Mercurial > repos > bgruening > rnaz_annotate
annotate rnazAnnotate.xml @ 0:e123d5c6f489 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
author | bgruening |
---|---|
date | Wed, 30 Jan 2019 04:12:06 -0500 |
parents | |
children |
rev | line source |
---|---|
0
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
1 <tool id="rnaz_annotate" name="Annotate RNAz" version="2.1"> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
2 <requirements> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
3 <requirement type="package" version="2.1">rnaz</requirement> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
4 <requirement type="package" version="3.6.7">python</requirement> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
5 <requirement type="package" version="0.8.0">pybedtools</requirement> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
6 </requirements> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
7 <command detect_errors="exit_code"><![CDATA[ |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
8 python3 '$__tool_directory__/AnnotateRNAz.py' |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
9 --bed '$bed' |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
10 --input '$input' |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
11 --bedout '$output1' |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
12 --rnazout '$output2' |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
13 ]]></command> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
14 <inputs> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
15 <param format="txt" name="input" type="data" label="RNAz output to annotate" /> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
16 <param type="data" name="bed" format="bed" label="Bed file with annotation" /> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
17 </inputs> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
18 <outputs> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
19 <data name="output1" format="bed" /> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
20 <data name="output2" format="txt" /> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
21 </outputs> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
22 <tests> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
23 <test> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
24 <param name="input" value="unknown.rnaz.clustered"/> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
25 <param name="bed" value="Annotation.bed"/> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
26 <output name="output1" file="unknown.rnaz.clustered.annotated.bed"/> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
27 <output name="output2" file="unknown.rnaz.clustered.annotated.rnaz"/> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
28 </test> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
29 <test> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
30 <param name="input" value="tRNA.rnaz.clustered"/> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
31 <param name="bed" value="Annotation.bed"/> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
32 <output name="output1" file="tRNA.rnaz.clustered.annotated.bed"/> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
33 <output name="output2" file="tRNA.rnaz.clustered.annotated.rnaz"/> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
34 </test> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
35 </tests> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
36 <help><![CDATA[ |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
37 |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
38 Annotated rnaz hits with an annotation BED file, |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
39 replaces rnazAnnotate.pl and rnazIndex.pl. |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
40 Best used after clustering of RNAz hits. |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
41 |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
42 usage: AnnotateRNAz.py [-h] [-b BED] [-i INPUT] [-o BEDOUT] [-r RNAZOUT] |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
43 |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
44 Intersect RNAz output with Annotation from BED |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
45 |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
46 optional arguments: |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
47 -h, --help show this help message and exit |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
48 -b BED, --bed BED Annotation BED file |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
49 -i INPUT, --input INPUT (RNAz output) |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
50 -o BEDOUT, --bedout BEDOUT (Annotated BED output) |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
51 -r RNAZOUT, --rnazout RNAZOUT (Annotated rnaz-format output) |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
52 ]]> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
53 </help> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
54 |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
55 <citations> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
56 <citation type="doi">10.1142/9789814295291_0009</citation> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
57 </citations> |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
58 |
e123d5c6f489
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
bgruening
parents:
diff
changeset
|
59 </tool> |