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comparison dunovo.xml @ 2:a9cb6fb9ea94 draft

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Update to Du Novo 0.7.6.
author nick
date Thu, 24 Aug 2017 02:13:33 -0400
parents ea832c221ec9
children 00dde366870a
comparison
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1:ea832c221ec9 2:a9cb6fb9ea94
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="dunovo" name="Du Novo: Make consensus reads" version="0.7"> 2 <tool id="dunovo" name="Du Novo: Make consensus reads" version="0.7.6">
3 <description>from duplex sequencing alignments</description> 3 <description>from duplex sequencing alignments</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.7.1">dunovo</requirement> 5 <requirement type="package" version="0.7.6">dunovo</requirement>
6 <!-- TODO: require Python 2.7 --> 6 <!-- TODO: require Python 2.7 -->
7 </requirements> 7 </requirements>
8 <command detect_errors="exit_code">dunovo.sh -r $min_reads -q $qual_thres -F $qual_format '$input' '$dcs1' '$dcs2' 8 <command detect_errors="exit_code"><![CDATA[
9 dunovo.py --galaxy $phone -r $min_reads -q $qual_thres -F $qual_format '$input'
9 #if $keep_sscs: 10 #if $keep_sscs:
10 '$sscs1' '$sscs2' 11 --sscs-file sscs.fa
11 #end if 12 #end if
13 > duplex.fa
14 && outconv.py duplex.fa -1 '$dcs1' -2 '$dcs2'
15 #if $keep_sscs:
16 && outconv.py sscs.fa -1 '$sscs1' -2 '$sscs2'
17 #end if
18 ]]>
12 </command> 19 </command>
13 <inputs> 20 <inputs>
14 <param name="input" type="data" format="tabular" label="Aligned input reads" /> 21 <param name="input" type="data" format="tabular" label="Aligned input reads" />
15 <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/> 22 <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/>
16 <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/> 23 <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/>
17 <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+"> 24 <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+">
18 <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option> 25 <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option>
19 <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option> 26 <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option>
20 </param> 27 </param>
21 <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" /> 28 <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" />
29 <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send anonymous usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the time taken to process it, and the IP address of the machine running it. No parameters or filenames are sent."/>
22 </inputs> 30 </inputs>
23 <outputs> 31 <outputs>
24 <data name="dcs1" format="fasta" label="$tool.name on $on_string (mate 1)"/> 32 <data name="dcs1" format="fasta" label="$tool.name on $on_string (mate 1)"/>
25 <data name="dcs2" format="fasta" label="$tool.name on $on_string (mate 2)"/> 33 <data name="dcs2" format="fasta" label="$tool.name on $on_string (mate 2)"/>
26 <data name="sscs1" format="fasta" label="$tool.name on $on_string (SSCS mate 1)"> 34 <data name="sscs1" format="fasta" label="$tool.name on $on_string (SSCS mate 1)">