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comparison polypolish.xml @ 1:a38f6a0ebbf9 draft

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"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/polypolish commit f361210f97bf2dfa63c2267193eca3163e17f78a-dirty"
author thanhlv
date Fri, 23 Sep 2022 23:26:59 +0000
parents 3c7cbfb8f43d
children 96580cd76488
comparison
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0:3c7cbfb8f43d 1:a38f6a0ebbf9
3 <macros> 3 <macros>
4 <token name="@VERSION@">0.5.0</token> 4 <token name="@VERSION@">0.5.0</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@VERSION@">polypolish</requirement> 7 <requirement type="package" version="@VERSION@">polypolish</requirement>
8 <requirement type="package" version="1.15.1">samtools</requirement> 8 <!--<requirement type="package" version="1.15.1">samtools</requirement> -->
9 <requirement type="package" version="0.7.17">bwa</requirement> 9 <requirement type="package" version="0.7.17">bwa</requirement>
10 </requirements> 10 </requirements>
11 <version_command>polypolish --version</version_command> 11 <version_command>polypolish --version</version_command>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 #if $short_reads.sr_type == 'paired' 13 #if $short_reads.sr_type == 'paired'
14 ln -s '$short_read.R1' reads_1.fastq.gz && 14 ln -s '$short_reads.R1' reads_1.fastq.gz &&
15 ln -s '$short_read.R2' reads_2.fastq.gz && 15 ln -s '$short_reads.R2' reads_2.fastq.gz &&
16 #else if str($short_reads.sr_type) == "collection" 16 #else if str($short_reads.sr_type) == "collection"
17 ln -s '$short_read.input1.forward' reads_1.fastq.gz && 17 ln -s '$short_reads.input1.forward' reads_1.fastq.gz &&
18 ln -s '$short_read.input1.reverse' reads_2.fastq.gz && 18 ln -s '$short_reads.input1.reverse' reads_2.fastq.gz &&
19 #end if 19 #end if
20 20
21 ln -s '${assembly}' draft.fa && 21 ln -s '${assembly}' draft.fa &&
22 bwa index draft.fa && 22 bwa index draft.fa &&
23 bwa mem -t \${GALAXY_SLOTS:-4} -a draft.fa reads_1.fastq.gz > alignments_1.sam && 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 && 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 && 25 polypolish_insert_filter.py --in1 alignments_1.sam --in2 alignments_2.sam --out1 filtered_1.sam --out2 filtered_2.sam &&
26 polypolish 26 polypolish
27 #if $debug 27 #if $debug
28 $debug debug.tsv 28 $debug debug.tsv
29 #end if 29 #end if
30 -d ${min_depth} 30 -d ${min_depth}
31 -i ${fraction_invalid} 31 -i ${fraction_invalid}
32 -m ${max_errors} 32 -m ${max_errors}
33 -v ${fraction_valid} 33 -v ${fraction_valid}
34 draft.fasta filtered_1.sam filtered_2.sam 34 draft.fasta filtered_1.sam filtered_2.sam
35 > polished.fasta 35 > polished.fasta
36 ]]> </command> 36 ]]> </command>
37 37
38 <inputs> 38 <inputs>
39 <param name="basecalled" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Basecalled data"/> 39 <param name="assembly" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Assembly"/>
40 <conditional name="short_reads"> 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"> 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> 42 <option value="paired" selected="true">Paired End</option>
43 <option value="collection">Paired Collection</option> 43 <option value="collection">Paired Collection</option>
44 </param> 44 </param>
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"/> 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> 51 </when>
52 </conditional> 52 </conditional>
53 <param argument="min_depth" type="integer" value="5" min="1" label="Minimum depth" /> 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" /> 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" /> 55 <param argument="fraction_valid" type="integer" value="0.2" min="0.0" max="1.0" 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" /> 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" /> 57 <param argument="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Debug output" />
58 </inputs> 58 </inputs>
59 <outputs> 59 <outputs>
60 <data name="polished" format="fasta" from_work_dir="polished.fasta" label="${tool.name} on ${on_string} Polished assembly" /> 60 <data name="polished" format="fasta" from_work_dir="polished.fasta" label="${tool.name} on ${on_string} Polished assembly" />