Mercurial > repos > jjohnson > arriba
diff arriba_get_filters.xml @ 2:7420753b0671 draft
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
author | jjohnson |
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date | Fri, 08 Oct 2021 19:23:48 +0000 |
parents | |
children | 77021ad5037d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/arriba_get_filters.xml Fri Oct 08 19:23:48 2021 +0000 @@ -0,0 +1,52 @@ +<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}*" '$cytobands' + *# + ]]></command> + <inputs> + <param name="arriba_reference_name" type="text" label="Select reference"> + <help>GRCh38 GRCh37 hg38 hg19 GRCm38 mm10</help> + <option value="GRCh38">GRCh38</option> + <option value="GRCh37">GRCh37</option> + <option value="hg38">hg38</option> + <option value="hg19">hg19</option> + <option value="GRCm38">GRCm38</option> + <option value="mm10">mm10</option> + </param> + </inputs> + <outputs> + <data name="blacklist" format="tabular" label="${tool.name} ${arriba_reference_name} blacklist"/> + <data name="known_fusions" format="tabular" label="${tool.name} ${arriba_reference_name} known_fusions"/> + <data name="protein_domains" format="tabular" label="${tool.name} ${arriba_reference_name} protein_domains"/> + <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands"/> + </outputs> + <help><![CDATA[ +** Arriba ** + +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. + +.. _Arriba: https://arriba.readthedocs.io/en/latest/ + +]]></help> + <expand macro="citations" /> +</tool>