Mercurial > repos > simon-gladman > trimmomatic_032

comparison trimmomatic.xml @ 13:476184b9b2f7 draft

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author simon-gladman
date Thu, 10 Jul 2014 14:38:25 -0400
parents 70953ccd575a
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12:e99104027742 13:476184b9b2f7
6 </requirements> 6 </requirements>
7 7
8 <command interpreter="perl"> 8 <command interpreter="perl">
9 trimmomatic_wrapper.pl 9 trimmomatic_wrapper.pl
10 paired ${paired.is_paired} 10 paired ${paired.is_paired}
11 fwdfile ${paired.forwards_file} 11 #if $paired.is_paired == "single":
12 #if $paired.is_paired: 12 fwdfile ${paired.forwards_file}
13 #end if
14 #if $paired.is_paired == "paired":
15 fwdfile ${paired.forwards_file}
13 revfile ${paired.reverse_file} 16 revfile ${paired.reverse_file}
17 #end if
18 #if $paired.is_paired == "collection":
19 fwdfile ${paired.collection_data.forward}
20 revfile ${paired.collection_data.reverse}
14 #end if 21 #end if
15 phred $phred 22 phred $phred
16 cutadapt ${adapt.adapters} 23 cutadapt ${adapt.adapters}
17 #if $adapt.adapters: 24 #if $adapt.adapters:
18 adaptfile ${adapt.adapt_file} 25 adaptfile ${adapt.adapt_file}
57 </command> 64 </command>
58 65
59 <inputs> 66 <inputs>
60 67
61 <conditional name="paired"> 68 <conditional name="paired">
62 <param name="is_paired" type="boolean" checked="true" truevalue="paired" falsevalue="single" label="Paired end reads?" help="Do you have 2 separate paired end read files?"/> 69 <!-- <param name="is_paired" type="boolean" checked="true" truevalue="paired" falsevalue="single" label="Paired end reads?" help="Do you have 2 separate paired end read files?"/> -->
70 <param name="is_paired" type="select" label="Read type selector" help="single file (not pair aware), two files (paired reads) or a dataset collection of pairs">
71 <option value="single" selected="true">Single File</option>
72 <option value="paired">Two Files</option>
73 <option value="collection">Single dataset collection pair</option>
74 </param>
63 <when value="paired"> 75 <when value="paired">
64 <param name="forwards_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Direction 1 fastq reads to trim"/> 76 <param name="forwards_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Direction 1 fastq reads to trim"/>
65 <param name="reverse_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Direction 2 fastq reads to trim"/> 77 <param name="reverse_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Direction 2 fastq reads to trim"/>
66 </when> 78 </when>
67 <when value="single"> 79 <when value="single">
68 <param name="forwards_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Fastq reads to trim"/> 80 <param name="forwards_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Fastq reads to trim"/>
81 </when>
82 <when value="collection">
83 <param name="collection_data" type="data_collection" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Paired end dataset collection" collection_type="paired"/>
69 </when> 84 </when>
70 </conditional> 85 </conditional>
71 <param name="phred" type="select" label="Quality encoding." help="Phred33 or Phred 64, probably Phred64"> 86 <param name="phred" type="select" label="Quality encoding." help="Phred33 or Phred 64, probably Phred64">
72 <option value="phred64">phred64</option> 87 <option value="phred64">phred64</option>
73 <option value="phred33" selected="True">phred33</option> 88 <option value="phred33" selected="True">phred33</option>
137 </inputs> 152 </inputs>
138 153
139 <outputs> 154 <outputs>
140 <data name="log" format="tabular" label="${tool.name} on ${on_string}: Trimmomatic Log" hidden="True"> 155 <data name="log" format="tabular" label="${tool.name} on ${on_string}: Trimmomatic Log" hidden="True">
141 </data> 156 </data>
142 <data name="fwdpairs" format="fastq" label="${tool.name} on ${on_string}: Dir1 trimmed pairs"> 157 <data name="fwdpairs" format="input" label="${tool.name} on ${on_string}: Dir1 trimmed pairs">
143 <filter>(paired['is_paired'])</filter> 158 <filter>(paired['is_paired']=="single")</filter>
144 </data> 159 </data>
145 <data name="revpairs" format="fastq" label="${tool.name} on ${on_string}: Dir2 trimmed pairs"> 160 <data name="revpairs" format="input" label="${tool.name} on ${on_string}: Dir2 trimmed pairs">
146 <filter>(paired['is_paired'])</filter> 161 <filter>(paired['is_paired'] == "paired" or paired['is_paired'] == "collection")</filter>
147 </data> 162 </data>
148 <data name="singles" format="fastq" label="${tool.name} on ${on_string}: trimmed reads"/> 163 <data name="singles" format="input" label="${tool.name} on ${on_string}: trimmed reads"/>
149 <data name="dummy_out" format="tabular" label="${tool.name} on ${on_string}: DEBUG OUTPUT" hidden="True"/> 164 <data name="dummy_out" format="tabular" label="${tool.name} on ${on_string}: DEBUG OUTPUT" hidden="True"/>
150 </outputs> 165 </outputs>
151 166
152 <stdio> 167 <stdio>
153 <exit_code range="1:" level="fatal" description="Trimmomatic error" /> 168 <exit_code range="1:" level="fatal" description="Trimmomatic error" />