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comparison arriba_download_reference.xml @ 2:7420753b0671 draft

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"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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1:9f2665b32c45 2:7420753b0671
1 <tool id="arriba_download_reference" name="Arriba Download Reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5"> 1 <tool id="arriba_download_reference" name="Arriba Reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
2 <description></description> 2 <description>Download to history</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="version_command" /> 7 <expand macro="version_command" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 echo $arriba_reference_name > '$arriba_reference' 9 echo $arriba_reference_name > '$star_index' &&
10 mkdir -p '$arriba_reference.files_path' && 10 BASE_DIR=\$(dirname \$(dirname `which arriba`)) &&
11 cd '$arriba_reference.files_path' && 11 REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` &&
12 BASE_DIR=$(dirname $(dirname `which arriba`)) && 12 \$REF_SCRIPT '$arriba_reference_name' &&
13 REF_SCRIPT=`find $BASE_DIR -name 'download_references.sh'` && 13 cp *.fa* > '$genome_fasta' &&
14 $REF_SCRIPT '$arriba_reference_name' 14 cp *.gtf* > '$genome_gtf' &&
15 mv STAR*/* '$star_index.extra_files_path'
15 ]]></command> 16 ]]></command>
16 <inputs> 17 <inputs>
17 <param name="arriba_reference_name" type="select" label="Select reference"> 18 <param name="arriba_reference_name" type="select" label="Select reference">
18 <option value="GRCh37+ENSEMBL87">GRCh37+ENSEMBL87</option> 19 <option value="GRCh37+ENSEMBL87">GRCh37+ENSEMBL87</option>
19 <option value="GRCh37+GENCODE19">GRCh37+GENCODE19</option> 20 <option value="GRCh37+GENCODE19">GRCh37+GENCODE19</option>
54 <option value="mm10viral+GENCODEM25">mm10viral+GENCODEM25</option> 55 <option value="mm10viral+GENCODEM25">mm10viral+GENCODEM25</option>
55 <option value="mm10viral+RefSeq">mm10viral+RefSeq</option> 56 <option value="mm10viral+RefSeq">mm10viral+RefSeq</option>
56 </param> 57 </param>
57 </inputs> 58 </inputs>
58 <outputs> 59 <outputs>
59 <data name="arriba_reference" format="txt" label="$arriba_reference_name"/> 60 <data name="genome_fasta" format="fasta" label="${tool.name} ${arriba_reference_name} fasta"/>
61 <data name="genome_gtf" format="gtf" label="${tool.name} ${arriba_reference_name} GTF"/>
62 <data name="star_index" format="txt" label="${tool.name} ${arriba_reference_name} STAR index"/>
60 </outputs> 63 </outputs>
61 <help><![CDATA[ 64 <help><![CDATA[
62 ** Arriba ** 65 ** Arriba **
63 66
64 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions. 67 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.