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comparison rnazAnnotate.xml @ 0:e123d5c6f489 draft default tip

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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
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-1:000000000000 0:e123d5c6f489
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>