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comparison dunovo.xml @ 3:00dde366870a draft

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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'a3ad9fbb3f010253808fc0c7329897a741ec9feb\n'
author nick
date Mon, 11 Sep 2017 16:59:44 -0400
parents a9cb6fb9ea94
children 5fbeaa41b223
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2:a9cb6fb9ea94 3:00dde366870a
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="dunovo" name="Du Novo: Make consensus reads" version="0.7.6"> 2 <tool id="dunovo" name="Du Novo: Make consensus reads" version="0.8.1">
3 <description>from duplex sequencing alignments</description> 3 <description>from duplex sequencing alignments</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.7.6">dunovo</requirement> 5 <requirement type="package" version="0.8.1">dunovo</requirement>
6 <!-- TODO: require Python 2.7 --> 6 <!-- TODO: require Python 2.7 -->
7 </requirements> 7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code">
9 dunovo.py --galaxy $phone -r $min_reads -q $qual_thres -F $qual_format '$input' 9 dunovo.py --galaxy $phone --processes \${GALAXY_SLOTS:-1} --min-reads $min_reads --qual $qual_thres --qual-format $qual_format --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2'
10 #if $keep_sscs: 10 #if $keep_sscs:
11 --sscs-file sscs.fa 11 --sscs1 '$sscs1' --sscs2 '$sscs2'
12 #end if 12 #end if
13 > duplex.fa
14 && outconv.py duplex.fa -1 '$dcs1' -2 '$dcs2'
15 #if $keep_sscs:
16 && outconv.py sscs.fa -1 '$sscs1' -2 '$sscs2'
17 #end if
18 ]]>
19 </command> 13 </command>
20 <inputs> 14 <inputs>
21 <param name="input" type="data" format="tabular" label="Aligned input reads" /> 15 <param name="input" type="data" format="tabular" label="Aligned input reads" />
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="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."/>
17 <param name="cons_thres" type="float" value="0.5" min="0.5" max="1.0" label="The threshold to use when making consensus sequences. The consensus base must be present in more than this fraction of the reads, or &quot;N&quot; will be used."/>
18 <param name="min_cons_reads" type="integer" value="0" min="0" label="The minimum number of reads a base must appear in to be used as the consensus base. If no base at the position appears in at least this many reads, &quot;N&quot; will be used."/>
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."/> 19 <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_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+"> 20 <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 <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option> 21 <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option>
26 <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option> 22 <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option>
27 </param> 23 </param>
39 </data> 35 </data>
40 </outputs> 36 </outputs>
41 <tests> 37 <tests>
42 <test> 38 <test>
43 <param name="input" value="families.msa.tsv"/> 39 <param name="input" value="families.msa.tsv"/>
44 <output name="dcs1" file="families.cons_1.fa"/> 40 <output name="dcs1" file="families.dcs_1.fa"/>
45 <output name="dcs2" file="families.cons_2.fa"/> 41 <output name="dcs2" file="families.dcs_2.fa"/>
46 </test> 42 </test>
47 </tests> 43 </tests>
48 <citations> 44 <citations>
49 <citation type="bibtex">@article{Stoler2016, 45 <citation type="bibtex">@article{Stoler2016,
50 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton}, 46 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},