Mercurial > repos > jjohnson > arriba_get_filters
diff arriba_get_filters.xml @ 0:463dd21dc267 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
author | jjohnson |
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date | Fri, 11 Feb 2022 19:08:51 +0000 |
parents | |
children | f1e60cf0823a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/arriba_get_filters.xml Fri Feb 11 19:08:51 2022 +0000 @@ -0,0 +1,71 @@ +<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>