
479 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/> 476 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
480 </conditional> 477 </conditional>