Mercurial > repos > iuc > lofreq_indelqual

comparison lofreq_indelqual.xml @ 0:5d6a078d30b0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
author iuc
date Tue, 17 Dec 2019 17:26:54 -0500
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children 354b534eeab7
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-1:000000000000 0:5d6a078d30b0
1 <tool id="lofreq_indelqual" name="Insert indel qualities" version="@WRAPPER_VERSION@0">
2 <description>into a BAM file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 #if $strategy.selector == 'dindel'
9 #set $reference_source = $strategy.reference_source
10 @PREPARE_REF@
11 #end if
12 lofreq indelqual
13 #if $strategy.selector == 'dindel'
14 --dindel
15 --ref $reference_fasta_fn
16 #else
17 #if $strategy.deletions
18 --uniform $strategy.insertions,$strategy.deletions
19 #else
20 --uniform $strategy.insertions
21 #end if
22 #end if
23 -o output.bam $reads
24 ]]></command>
25 <inputs>
26 <param type="data" name="reads" format="bam" label="Reads" />
27 <conditional name="strategy">
28 <param name="selector" type="select" label="Indel calculation approach">
29 <option value="uniform">Uniform</option>
30 <option value="dindel">Dindel</option>
31 </param>
32 <when value="uniform">
33 <param name="insertions" type="integer" value="30" label="Indel quality to add" help="Should probably not be left at the default value" />
34 <param name="deletions" type="integer" optional="true" label="Separate deletion quality" help="Leave blank to use the same values for insertions and deletions" />
35 </when>
36 <when value="dindel">
37 <expand macro="reference_interface" />
38 </when>
39 </conditional>
40 </inputs>
41 <outputs>
42 <data name="output" format="bam" from_work_dir="output.bam" label="Add indel qualities to data ${reads.dataset.hid}" />
43 </outputs>
44 <tests>
45 <test>
46 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
47 <param name="selector" value="uniform" />
48 <param name="insertions" value="20" />
49 <param name="deletions" value="30" />
50 <output name="output" file="indelqual-out1.bam" />
51 </test>
52 <test>
53 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
54 <param name="selector" value="dindel" />
55 <param name="ref_selector" value="history" />
56 <param name="ref" ftype="fasta" value="pBR322.fa" />
57 <output name="output" file="indelqual-out2.bam" />
58 </test>
59 <test>
60 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
61 <param name="selector" value="uniform" />
62 <param name="insertions" value="20" />
63 <output name="output" file="indelqual-out3.bam" />
64 </test>
65 </tests>
66 <help><![CDATA[
67 Insert indel qualities into BAM file
68
69 The tool has two modes: 'uniform' and 'dindel':
70 - 'uniform' will assign a given value uniformly, whereas
71 - 'dindel' will insert indel qualities based on Dindel.
72
73 Both will overwrite any existing values. Do not realign your BAM file afterwards!
74 ]]></help>
75 <expand macro="citations">
76 <citation type="doi">10.1101/gr.112326.110</citation>
77 </expand>
78 </tool>