Mercurial > repos > bgruening > rnaz_annotate
comparison 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 |
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date | Wed, 30 Jan 2019 04:12:06 -0500 |
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-1:000000000000 | 0:e123d5c6f489 |
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1 <tool id="rnaz_annotate" name="Annotate RNAz" version="2.1"> | |
2 <requirements> | |
3 <requirement type="package" version="2.1">rnaz</requirement> | |
4 <requirement type="package" version="3.6.7">python</requirement> | |
5 <requirement type="package" version="0.8.0">pybedtools</requirement> | |
6 </requirements> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 python3 '$__tool_directory__/AnnotateRNAz.py' | |
9 --bed '$bed' | |
10 --input '$input' | |
11 --bedout '$output1' | |
12 --rnazout '$output2' | |
13 ]]></command> | |
14 <inputs> | |
15 <param format="txt" name="input" type="data" label="RNAz output to annotate" /> | |
16 <param type="data" name="bed" format="bed" label="Bed file with annotation" /> | |
17 </inputs> | |
18 <outputs> | |
19 <data name="output1" format="bed" /> | |
20 <data name="output2" format="txt" /> | |
21 </outputs> | |
22 <tests> | |
23 <test> | |
24 <param name="input" value="unknown.rnaz.clustered"/> | |
25 <param name="bed" value="Annotation.bed"/> | |
26 <output name="output1" file="unknown.rnaz.clustered.annotated.bed"/> | |
27 <output name="output2" file="unknown.rnaz.clustered.annotated.rnaz"/> | |
28 </test> | |
29 <test> | |
30 <param name="input" value="tRNA.rnaz.clustered"/> | |
31 <param name="bed" value="Annotation.bed"/> | |
32 <output name="output1" file="tRNA.rnaz.clustered.annotated.bed"/> | |
33 <output name="output2" file="tRNA.rnaz.clustered.annotated.rnaz"/> | |
34 </test> | |
35 </tests> | |
36 <help><![CDATA[ | |
37 | |
38 Annotated rnaz hits with an annotation BED file, | |
39 replaces rnazAnnotate.pl and rnazIndex.pl. | |
40 Best used after clustering of RNAz hits. | |
41 | |
42 usage: AnnotateRNAz.py [-h] [-b BED] [-i INPUT] [-o BEDOUT] [-r RNAZOUT] | |
43 | |
44 Intersect RNAz output with Annotation from BED | |
45 | |
46 optional arguments: | |
47 -h, --help show this help message and exit | |
48 -b BED, --bed BED Annotation BED file | |
49 -i INPUT, --input INPUT (RNAz output) | |
50 -o BEDOUT, --bedout BEDOUT (Annotated BED output) | |
51 -r RNAZOUT, --rnazout RNAZOUT (Annotated rnaz-format output) | |
52 ]]> | |
53 </help> | |
54 | |
55 <citations> | |
56 <citation type="doi">10.1142/9789814295291_0009</citation> | |
57 </citations> | |
58 | |
59 </tool> |