Mercurial > repos > jjohnson > arriba
diff arriba_download_reference.xml @ 2:7420753b0671 draft
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
author | jjohnson |
---|---|
date | Fri, 08 Oct 2021 19:23:48 +0000 |
parents | 9f2665b32c45 |
children | 2d32e6c86c48 |
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--- a/arriba_download_reference.xml Fri Oct 08 11:16:21 2021 +0000 +++ b/arriba_download_reference.xml Fri Oct 08 19:23:48 2021 +0000 @@ -1,17 +1,18 @@ -<tool id="arriba_download_reference" name="Arriba Download Reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5"> - <description></description> +<tool id="arriba_download_reference" name="Arriba Reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5"> + <description>Download to history</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ - echo $arriba_reference_name > '$arriba_reference' - mkdir -p '$arriba_reference.files_path' && - cd '$arriba_reference.files_path' && - BASE_DIR=$(dirname $(dirname `which arriba`)) && - REF_SCRIPT=`find $BASE_DIR -name 'download_references.sh'` && - $REF_SCRIPT '$arriba_reference_name' + echo $arriba_reference_name > '$star_index' && + 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* > '$genome_gtf' && + mv STAR*/* '$star_index.extra_files_path' ]]></command> <inputs> <param name="arriba_reference_name" type="select" label="Select reference"> @@ -56,7 +57,9 @@ </param> </inputs> <outputs> - <data name="arriba_reference" format="txt" label="$arriba_reference_name"/> + <data name="genome_fasta" format="fasta" label="${tool.name} ${arriba_reference_name} fasta"/> + <data name="genome_gtf" format="gtf" label="${tool.name} ${arriba_reference_name} GTF"/> + <data name="star_index" format="txt" label="${tool.name} ${arriba_reference_name} STAR index"/> </outputs> <help><![CDATA[ ** Arriba **