Mercurial > repos > jjohnson > arriba
comparison 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 |
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date | Fri, 08 Oct 2021 19:23:48 +0000 |
parents | 9f2665b32c45 |
children | 2d32e6c86c48 |
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1:9f2665b32c45 | 2:7420753b0671 |
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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. |