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comparison dunovo.xml @ 5:4bc49a5769ee draft

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Version 0.5: Split interleaved SSCS output file into two paired files.
author nick
date Thu, 01 Dec 2016 23:22:52 -0500
parents 7f513b9b1b1e
children 9a0bee12b583
comparison
equal deleted inserted replaced
4:7f513b9b1b1e 5:4bc49a5769ee
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="duplex" name="Du Novo: Make consensus reads" version="0.3"> 2 <tool id="duplex" name="Du Novo: Make consensus reads" version="0.5">
3 <description>from duplex sequencing alignments</description> 3 <description>from duplex sequencing alignments</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.3">duplex</requirement> 5 <requirement type="package" version="0.5">duplex</requirement>
6 <requirement type="set_environment">DUPLEX_DIR</requirement> 6 <requirement type="set_environment">DUPLEX_DIR</requirement>
7 <!-- TODO: require Python 2.7 --> 7 <!-- TODO: require Python 2.7 -->
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 python \$DUPLEX_DIR/dunovo.py -r $min_reads -q $qual_thres -F $qual_format $input 10 python \$DUPLEX_DIR/dunovo.py -r $min_reads -q $qual_thres -F $qual_format $input
11 #if $keep_sscs: 11 #if $keep_sscs:
12 --sscs-file $sscs 12 --sscs-file sscs.fa
13 #end if 13 #end if
14 > duplex.fa 14 > duplex.fa
15 && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=1 duplex.fa > $output1 15 && python \$DUPLEX_DIR/utils/outconv.py duplex.fa -1 $dcs1 -2 $dcs2
16 && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=2 duplex.fa > $output2 16 #if $keep_sscs:
17 && python \$DUPLEX_DIR/utils/outconv.py sscs.fa -1 $sscs1 -2 $sscs2
18 #end if
17 ]]> 19 ]]>
18 </command> 20 </command>
19 <inputs> 21 <inputs>
20 <param name="input" type="data" format="tabular" label="Aligned input reads" /> 22 <param name="input" type="data" format="tabular" label="Aligned input reads" />
21 <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/> 23 <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/>
22 <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/> 24 <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/>
23 <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+"> 25 <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+">
24 <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option> 26 <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option>
25 <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option> 27 <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option>
26 </param> 28 </param>
27 <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences" /> 29 <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" />
28 </inputs> 30 </inputs>
29 <outputs> 31 <outputs>
30 <data name="output1" format="fasta" label="$tool.name on $on_string (mate 1)"/> 32 <data name="dcs1" format="fasta" label="$tool.name on $on_string (mate 1)"/>
31 <data name="output2" format="fasta" label="$tool.name on $on_string (mate 2)"/> 33 <data name="dcs2" format="fasta" label="$tool.name on $on_string (mate 2)"/>
32 <data name="sscs" format="fasta" label="$tool.name on $on_string (SSCS)"> 34 <data name="sscs1" format="fasta" label="$tool.name on $on_string (SSCS mate 1)">
35 <filter>keep_sscs</filter>
36 </data>
37 <data name="sscs2" format="fasta" label="$tool.name on $on_string (SSCS mate 2)">
33 <filter>keep_sscs</filter> 38 <filter>keep_sscs</filter>
34 </data> 39 </data>
35 </outputs> 40 </outputs>
36 <tests> 41 <tests>
37 <test> 42 <test>
38 <param name="input" value="families.msa.tsv"/> 43 <param name="input" value="families.msa.tsv"/>
39 <output name="output1" file="families.cons_1.fa"/> 44 <output name="dcs1" file="families.cons_1.fa"/>
40 <output name="output2" file="families.cons_2.fa"/> 45 <output name="dcs2" file="families.cons_2.fa"/>
41 </test> 46 </test>
42 </tests> 47 </tests>
43 <help> 48 <help>
44 49
45 **What it does** 50 **What it does**