Mercurial > repos > jjohnson > arriba_download_reference
diff arriba_download_reference.xml @ 0:7345cb1bb772 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
| author | jjohnson |
|---|---|
| date | Fri, 11 Feb 2022 19:09:19 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/arriba_download_reference.xml Fri Feb 11 19:09:19 2022 +0000 @@ -0,0 +1,116 @@ +<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 $arriba_reference_name > '$star_index' && + BASE_DIR=\$(dirname \$(dirname `which arriba`)) && + REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` && + #if $is_test != 'yes' + \$REF_SCRIPT '$arriba_reference_name' && + cp *.fa* '$genome_fasta' && + cp *.gtf* '$genome_gtf' && + mv STAR_index_* '$star_index.extra_files_path' + #else + [[ -x \$REF_SCRIPT ]] + #end if + ]]></command> + <inputs> + <param name="is_test" type="hidden" value="no"/> + <param name="arriba_reference_name" type="select" label="Select reference"> + <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="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="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="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="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="GRCm39+GENCODEM26">GRCm39+GENCODEM26</option> + <option value="GRCm39+RefSeq">GRCm39+RefSeq</option> + <option value="GRCm39viral+GENCODEM26">GRCm39viral+GENCODEM26</option> + <option value="GRCm39viral+RefSeq">GRCm39viral+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="mm39+GENCODEM26">mm39+GENCODEM26</option> + <option value="mm39+RefSeq">mm39+RefSeq</option> + <option value="mm39viral+GENCODEM26">mm39viral+GENCODEM26</option> + <option value="mm39viral+RefSeq">mm39viral+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="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> + <tests> + <!-- Downloading a genome and annotation plus build a STAR index requires too many resources for testing. + Just test that we can locate the script. --> + <test> + <param name="is_test" value="yes"/> + <param name="arriba_reference_name" value="GRCh38+ENSEMBL93"/> + <output name="star_index"> + <assert_contents> + <has_text text="GRCh38+ENSEMBL93"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +** Arriba Reference ** + +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 Reference** downloads a genome sequence fasta and its related annotation GTF, and then build a STAR index for the RNA STAR aligner. + +These datasets will be added to your Galaxy history: + + - genome assembly fasta + - genome annotation GTF + - STAR index + +See Arriba manual pages: + + - https://arriba.readthedocs.io/en/latest/workflow/ + - https://arriba.readthedocs.io/en/latest/input-files/ + + +**NOTE:** This is a resource intensive process, so the results should be copied to new histories as needed rather than running this in each workflow. + +.. _Arriba: https://arriba.readthedocs.io/en/latest/ + +]]></help> + <expand macro="citations" /> +</tool>