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"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
author thanhlv
date Thu, 22 Sep 2022 15:01:09 +0000
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-1:000000000000 0:b40614f1e3c7
1 <tool id="polca" name="polca" version="@VERSION@">
2 <description> Minimal but speedy quality control for nanopore reads</description>
3 <macros>
4 <token name="@VERSION@">4.0.9</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@VERSION@">masurca</requirement>
8 </requirements>
9 <version_command>polca --version</version_command>
10 <command detect_errors="exit_code"><![CDATA[
11 #if $short_reads.sr_type == 'paired'
12 ln -s '$short_read.R1' reads_1.fastq.gz &&
13 ln -s '$short_read.R2' reads_2.fastq.gz &&
14 #else if str($short_reads.sr_type) == "collection"
15 ln -s '$short_read.input1.forward' reads_1.fastq.gz &&
16 ln -s '$short_read.input1.reverse' reads_2.fastq.gz &&
17 #end if
18 ln -s '${contigs}' contigs &&
19 polca.sh -a contigs.fa
20 -r reads1.fastq.gz reads2.fastq.gz
21 -t \${GALAXY_SLOTS:-4}
22 -m 1G
23 $no_fix
24 ]]> </command>
25
26 <inputs>
27 <param name="contigs" type="data" format="fasta,fasta.gz" label="Assembly"/>
28 <conditional name="short_reads">
29 <param name="sr_type" type="select" label="Input reads type or collection" help="Select 'paired end' for a single library or 'collection' for a paired end collection">
30 <option value="paired" selected="true">Paired End</option>
31 <option value="collection">Paired Collection</option>
32 </param>
33 <when value="paired">
34 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
35 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
36 </when>
37 <when value="collection">
38 <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/>
39 </when>
40 </conditional>
41 <param argument="no_fix" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Do not fix errors when found." />
42 </inputs>
43 <outputs>
44 <data name="contigs" format="fasta" from_work_dir="contigs.PolcaCorrected.fa" label="${tool.name} on ${on_string} Polished assembly" />
45 <data name="report" format="fasta" from_work_dir="contigs.report" label="${tool.name} on ${on_string} Polished assembly" />
46 </outputs>
47 <help><![CDATA[
48 ]]> </help>
49 </tool>