annotate arriba_download_reference.xml @ 2:7420753b0671 draft

"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
author jjohnson
date Fri, 08 Oct 2021 19:23:48 +0000
parents 9f2665b32c45
children 2d32e6c86c48
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
jjohnson
parents: 1
diff changeset
1 <tool id="arriba_download_reference" name="Arriba Reference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
jjohnson
parents: 1
diff changeset
2 <description>Download to history</description>
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
3 <macros>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
4 <import>macros.xml</import>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
5 </macros>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
6 <expand macro="requirements" />
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
7 <expand macro="version_command" />
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
2
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
jjohnson
parents: 1
diff changeset
9 echo $arriba_reference_name > '$star_index' &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
jjohnson
parents: 1
diff changeset
10 BASE_DIR=\$(dirname \$(dirname `which arriba`)) &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
jjohnson
parents: 1
diff changeset
11 REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
jjohnson
parents: 1
diff changeset
12 \$REF_SCRIPT '$arriba_reference_name' &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
jjohnson
parents: 1
diff changeset
13 cp *.fa* > '$genome_fasta' &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
jjohnson
parents: 1
diff changeset
14 cp *.gtf* > '$genome_gtf' &&
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
jjohnson
parents: 1
diff changeset
15 mv STAR*/* '$star_index.extra_files_path'
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
16 ]]></command>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
17 <inputs>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
18 <param name="arriba_reference_name" type="select" label="Select reference">
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
19 <option value="GRCh37+ENSEMBL87">GRCh37+ENSEMBL87</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
20 <option value="GRCh37+GENCODE19">GRCh37+GENCODE19</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
21 <option value="GRCh37+RefSeq">GRCh37+RefSeq</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
22 <option value="GRCh37viral+ENSEMBL87">GRCh37viral+ENSEMBL87</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
23 <option value="GRCh37viral+GENCODE19">GRCh37viral+GENCODE19</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
24 <option value="GRCh37viral+RefSeq">GRCh37viral+RefSeq</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
25 <option value="GRCh38+ENSEMBL93">GRCh38+ENSEMBL93</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
26 <option value="GRCh38+GENCODE28">GRCh38+GENCODE28</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
27 <option value="GRCh38+RefSeq">GRCh38+RefSeq</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
28 <option value="GRCh38viral+ENSEMBL93">GRCh38viral+ENSEMBL93</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
29 <option value="GRCh38viral+GENCODE28">GRCh38viral+GENCODE28</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
30 <option value="GRCh38viral+RefSeq">GRCh38viral+RefSeq</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
31 <option value="GRCm38+GENCODEM25">GRCm38+GENCODEM25</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
32 <option value="GRCm38+RefSeq">GRCm38+RefSeq</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
33 <option value="GRCm38viral+GENCODEM25">GRCm38viral+GENCODEM25</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
34 <option value="GRCm38viral+RefSeq">GRCm38viral+RefSeq</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
35 <option value="hg19+ENSEMBL87">hg19+ENSEMBL87</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
36 <option value="hg19+GENCODE19">hg19+GENCODE19</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
37 <option value="hg19+RefSeq">hg19+RefSeq</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
38 <option value="hg19viral+ENSEMBL87">hg19viral+ENSEMBL87</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
39 <option value="hg19viral+GENCODE19">hg19viral+GENCODE19</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
40 <option value="hg19viral+RefSeq">hg19viral+RefSeq</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
41 <option value="hg38+ENSEMBL93">hg38+ENSEMBL93</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
42 <option value="hg38+GENCODE28">hg38+GENCODE28</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
43 <option value="hg38+RefSeq">hg38+RefSeq</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
44 <option value="hg38viral+ENSEMBL93">hg38viral+ENSEMBL93</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
45 <option value="hg38viral+GENCODE28">hg38viral+GENCODE28</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
46 <option value="hg38viral+RefSeq">hg38viral+RefSeq</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
47 <option value="hs37d5+ENSEMBL87">hs37d5+ENSEMBL87</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
48 <option value="hs37d5+GENCODE19">hs37d5+GENCODE19</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
49 <option value="hs37d5+RefSeq">hs37d5+RefSeq</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
50 <option value="hs37d5viral+ENSEMBL87">hs37d5viral+ENSEMBL87</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
51 <option value="hs37d5viral+GENCODE19">hs37d5viral+GENCODE19</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
52 <option value="hs37d5viral+RefSeq">hs37d5viral+RefSeq</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
53 <option value="mm10+GENCODEM25">mm10+GENCODEM25</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
54 <option value="mm10+RefSeq">mm10+RefSeq</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
55 <option value="mm10viral+GENCODEM25">mm10viral+GENCODEM25</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
56 <option value="mm10viral+RefSeq">mm10viral+RefSeq</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
57 </param>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
58 </inputs>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
59 <outputs>
2
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
jjohnson
parents: 1
diff changeset
60 <data name="genome_fasta" format="fasta" label="${tool.name} ${arriba_reference_name} fasta"/>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
jjohnson
parents: 1
diff changeset
61 <data name="genome_gtf" format="gtf" label="${tool.name} ${arriba_reference_name} GTF"/>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
jjohnson
parents: 1
diff changeset
62 <data name="star_index" format="txt" label="${tool.name} ${arriba_reference_name} STAR index"/>
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
63 </outputs>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
64 <help><![CDATA[
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
65 ** Arriba **
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
66
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
67 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
68 It is based on chimeric alignments found by the STAR RNA-Seq aligner.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
69
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
70 .. _Arriba: https://arriba.readthedocs.io/en/latest/
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
71
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
72 ]]></help>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
73 <expand macro="citations" />
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents:
diff changeset
74 </tool>