Mercurial > repos > thanhlv > polca
comparison polca.xml.bk @ 0:b40614f1e3c7 draft default tip
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polca commit 5fc36e31ac584a66ab3dddab9e6149a3ef5c9ad3-dirty"
author | thanhlv |
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date | Thu, 22 Sep 2022 15:01:09 +0000 (2022-09-22) |
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-1:000000000000 | 0:b40614f1e3c7 |
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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> |