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comparison arriba_download_reference.xml @ 5:005b200c8841 draft

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"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
author jjohnson
date Sun, 10 Oct 2021 13:00:45 +0000
parents 77021ad5037d
children 8c4c97fd0555
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4:77021ad5037d 5:005b200c8841
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 $arriba_reference_name > '$star_index' && 9 echo $arriba_reference_name > '$star_index' &&
10 BASE_DIR=\$(dirname \$(dirname `which arriba`)) && 10 BASE_DIR=\$(dirname \$(dirname `which arriba`)) &&
11 REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` && 11 REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` &&
12 #if $is_test != 'yes'
12 \$REF_SCRIPT '$arriba_reference_name' && 13 \$REF_SCRIPT '$arriba_reference_name' &&
13 cp *.fa* '$genome_fasta' && 14 cp *.fa* '$genome_fasta' &&
14 cp *.gtf* '$genome_gtf' && 15 cp *.gtf* '$genome_gtf' &&
15 mv STAR_index_* '$star_index.extra_files_path' 16 mv STAR_index_* '$star_index.extra_files_path'
17 #else
18 [[ -x \$REF_SCRIPT ]]
19 #end if
16 ]]></command> 20 ]]></command>
17 <inputs> 21 <inputs>
22 <param name="is_test" type="hidden" value="no"/>
18 <param name="arriba_reference_name" type="select" label="Select reference"> 23 <param name="arriba_reference_name" type="select" label="Select reference">
19 <option value="GRCh37+ENSEMBL87">GRCh37+ENSEMBL87</option> 24
20 <option value="GRCh37+GENCODE19">GRCh37+GENCODE19</option>
21 <option value="GRCh37+RefSeq">GRCh37+RefSeq</option>
22 <option value="GRCh37viral+ENSEMBL87">GRCh37viral+ENSEMBL87</option>
23 <option value="GRCh37viral+GENCODE19">GRCh37viral+GENCODE19</option>
24 <option value="GRCh37viral+RefSeq">GRCh37viral+RefSeq</option>
25 <option value="GRCh38+ENSEMBL93">GRCh38+ENSEMBL93</option> 25 <option value="GRCh38+ENSEMBL93">GRCh38+ENSEMBL93</option>
26 <option value="GRCh38+GENCODE28">GRCh38+GENCODE28</option> 26 <option value="GRCh38+GENCODE28">GRCh38+GENCODE28</option>
27 <option value="GRCh38+RefSeq">GRCh38+RefSeq</option> 27 <option value="GRCh38+RefSeq">GRCh38+RefSeq</option>
28 <option value="GRCh38viral+ENSEMBL93">GRCh38viral+ENSEMBL93</option> 28 <option value="GRCh38viral+ENSEMBL93">GRCh38viral+ENSEMBL93</option>
29 <option value="GRCh38viral+GENCODE28">GRCh38viral+GENCODE28</option> 29 <option value="GRCh38viral+GENCODE28">GRCh38viral+GENCODE28</option>
30 <option value="GRCh38viral+RefSeq">GRCh38viral+RefSeq</option> 30 <option value="GRCh38viral+RefSeq">GRCh38viral+RefSeq</option>
31 <option value="GRCm38+GENCODEM25">GRCm38+GENCODEM25</option> 31 <option value="GRCm38+GENCODEM25">GRCm38+GENCODEM25</option>
32 <option value="GRCm38+RefSeq">GRCm38+RefSeq</option> 32 <option value="GRCm38+RefSeq">GRCm38+RefSeq</option>
33 <option value="GRCm38viral+GENCODEM25">GRCm38viral+GENCODEM25</option> 33 <option value="GRCm38viral+GENCODEM25">GRCm38viral+GENCODEM25</option>
34 <option value="GRCm38viral+RefSeq">GRCm38viral+RefSeq</option> 34 <option value="GRCm38viral+RefSeq">GRCm38viral+RefSeq</option>
35 <option value="hg38+ENSEMBL93">hg38+ENSEMBL93</option>
36 <option value="hg38+GENCODE28">hg38+GENCODE28</option>
37 <option value="hg38+RefSeq">hg38+RefSeq</option>
38 <option value="hg38viral+ENSEMBL93">hg38viral+ENSEMBL93</option>
39 <option value="hg38viral+GENCODE28">hg38viral+GENCODE28</option>
40 <option value="hg38viral+RefSeq">hg38viral+RefSeq</option>
41 <option value="GRCh37+ENSEMBL87">GRCh37+ENSEMBL87</option>
42 <option value="GRCh37+GENCODE19">GRCh37+GENCODE19</option>
43 <option value="GRCh37+RefSeq">GRCh37+RefSeq</option>
44 <option value="GRCh37viral+ENSEMBL87">GRCh37viral+ENSEMBL87</option>
45 <option value="GRCh37viral+GENCODE19">GRCh37viral+GENCODE19</option>
46 <option value="GRCh37viral+RefSeq">GRCh37viral+RefSeq</option>
