Mercurial > repos > jjohnson > arriba
comparison arriba_download_reference.xml @ 1:9f2665b32c45 draft
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
| author | jjohnson |
|---|---|
| date | Fri, 08 Oct 2021 11:16:21 +0000 |
| parents | |
| children | 7420753b0671 |
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| 0:5ebf2354cc9b | 1:9f2665b32c45 |
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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"> | |
| 2 <description></description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="version_command" /> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 echo $arriba_reference_name > '$arriba_reference' | |
| 10 mkdir -p '$arriba_reference.files_path' && | |
| 11 cd '$arriba_reference.files_path' && | |
| 12 BASE_DIR=$(dirname $(dirname `which arriba`)) && | |
| 13 REF_SCRIPT=`find $BASE_DIR -name 'download_references.sh'` && | |
| 14 $REF_SCRIPT '$arriba_reference_name' | |
| 15 ]]></command> | |
| 16 <inputs> | |
| 17 <param name="arriba_reference_name" type="select" label="Select reference"> | |
| 18 <option value="GRCh37+ENSEMBL87">GRCh37+ENSEMBL87</option> | |
| 19 <option value="GRCh37+GENCODE19">GRCh37+GENCODE19</option> | |
| 20 <option value="GRCh37+RefSeq">GRCh37+RefSeq</option> | |
| 21 <option value="GRCh37viral+ENSEMBL87">GRCh37viral+ENSEMBL87</option> | |
| 22 <option value="GRCh37viral+GENCODE19">GRCh37viral+GENCODE19</option> | |
| 23 <option value="GRCh37viral+RefSeq">GRCh37viral+RefSeq</option> | |
| 24 <option value="GRCh38+ENSEMBL93">GRCh38+ENSEMBL93</option> | |
| 25 <option value="GRCh38+GENCODE28">GRCh38+GENCODE28</option> | |
| 26 <option value="GRCh38+RefSeq">GRCh38+RefSeq</option> | |
| 27 <option value="GRCh38viral+ENSEMBL93">GRCh38viral+ENSEMBL93</option> | |
| 28 <option value="GRCh38viral+GENCODE28">GRCh38viral+GENCODE28</option> | |
| 29 <option value="GRCh38viral+RefSeq">GRCh38viral+RefSeq</option> | |
| 30 <option value="GRCm38+GENCODEM25">GRCm38+GENCODEM25</option> | |
| 31 <option value="GRCm38+RefSeq">GRCm38+RefSeq</option> | |
| 32 <option value="GRCm38viral+GENCODEM25">GRCm38viral+GENCODEM25</option> | |
| 33 <option value="GRCm38viral+RefSeq">GRCm38viral+RefSeq</option> | |
| 34 <option value="hg19+ENSEMBL87">hg19+ENSEMBL87</option> | |
| 35 <option value="hg19+GENCODE19">hg19+GENCODE19</option> | |
| 36 <option value="hg19+RefSeq">hg19+RefSeq</option> | |
| 37 <option value="hg19viral+ENSEMBL87">hg19viral+ENSEMBL87</option> | |
| 38 <option value="hg19viral+GENCODE19">hg19viral+GENCODE19</option> | |
| 39 <option value="hg19viral+RefSeq">hg19viral+RefSeq</option> | |
| 40 <option value="hg38+ENSEMBL93">hg38+ENSEMBL93</option> | |
| 41 <option value="hg38+GENCODE28">hg38+GENCODE28</option> | |
| 42 <option value="hg38+RefSeq">hg38+RefSeq</option> | |
| 43 <option value="hg38viral+ENSEMBL93">hg38viral+ENSEMBL93</option> | |
| 44 <option value="hg38viral+GENCODE28">hg38viral+GENCODE28</option> | |
| 45 <option value="hg38viral+RefSeq">hg38viral+RefSeq</option> | |
| 46 <option value="hs37d5+ENSEMBL87">hs37d5+ENSEMBL87</option> | |
| 47 <option value="hs37d5+GENCODE19">hs37d5+GENCODE19</option> | |
| 48 <option value="hs37d5+RefSeq">hs37d5+RefSeq</option> | |
| 49 <option value="hs37d5viral+ENSEMBL87">hs37d5viral+ENSEMBL87</option> | |
| 50 <option value="hs37d5viral+GENCODE19">hs37d5viral+GENCODE19</option> | |
| 51 <option value="hs37d5viral+RefSeq">hs37d5viral+RefSeq</option> | |
| 52 <option value="mm10+GENCODEM25">mm10+GENCODEM25</option> | |
| 53 <option value="mm10+RefSeq">mm10+RefSeq</option> | |
| 54 <option value="mm10viral+GENCODEM25">mm10viral+GENCODEM25</option> | |
| 55 <option value="mm10viral+RefSeq">mm10viral+RefSeq</option> | |
| 56 </param> | |
| 57 </inputs> | |
| 58 <outputs> | |
| 59 <data name="arriba_reference" format="txt" label="$arriba_reference_name"/> | |
| 60 </outputs> | |
| 61 <help><![CDATA[ | |
| 62 ** Arriba ** | |
| 63 | |
| 64 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions. | |
| 65 It is based on chimeric alignments found by the STAR RNA-Seq aligner. | |
| 66 | |
| 67 .. _Arriba: https://arriba.readthedocs.io/en/latest/ | |
| 68 | |
| 69 ]]></help> | |
| 70 <expand macro="citations" /> | |
| 71 </tool> |