Mercurial > repos > iuc > lofreq_viterbi

comparison lofreq_viterbi.xml @ 0:33a416e1659e 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 17:25:37 -0500
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1 <tool id="lofreq_viterbi" name="Realign reads" version="@WRAPPER_VERSION@0" python_template_version="3.5">
2 <description>with LoFreq viterbi</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="1.9">samtools</requirement>
8 </expand>
9 <command detect_errors="exit_code"><![CDATA[
10 @PREPARE_REF@
11 lofreq viterbi --ref '$reference_fasta_fn' --out - $keepflags --defqual $defqual '$reads' | samtools sort - -O BAM -o '$realigned'
12 ]]></command>
13 <inputs>
14 <param name="reads" type="data" format="bam" label="Reads to realign" />
15 <expand macro="reference_interface" />
16 <param argument="--keepflags" type="boolean" truevalue="--keepflags" label="Don't delete flags MC, MD, NM, and A" help="These flags are all prone to changing during realignment" />
17 <param argument="--defqual" type="integer" value="-1" label="Quality to assume for all bases with BQ2" />
18 </inputs>
19 <outputs>
20 <data name="realigned" format="bam" label="${tool.name} on ${on_string}: Realigned reads" />
21 </outputs>
22 <tests>
23 <test>
24 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
25 <param name="ref_selector" value="history" />
26 <param name="ref" ftype="fasta" value="pBR322.fa" />
27 <output name="realigned" file="viterbi-out1.bam" />
28 </test>
29 <test>
30 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
31 <param name="ref_selector" value="history" />
32 <param name="keepflags" value="true" />
33 <param name="ref" ftype="fasta" value="pBR322.fa" />
34 <output name="realigned" file="viterbi-out2.bam" />
35 </test>
36 </tests>
37 <help><![CDATA[
38 Usage: lofreq viterbi [options] in.bam
39
40 Options:
41 -f | --ref FILE Indexed reference fasta file [null]
42 -k | --keepflags Don't delete flags MC, MD, NM and A, which are all prone to change during realignment.
43 -q | --defqual INT Assume INT as quality for all bases with BQ2. Default (=-1) is to use median quality of bases in read.
44 -o | --out FILE Output BAM file [- = stdout = default]
45 --verbose Be verbose
46
47 NOTE: Output BAM file will (likely) be unsorted (use samtools sort, e.g. lofreq viterbi ... | samtools sort -')
48
49 ]]></help>
50 <expand macro="citations" />
51 </tool>