Mercurial > repos > thanhlv > polypolish

comparison polypolish.xml @ 0:3c7cbfb8f43d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polypolish commit e855ff93b8b8493f8f061895d111885b938655e8-dirty"
author thanhlv
date Thu, 22 Sep 2022 13:42:49 +0000
parents
children a38f6a0ebbf9
comparison
equal deleted inserted replaced
-1:000000000000 0:3c7cbfb8f43d
1 <tool id="polypolish" name="polypolish" version="@VERSION@">
2 <description> Polishing genome assemblies with short reads</description>
3 <macros>
4 <token name="@VERSION@">0.5.0</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@VERSION@">polypolish</requirement>
8 <requirement type="package" version="1.15.1">samtools</requirement>
9 <requirement type="package" version="0.7.17">bwa</requirement>
10 </requirements>
11 <version_command>polypolish --version</version_command>
12 <command detect_errors="exit_code"><![CDATA[
13 #if $short_reads.sr_type == 'paired'
14 ln -s '$short_read.R1' reads_1.fastq.gz &&
15 ln -s '$short_read.R2' reads_2.fastq.gz &&
16 #else if str($short_reads.sr_type) == "collection"
17 ln -s '$short_read.input1.forward' reads_1.fastq.gz &&
18 ln -s '$short_read.input1.reverse' reads_2.fastq.gz &&
19 #end if
20
21 ln -s '${assembly}' draft.fa &&
22 bwa index draft.fa &&
23 bwa mem -t \${GALAXY_SLOTS:-4} -a draft.fa reads_1.fastq.gz > alignments_1.sam &&
24 bwa mem -t \${GALAXY_SLOTS:-4} -a draft.fa reads_2.fastq.gz > alignments_2.sam &&
25 polypolish_insert_filter.py --in1 alignments_1.sam --in2 alignments_2.sam --out1 filtered_1.sam --out2 filtered_2.sam &&
26 polypolish
27 #if $debug
28 $debug debug.tsv
29 #end if
30 -d ${min_depth}
31 -i ${fraction_invalid}
32 -m ${max_errors}
33 -v ${fraction_valid}
34 draft.fasta filtered_1.sam filtered_2.sam
35 > polished.fasta
36 ]]> </command>
37
38 <inputs>
39 <param name="basecalled" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Basecalled data"/>
40 <conditional name="short_reads">
41 <param name="sr_type" type="select" label="Input reads type or collection" help="Select 'paired end' for a single library or 'collection' for a paired end collection">
42 <option value="paired" selected="true">Paired End</option>
43 <option value="collection">Paired Collection</option>
44 </param>
45 <when value="paired">
46 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
47 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
48 </when>
49 <when value="collection">
50 <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/>
51 </when>
52 </conditional>
53 <param argument="min_depth" type="integer" value="5" min="1" label="Minimum depth" />
54 <param argument="fraction_invalid" type="float" value="0.2" min="0.0" max="1.0" label="Fraction value of the read depth to be considered invalid" />
55 <param argument="fraction_valid" type="integer" value="10" min="1" label="Ignore alignments with more than this many mismatches and indels" />
56 <param argument="max_errors" type="integer" value="10" min="1" label="Fraction value of the read depth to be considered invalid" />
57 <param argument="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Debug output" />
58 </inputs>
59 <outputs>
60 <data name="polished" format="fasta" from_work_dir="polished.fasta" label="${tool.name} on ${on_string} Polished assembly" />
61 <data name="debug" format="tabular" from_work_dir="debug.tsv" label="${tool.name} on ${on_string} Polished assembly" >
62 <filter>debug is True</filter>
63 </data>
64 </outputs>
65 <help><![CDATA[
66 ]]> </help>
67 </tool>