Mercurial > repos > jjohnson > arriba_download_reference

comparison arriba_download_reference.xml @ 0:7345cb1bb772 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
comparison
equal deleted inserted replaced
-1:000000000000 0:7345cb1bb772
1 <tool id="arriba_download_reference" name="Arriba Reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
2 <description>Download to history</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 $arriba_reference_name > '$star_index' &&
10 BASE_DIR=\$(dirname \$(dirname `which arriba`)) &&
11 REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` &&
12 #if $is_test != 'yes'
13 \$REF_SCRIPT '$arriba_reference_name' &&
14 cp *.fa* '$genome_fasta' &&
15 cp *.gtf* '$genome_gtf' &&
16 mv STAR_index_* '$star_index.extra_files_path'
17 #else
18 [[ -x \$REF_SCRIPT ]]
19 #end if
20 ]]></command>
21 <inputs>
22 <param name="is_test" type="hidden" value="no"/>
23 <param name="arriba_reference_name" type="select" label="Select reference">
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="hg38+ENSEMBL93">hg38+ENSEMBL93</option>
31 <option value="hg38+GENCODE28">hg38+GENCODE28</option>
32 <option value="hg38+RefSeq">hg38+RefSeq</option>
33 <option value="hg38viral+ENSEMBL93">hg38viral+ENSEMBL93</option>
34 <option value="hg38viral+GENCODE28">hg38viral+GENCODE28</option>
35 <option value="hg38viral+RefSeq">hg38viral+RefSeq</option>
36 <option value="GRCh37+ENSEMBL87">GRCh37+ENSEMBL87</option>
37 <option value="GRCh37+GENCODE19">GRCh37+GENCODE19</option>
38 <option value="GRCh37+RefSeq">GRCh37+RefSeq</option>
39 <option value="GRCh37viral+ENSEMBL87">GRCh37viral+ENSEMBL87</option>
40 <option value="GRCh37viral+GENCODE19">GRCh37viral+GENCODE19</option>
41 <option value="GRCh37viral+RefSeq">GRCh37viral+RefSeq</option>
42 <option value="hg19+ENSEMBL87">hg19+ENSEMBL87</option>
43 <option value="hg19+GENCODE19">hg19+GENCODE19</option>
44 <option value="hg19+RefSeq">hg19+RefSeq</option>
45 <option value="hg19viral+ENSEMBL87">hg19viral+ENSEMBL87</option>
46 <option value="hg19viral+GENCODE19">hg19viral+GENCODE19</option>
47 <option value="hg19viral+RefSeq">hg19viral+RefSeq</option>
48 <option value="hs37d5+ENSEMBL87">hs37d5+ENSEMBL87</option>
49 <option value="hs37d5+GENCODE19">hs37d5+GENCODE19</option>
50 <option value="hs37d5+RefSeq">hs37d5+RefSeq</option>
51 <option value="hs37d5viral+ENSEMBL87">hs37d5viral+ENSEMBL87</option>
52 <option value="hs37d5viral+GENCODE19">hs37d5viral+GENCODE19</option>
53 <option value="hs37d5viral+RefSeq">hs37d5viral+RefSeq</option>
54 <option value="GRCm39+GENCODEM26">GRCm39+GENCODEM26</option>
55 <option value="GRCm39+RefSeq">GRCm39+RefSeq</option>
56 <option value="GRCm39viral+GENCODEM26">GRCm39viral+GENCODEM26</option>
57 <option value="GRCm39viral+RefSeq">GRCm39viral+RefSeq</option>
58 <option value="GRCm38+GENCODEM25">GRCm38+GENCODEM25</option>
59 <option value="GRCm38+RefSeq">GRCm38+RefSeq</option>
60 <option value="GRCm38viral+GENCODEM25">GRCm38viral+GENCODEM25</option>
61 <option value="GRCm38viral+RefSeq">GRCm38viral+RefSeq</option>
62 <option value="mm39+GENCODEM26">mm39+GENCODEM26</option>
63 <option value="mm39+RefSeq">mm39+RefSeq</option>
64 <option value="mm39viral+GENCODEM26">mm39viral+GENCODEM26</option>
65 <option value="mm39viral+RefSeq">mm39viral+RefSeq</option>
66 <option value="mm10+GENCODEM25">mm10+GENCODEM25</option>
67 <option value="mm10+RefSeq">mm10+RefSeq</option>
68 <option value="mm10viral+GENCODEM25">mm10viral+GENCODEM25</option>
69 <option value="mm10viral+RefSeq">mm10viral+RefSeq</option>
70 </param>
71 </inputs>
72 <outputs>
73 <data name="genome_fasta" format="fasta" label="${tool.name} ${arriba_reference_name} fasta"/>
74 <data name="genome_gtf" format="gtf" label="${tool.name} ${arriba_reference_name} GTF"/>
75 <data name="star_index" format="txt" label="${tool.name} ${arriba_reference_name} STAR index"/>
76 </outputs>
77 <tests>
78 <!-- Downloading a genome and annotation plus build a STAR index requires too many resources for testing.
79 Just test that we can locate the script. -->
80 <test>
81 <param name="is_test" value="yes"/>
82 <param name="arriba_reference_name" value="GRCh38+ENSEMBL93"/>
83 <output name="star_index">
84 <assert_contents>
85 <has_text text="GRCh38+ENSEMBL93"/>
86 </assert_contents>
87 </output>
88 </test>
89 </tests>
90 <help><![CDATA[
91 ** Arriba Reference **
92
93 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.
94 It is based on chimeric alignments found by the STAR RNA-Seq aligner.
95
96 **Arriba Reference** downloads a genome sequence fasta and its related annotation GTF, and then build a STAR index for the RNA STAR aligner.
97
98 These datasets will be added to your Galaxy history:
99
100 - genome assembly fasta
101 - genome annotation GTF
102 - STAR index
103
104 See Arriba manual pages:
105
106 - https://arriba.readthedocs.io/en/latest/workflow/
107 - https://arriba.readthedocs.io/en/latest/input-files/
108
109
110 **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.
111
112 .. _Arriba: https://arriba.readthedocs.io/en/latest/
113
114 ]]></help>
115 <expand macro="citations" />
116 </tool>