Mercurial > repos > jjohnson > arriba
diff 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 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/arriba_download_reference.xml Fri Oct 08 11:16:21 2021 +0000 @@ -0,0 +1,71 @@ +<tool id="arriba_download_reference" name="Arriba Download Reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5"> + <description></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' + ]]></command> + <inputs> + <param name="arriba_reference_name" type="select" label="Select reference"> + <option value="GRCh37+ENSEMBL87">GRCh37+ENSEMBL87</option> + <option value="GRCh37+GENCODE19">GRCh37+GENCODE19</option> + <option value="GRCh37+RefSeq">GRCh37+RefSeq</option> + <option value="GRCh37viral+ENSEMBL87">GRCh37viral+ENSEMBL87</option> + <option value="GRCh37viral+GENCODE19">GRCh37viral+GENCODE19</option> + <option value="GRCh37viral+RefSeq">GRCh37viral+RefSeq</option> + <option value="GRCh38+ENSEMBL93">GRCh38+ENSEMBL93</option> + <option value="GRCh38+GENCODE28">GRCh38+GENCODE28</option> + <option value="GRCh38+RefSeq">GRCh38+RefSeq</option> + <option value="GRCh38viral+ENSEMBL93">GRCh38viral+ENSEMBL93</option> + <option value="GRCh38viral+GENCODE28">GRCh38viral+GENCODE28</option> + <option value="GRCh38viral+RefSeq">GRCh38viral+RefSeq</option> + <option value="GRCm38+GENCODEM25">GRCm38+GENCODEM25</option> + <option value="GRCm38+RefSeq">GRCm38+RefSeq</option> + <option value="GRCm38viral+GENCODEM25">GRCm38viral+GENCODEM25</option> + <option value="GRCm38viral+RefSeq">GRCm38viral+RefSeq</option> + <option value="hg19+ENSEMBL87">hg19+ENSEMBL87</option> + <option value="hg19+GENCODE19">hg19+GENCODE19</option> + <option value="hg19+RefSeq">hg19+RefSeq</option> + <option value="hg19viral+ENSEMBL87">hg19viral+ENSEMBL87</option> + <option value="hg19viral+GENCODE19">hg19viral+GENCODE19</option> + <option value="hg19viral+RefSeq">hg19viral+RefSeq</option> + <option value="hg38+ENSEMBL93">hg38+ENSEMBL93</option> + <option value="hg38+GENCODE28">hg38+GENCODE28</option> + <option value="hg38+RefSeq">hg38+RefSeq</option> + <option value="hg38viral+ENSEMBL93">hg38viral+ENSEMBL93</option> + <option value="hg38viral+GENCODE28">hg38viral+GENCODE28</option> + <option value="hg38viral+RefSeq">hg38viral+RefSeq</option> + <option value="hs37d5+ENSEMBL87">hs37d5+ENSEMBL87</option> + <option value="hs37d5+GENCODE19">hs37d5+GENCODE19</option> + <option value="hs37d5+RefSeq">hs37d5+RefSeq</option> + <option value="hs37d5viral+ENSEMBL87">hs37d5viral+ENSEMBL87</option> + <option value="hs37d5viral+GENCODE19">hs37d5viral+GENCODE19</option> + <option value="hs37d5viral+RefSeq">hs37d5viral+RefSeq</option> + <option value="mm10+GENCODEM25">mm10+GENCODEM25</option> + <option value="mm10+RefSeq">mm10+RefSeq</option> + <option value="mm10viral+GENCODEM25">mm10viral+GENCODEM25</option> + <option value="mm10viral+RefSeq">mm10viral+RefSeq</option> + </param> + </inputs> + <outputs> + <data name="arriba_reference" format="txt" label="$arriba_reference_name"/> + </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>