Mercurial > repos > simon-gladman > trimmomatic_032

comparison trimmomatic.xml @ 11:70953ccd575a draft

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author simon-gladman
date Thu, 10 Jul 2014 14:06:14 -0400
parents 2c4e0eab2cae
children 476184b9b2f7
comparison
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10:f6cf40363396 11:70953ccd575a
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 #if $paired.is_paired == "single": 11 fwdfile ${paired.forwards_file}
12 fwdfile ${paired.forwards_file} 12 #if $paired.is_paired:
13 #end if
14 #if $paired.is_paired == "paired":
15 fwdfile ${paired.forwards_file}
16 revfile ${paired.reverse_file} 13 revfile ${paired.reverse_file}
17 #end if
18 #if $paired.is_paired == "collection":
19 fwdfile ${collection_data.forward}
20 revfile ${collection_data.reverse}
21 #end if 14 #end if
22 phred $phred 15 phred $phred
23 cutadapt ${adapt.adapters} 16 cutadapt ${adapt.adapters}
24 #if $adapt.adapters: 17 #if $adapt.adapters:
25 adaptfile ${adapt.adapt_file} 18 adaptfile ${adapt.adapt_file}
64 </command> 57 </command>
65 58
66 <inputs> 59 <inputs>
67 60
68 <conditional name="paired"> 61 <conditional name="paired">
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?"/> --> 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?"/>
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>
75 <when value="paired"> 63 <when value="paired">
76 <param name="forwards_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Direction 1 fastq reads to trim"/> 64 <param name="forwards_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Direction 1 fastq reads to trim"/>
77 <param name="reverse_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Direction 2 fastq reads to trim"/> 65 <param name="reverse_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Direction 2 fastq reads to trim"/>
78 </when> 66 </when>
79 <when value="single"> 67 <when value="single">
80 <param name="forwards_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Fastq reads to trim"/> 68 <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"/>
84 </when> 69 </when>
85 </conditional> 70 </conditional>
86 <param name="phred" type="select" label="Quality encoding." help="Phred33 or Phred 64, probably Phred64"> 71 <param name="phred" type="select" label="Quality encoding." help="Phred33 or Phred 64, probably Phred64">
87 <option value="phred64">phred64</option> 72 <option value="phred64">phred64</option>
88 <option value="phred33" selected="True">phred33</option> 73 <option value="phred33" selected="True">phred33</option>
152 </inputs> 137 </inputs>
153 138
154 <outputs> 139 <outputs>
155 <data name="log" format="tabular" label="${tool.name} on ${on_string}: Trimmomatic Log" hidden="True"> 140 <data name="log" format="tabular" label="${tool.name} on ${on_string}: Trimmomatic Log" hidden="True">
156 </data> 141 </data>
157 <data name="fwdpairs" format="input" label="${tool.name} on ${on_string}: Dir1 trimmed pairs"> 142 <data name="fwdpairs" format="fastq" label="${tool.name} on ${on_string}: Dir1 trimmed pairs">
158 <filter>(paired['is_paired']=="single")</filter> 143 <filter>(paired['is_paired'])</filter>
159 </data> 144 </data>
160 <data name="revpairs" format="input" label="${tool.name} on ${on_string}: Dir2 trimmed pairs"> 145 <data name="revpairs" format="fastq" label="${tool.name} on ${on_string}: Dir2 trimmed pairs">
161 <filter>(paired['is_paired'] == "paired" or paired['is_paired'] == "collection")</filter> 146 <filter>(paired['is_paired'])</filter>
162 </data> 147 </data>
163 <data name="singles" format="input" label="${tool.name} on ${on_string}: trimmed reads"/> 148 <data name="singles" format="fastq" label="${tool.name} on ${on_string}: trimmed reads"/>
164 <data name="dummy_out" format="tabular" label="${tool.name} on ${on_string}: DEBUG OUTPUT" hidden="True"/> 149 <data name="dummy_out" format="tabular" label="${tool.name} on ${on_string}: DEBUG OUTPUT" hidden="True"/>
165 </outputs> 150 </outputs>
166 151
167 <stdio> 152 <stdio>
168 <exit_code range="1:" level="fatal" description="Trimmomatic error" /> 153 <exit_code range="1:" level="fatal" description="Trimmomatic error" />