Mercurial > repos > bvalot > panisa
comparison panisa.xml @ 0:349c2fbd38a0 draft default tip
"planemo upload for repository https://github.com/bvalot/panISa commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb"
author | bvalot |
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date | Thu, 16 Jun 2022 12:37:30 +0000 |
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-1:000000000000 | 0:349c2fbd38a0 |
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1 <tool id="panisa2_wrapper" name="PanISa: IS search" version="0.1.6"> | |
2 <description>Search integrative element (IS) insertion on a genome using BAM alignment</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.1.6">panisa</requirement> | |
5 </requirements> | |
6 <stdio> | |
7 <exit_code range="1:" level="fatal" /> | |
8 </stdio> | |
9 <version_command>panISa.py -v</version_command> | |
10 <command> | |
11 panISa.py | |
12 #if str($quality) | |
13 -q $quality | |
14 #end if | |
15 #if str($minimun) | |
16 -m $minimun | |
17 #end if | |
18 #if str($size) | |
19 -s $size | |
20 #end if | |
21 #if str($percentage) | |
22 -p $percentage | |
23 #end if | |
24 '$bam' > '$output' | |
25 </command> | |
26 <inputs> | |
27 <param name="bam" type="data" | |
28 format="bam" | |
29 label="Alignment result" | |
30 help="Bam format" /> | |
31 <param name="quality" type="integer" value="20" | |
32 optional="true" | |
33 label="Minimun alignment quality value to conserve a clipped" /> | |
34 <param name="minimun" type="integer" value="5" | |
35 optional="true" | |
36 label="Minimun number of clipped reads to look at IS on a position" /> | |
37 <param name="size" type="integer" value="20" | |
38 optional="true" | |
39 label="Maximun size of direct repeat region" /> | |
40 <param name="percentage" type="float" value="0.8" | |
41 optional="true" | |
42 label="Minimum percentage of same base to create consensus" /> | |
43 </inputs> | |
44 <outputs> | |
45 <data name="output" format="tabular" label="panISa on ${bam.name}"> | |
46 <!-- <actions> --> | |
47 <!-- <action name="column_names" type="metadata" default="Chromosome,End position,End clipped reads,Direct repeats,Start position,Start clipped reads,Inverted repeats,Left sequence,Right sequence" /> --> | |
48 <!-- </actions> --> | |
49 </data> | |
50 </outputs> | |
51 <tests> | |
52 <test expect_num_outputs="1"> | |
53 <param name="bam" value="input.bam" /> | |
54 <output name="output" file="panisa.txt" ftype="tabular" /> | |
55 </test> | |
56 </tests> | |
57 <help> | |
58 **What it does** | |
59 | |
60 Search integrative element (IS) insertion on a genome using BAM alignment. | |
61 | |
62 **License and citation** | |
63 | |
64 This Galaxy tool is Copyright © 2018 `B. Valot` and is released under the `GPL3 license`. | |
65 | |
66 PanISa program was publised : | |
67 | |
68 Treepong, P., Guyeux, C., Meunier, A., Couchoud, C., Hocquet, D. et Valot, B. (2018). PanISa : Ab initio detection of insertion sequences in bacterial genomes from short read sequence | |
69 data. Bioinformatics. | |
70 </help> | |
71 <citations> | |
72 <citation type="doi">10.1093/bioinformatics/bty479</citation> | |
73 </citations> | |
74 </tool> |