Mercurial > repos > jjohnson > arriba
view arriba_get_filters.xml @ 8:1a56888ddb7d draft
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit f5af83950615d8c77a3a43cf45f5ddf46000701b"
author | jjohnson |
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date | Mon, 11 Oct 2021 19:00:45 +0000 |
parents | 005b200c8841 |
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<tool id="arriba_get_filters" name="Arriba Get Filters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5"> <description>to history</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ BASE_DIR=\$(dirname \$(dirname `which arriba`)) && REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` && REF_DIR=\$(dirname \$REF_SCRIPT) && REF_NAME=${arriba_reference_name.split('+')[0].replace('viral','')} && echo \$REF_NAME && cp `find \$REF_DIR -name 'blacklist_*' | grep -i \$REF_NAME` '$blacklist' && cp `find \$REF_DIR -name 'known_fusions_*' | grep -i \$REF_NAME` '$known_fusions' && cp `find \$REF_DIR -name 'protein_domains_*' | grep -i \$REF_NAME` '$protein_domains' && cp `find \$REF_DIR -name 'cytobands_*' | grep -i \$REF_NAME` '$cytobands' #* cp "\$REF_DIR/blacklist_*${arriba_reference_name}*" '$blacklist' && cp "\$REF_DIR/known_fusions_*${arriba_reference_name}*" '$known_fusions' && cp "\$REF_DIR/protein_domains_*${arriba_reference_name}*" '$protein_domains' && cp "\$REF_DIR/cytobands_*${arriba_reference_name}*" '$cytobands' *# ]]></command> <inputs> <param name="arriba_reference_name" type="text" label="Select reference"> <help>GRCh38 GRCh37 hg38 hg19 GRCm38 mm10</help> <option value="GRCh38">GRCh38</option> <option value="GRCh37">GRCh37</option> <option value="hg38">hg38</option> <option value="hg19">hg19</option> <option value="GRCm38">GRCm38</option> <option value="mm10">mm10</option> </param> </inputs> <outputs> <data name="blacklist" format="tabular.gz" label="${tool.name} ${arriba_reference_name} blacklist.tsv.gz"/> <data name="known_fusions" format="tabular.gz" label="${tool.name} ${arriba_reference_name} known_fusions.tsv.gz"/> <data name="protein_domains" format="gff3" label="${tool.name} ${arriba_reference_name} protein_domains.gff3"/> <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands.tsv"/> </outputs> <tests> <test> <param name="arriba_reference_name" value="GRCh38"/> <output name="cytobands"> <assert_contents> <has_text_matching expression="1\t1\t\d+\tp36.33\tgneg"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ **Arriba Get Filters** Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions. It is based on chimeric alignments found by the STAR RNA-Seq aligner. The **Arriba Get Filters** tool adds the following Arriba distribution input_files_ to your galaxy history: - blacklist - known_fusions - protein_domains - cytobands .. _Arriba: https://arriba.readthedocs.io/en/latest/ .. _input_files: https://arriba.readthedocs.io/en/latest/input-files/ ]]></help> <expand macro="citations" /> </tool>