Mercurial > repos > jjohnson > arriba
diff arriba.xml @ 4:77021ad5037d draft
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
author | jjohnson |
---|---|
date | Sat, 09 Oct 2021 15:41:49 +0000 |
parents | 2d32e6c86c48 |
children | 005b200c8841 |
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--- a/arriba.xml Fri Oct 08 20:44:25 2021 +0000 +++ b/arriba.xml Sat Oct 09 15:41:49 2021 +0000 @@ -20,7 +20,7 @@ #end if ln -f -s '${input_params.right_fq}' ${read2} && #if str($input_params.index.index_source) == "history" - #set $star_index_dir = $input_params.index.star_index.files_path + #set $star_index_dir = $input_params.index.star_index.extra_files_path #end if STAR --runThreadN \${GALAXY_SLOTS:-1} @@ -56,29 +56,31 @@ #end if -a '$genome_assembly' -g '$gtf' - #if '$blacklist' + #if $blacklist -b '$blacklist' + #else + -f 'blacklist' #end if - #if '$protein_domains' + #if $protein_domains -p '$protein_domains' #end if - #if '$known_fusions' + #if $known_fusions -k '$known_fusions' #end if - #if '$tags' + #if $tags -t '$tags' #end if -o fusions.tsv -O fusions.discarded.tsv #if str($input_params.input_source) == "use_fastq" - && samtools sort -@ "$THREADS" -m 4G -T tmp -O bam Aligned.out.bam > Aligned.sortedByCoord.out.bam + && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam Aligned.out.bam > Aligned.sortedByCoord.out.bam && samtools index Aligned.sortedByCoord.out.bam #elif str($visualization.do_viz) == "yes" - && samtools sort -@ "$THREADS" -m 4G -T tmp -O bam '$input_params.input' > Aligned.sortedByCoord.out.bam + && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input_params.input' > Aligned.sortedByCoord.out.bam && samtools index Aligned.sortedByCoord.out.bam #end if #if str($visualization.do_viz) == "yes" -draw_fusions.R \ +&& draw_fusions.R --fusions=fusions.tsv --alignments=Aligned.sortedByCoord.out.bam --output=fusions.pdf @@ -87,7 +89,7 @@ --cytobands='$visualization.cytobands' #end if #if '$protein_domains' - --proteinDomains=database/protein_domains_hg19_hs37d5_GRCh37_v2.1.0.gff3 + --proteinDomains='$protein_domains' #end if #end if @@ -129,11 +131,12 @@ <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/> <param name="gtf" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/> <param name="blacklist" argument="-b" type="data" format="tabular" optional="true" label="File containing blacklisted ranges."/> - <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing blacklisted ranges."/> + <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/> <param name="known_fusions" argument="-k" type="data" format="tabular" optional="true" label="File containing known fusions"> <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help> </param> - <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion."/> + <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="visualization"> <param name="do_viz" type="select" label="Generate visualization"> <option value="yes">Yes</option> @@ -152,10 +155,29 @@ <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam"> <filter>input_params['input_source'] == "use_fastq"</filter> </data> - <data name="fusions_png" format="png" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf"> + <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf"> <filter>visualization['do_viz'] == "yes"</filter> </data> </outputs> + <tests> + <!-- Test 1 - From exisitng BAM --> + <test> + <conditional name="input_params"> + <param name="input_source" value="use_star"/> + <param name="input" ftype="sam" value="Aligned.out.sam"/> + </conditional> + <param name="genome_assembly" ftype="fasta" value="genome.fasta"/> + <param name="gtf" ftype="gtf" value="genome.gtf"/> + <conditional name="visualization"> + <param name="do_viz" value="no"/> + </conditional> + <output name="fusions"> + <assert_contents> + <has_text_matching expression="BCR\tABL1"/> + </assert_contents> + </output> + </test> + </tests> <help><![CDATA[ ** Arriba **