35 <option value="hg19+ENSEMBL87">hg19+ENSEMBL87</option> 47 <option value="hg19+ENSEMBL87">hg19+ENSEMBL87</option>
36 <option value="hg19+GENCODE19">hg19+GENCODE19</option> 48 <option value="hg19+GENCODE19">hg19+GENCODE19</option>
37 <option value="hg19+RefSeq">hg19+RefSeq</option> 49 <option value="hg19+RefSeq">hg19+RefSeq</option>
38 <option value="hg19viral+ENSEMBL87">hg19viral+ENSEMBL87</option> 50 <option value="hg19viral+ENSEMBL87">hg19viral+ENSEMBL87</option>
39 <option value="hg19viral+GENCODE19">hg19viral+GENCODE19</option> 51 <option value="hg19viral+GENCODE19">hg19viral+GENCODE19</option>
40 <option value="hg19viral+RefSeq">hg19viral+RefSeq</option> 52 <option value="hg19viral+RefSeq">hg19viral+RefSeq</option>
41 <option value="hg38+ENSEMBL93">hg38+ENSEMBL93</option>
42 <option value="hg38+GENCODE28">hg38+GENCODE28</option>
43 <option value="hg38+RefSeq">hg38+RefSeq</option>
44 <option value="hg38viral+ENSEMBL93">hg38viral+ENSEMBL93</option>
45 <option value="hg38viral+GENCODE28">hg38viral+GENCODE28</option>
46 <option value="hg38viral+RefSeq">hg38viral+RefSeq</option>
47 <option value="hs37d5+ENSEMBL87">hs37d5+ENSEMBL87</option> 53 <option value="hs37d5+ENSEMBL87">hs37d5+ENSEMBL87</option>
48 <option value="hs37d5+GENCODE19">hs37d5+GENCODE19</option> 54 <option value="hs37d5+GENCODE19">hs37d5+GENCODE19</option>
49 <option value="hs37d5+RefSeq">hs37d5+RefSeq</option> 55 <option value="hs37d5+RefSeq">hs37d5+RefSeq</option>
50 <option value="hs37d5viral+ENSEMBL87">hs37d5viral+ENSEMBL87</option> 56 <option value="hs37d5viral+ENSEMBL87">hs37d5viral+ENSEMBL87</option>
51 <option value="hs37d5viral+GENCODE19">hs37d5viral+GENCODE19</option> 57 <option value="hs37d5viral+GENCODE19">hs37d5viral+GENCODE19</option>
59 <outputs> 65 <outputs>
60 <data name="genome_fasta" format="fasta" label="${tool.name} ${arriba_reference_name} fasta"/> 66 <data name="genome_fasta" format="fasta" label="${tool.name} ${arriba_reference_name} fasta"/>
61 <data name="genome_gtf" format="gtf" label="${tool.name} ${arriba_reference_name} GTF"/> 67 <data name="genome_gtf" format="gtf" label="${tool.name} ${arriba_reference_name} GTF"/>
62 <data name="star_index" format="txt" label="${tool.name} ${arriba_reference_name} STAR index"/> 68 <data name="star_index" format="txt" label="${tool.name} ${arriba_reference_name} STAR index"/>
63 </outputs> 69 </outputs>
70 <tests>
71 <!-- Downloading a genome and annotation plus build a STAR index requires too many resources for testing.
72 Just test that we can locate the script. -->
73 <test>
74 <param name="is_test" value="yes"/>
75 <param name="arriba_reference_name" value="GRCh38+ENSEMBL93"/>
76 <output name="star_index">
77 <assert_contents>
78 <has_text text="GRCh38+ENSEMBL93"/>
79 </assert_contents>
80 </output>
81
82 </test>
83 </tests>
64 <help><![CDATA[ 84 <help><![CDATA[
65 ** Arriba ** 85 ** Arriba Reference **
66 86
67 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions. 87 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.
68 It is based on chimeric alignments found by the STAR RNA-Seq aligner. 88 It is based on chimeric alignments found by the STAR RNA-Seq aligner.
89
90 **Arriba Reference** downloads a genome sequence fasta and its related annoation GTF, and then build a STAR index for the RNA STAR aligner.
91
92 These datasets will be added to your Galaxy history:
93
94 - genome assembly fasta
95 - genome annotation GTF
96 - STAR index
97
98 See Arriba manual pages:
99
100 - https://arriba.readthedocs.io/en/latest/workflow/
101 - https://arriba.readthedocs.io/en/latest/input-files/
102
103
104 **NOTE:** This is a resource intensive process, so the results should be copies to new histories as needed rather than running this in each workflow.
69 105
70 .. _Arriba: https://arriba.readthedocs.io/en/latest/ 106 .. _Arriba: https://arriba.readthedocs.io/en/latest/
71 107
72 ]]></help> 108 ]]></help>
73 <expand macro="citations" /> 109 <expand macro="citations" />