| Previous changeset 2:7420753b0671 (2021-10-08) Next changeset 4:77021ad5037d (2021-10-09) |
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Commit message:
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" |
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modified:
arriba.xml arriba_download_reference.xml |
| b |
| diff -r 7420753b0671 -r 2d32e6c86c48 arriba.xml --- a/arriba.xml Fri Oct 08 19:23:48 2021 +0000 +++ b/arriba.xml Fri Oct 08 20:44:25 2021 +0000 |
| [ |
| @@ -70,6 +70,27 @@ #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 index Aligned.sortedByCoord.out.bam +#elif str($visualization.do_viz) == "yes" + && samtools sort -@ "$THREADS" -m 4G -T tmp -O bam '$input_params.input' > Aligned.sortedByCoord.out.bam + && samtools index Aligned.sortedByCoord.out.bam +#end if +#if str($visualization.do_viz) == "yes" +draw_fusions.R \ + --fusions=fusions.tsv + --alignments=Aligned.sortedByCoord.out.bam + --output=fusions.pdf + --annotation='$gtf' + #if $visualization.cytobands + --cytobands='$visualization.cytobands' + #end if + #if '$protein_domains' + --proteinDomains=database/protein_domains_hg19_hs37d5_GRCh37_v2.1.0.gff3 + #end if +#end if + ]]></command> <inputs> <conditional name="input_params"> @@ -107,16 +128,33 @@ </conditional> <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/> <param name="gtf" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/> - <param name="blacklist" argument="-b" type="data" format="tabular" label="File containing blacklisted ranges."/> + <param name="blacklist" argument="-b" type="data" format="tabular" optional="true" label="File containing blacklisted ranges."/> <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing blacklisted ranges."/> <param name="known_fusions" argument="-k" type="data" format="tabular" optional="true" label="File containing known fusions"> <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help> </param> <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion."/> + <conditional name="visualization"> + <param name="do_viz" type="select" label="Generate visualization"> + <option value="yes">Yes</option> + <option value="no">no</option> + </param> + <when value="yes"> + <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/> + </when> + <when value="no"/> + </conditional> + </inputs> <outputs> <data name="fusions" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"/> <data name="discarded" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv"/> + <data name="aligned_bam" format="bam" label="${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 ${on_string}: fusions.pdf" from_work_dir="fusions.pdf"> + <filter>visualization['do_viz'] == "yes"</filter> + </data> </outputs> <help><![CDATA[ ** Arriba ** |
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| diff -r 7420753b0671 -r 2d32e6c86c48 arriba_download_reference.xml --- a/arriba_download_reference.xml Fri Oct 08 19:23:48 2021 +0000 +++ b/arriba_download_reference.xml Fri Oct 08 20:44:25 2021 +0000 |
| b |
| @@ -10,8 +10,8 @@ BASE_DIR=\$(dirname \$(dirname `which arriba`)) && REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` && \$REF_SCRIPT '$arriba_reference_name' && - cp *.fa* > '$genome_fasta' && - cp *.gtf* > '$genome_gtf' && + cp *.fa* '$genome_fasta' && + cp *.gtf* '$genome_gtf' && mv STAR*/* '$star_index.extra_files_path' ]]></command> <inputs> |