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Added support for the "pair"-data collection type.
author yhoogstrate
date Fri, 20 Feb 2015 02:49:16 -0500
parents c6a790326d1e
children
comparison
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6:c6a790326d1e 7:dd2ec1b37e96
2 <description>Windowed Adaptive Trimming of FastQ data</description> 2 <description>Windowed Adaptive Trimming of FastQ data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.21.0">sickle</requirement> 4 <requirement type="package" version="1.21.0">sickle</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 sickle $readtype.single_or_paired --quiet 7 sickle
8 8
9 #if str($readtype.single_or_paired) == "se": 9 #if str($readtype.single_or_paired) == "se":
10 -f $input_single -t $qual_type -o $output_single 10 se
11 #else
12 pe
11 #end if 13 #end if
12 14
15 --quiet
16
17 #if str($readtype.single_or_paired) == "se":
18 -f $input_single -t $qual_type -o $output_single
19 #end if
20
13 #if str($readtype.single_or_paired) == "pe": 21 #if str($readtype.single_or_paired) == "pe":
14 -f $input_paired1 -r $input_paired2 -o $output_paired1 -p $output_paired2 -s $output_paired_single -t $qual_type 22 -f $input_paired1 -r $input_paired2 -o $output_paired1 -p $output_paired2 -s $output_paired_single -t $qual_type
15 #end if 23 #end if
16 24
25 #if str($readtype.single_or_paired) == "pe_collection":
26 -f "$readtype.input_paired.forward" -r "$readtype.input_paired.reverse" -o $output_paired1 -p $output_paired2 -s $output_paired_single -t $qual_type
27 #end if
28
17 #if str($qual_threshold) != "": 29 #if str($qual_threshold) != "":
18 -q $qual_threshold 30 -q $qual_threshold
19 #end if 31 #end if
20 32
21 #if str($length_threshold) != "": 33 #if str($length_threshold) != "":
22 -l $length_threshold 34 -l $length_threshold
23 #end if 35 #end if
24 36
25 #if $no_five_prime: 37 #if $no_five_prime:
26 -x 38 -x
27 #end if 39 #end if
28 40
29 #if $discard_n: 41 #if $discard_n:
30 -n 42 -n
31 #end if 43 #end if
32 </command> 44 </command>
33 45
34 <inputs> 46 <inputs>
47 <!-- original wrapper code -->
35 <conditional name="readtype"> 48 <conditional name="readtype">
36 <param name="single_or_paired" type="select" optional="false" label="Single-End or Paired-End reads?"> 49 <param name="single_or_paired" type="select" optional="false" label="Single-End or Paired-End reads?">
37 <option value="se" selected="true">Single-End</option> 50 <option value="se" selected="true">Single-End</option>
38 <option value="pe">Paired-End</option> 51 <option value="pe">Paired-End</option>
52 <option value="pe_collection">Paired-End (as collection)</option>
39 </param> 53 </param>
40 54
41 <when value="se"> 55 <when value="se">
42 <param format="fastq, fastqsanger" name="input_single" type="data" optional="false" label="Single-End FastQ Reads"/> 56 <param format="fastq, fastqsanger" name="input_single" type="data" optional="false" label="Single-End FastQ Reads"/>
43 </when> 57 </when>
44 58
45 <when value="pe"> 59 <when value="pe">
46 <param format="fastq, fastqsanger" name="input_paired1" type="data" optional="false" label="Paired-End Forward Strand FastQ Reads"/> 60 <param format="fastq, fastqsanger" name="input_paired1" type="data" optional="false" label="Paired-End Forward Strand FastQ Reads"/>
47 <param format="fastq, fastqsanger" name="input_paired2" type="data" optional="false" label="Paired-End Reverse Strand FastQ Reads"/> 61 <param format="fastq, fastqsanger" name="input_paired2" type="data" optional="false" label="Paired-End Reverse Strand FastQ Reads"/>
48 </when> 62 </when>
63
64 <when value="pe_collection">
65 <param format="fastq, fastqsanger" name="input_paired" type="data_collection" collection_type="paired" optional="false" label="Paired-End FastQ Reads as paired collection" />
66 </when>
49 </conditional> 67 </conditional>
50 68
51 <param name="qual_type" type="select" optional="false" label="Quality type"> 69 <param name="qual_type" type="select" optional="false" label="Quality type">
52 <option value="illumina" selected="true">Illumina</option> 70 <option value="illumina" selected="true">Illumina</option>
53 <option value="solexa">Solexa</option> 71 <option value="solexa">Solexa</option>
54 <option value="sanger">Sanger</option> 72 <option value="sanger">Sanger</option>
55 </param> 73 </param>
70 <data format_source="input_single" name="output_single" label="Single-End output of ${tool.name} on ${on_string}"> 88 <data format_source="input_single" name="output_single" label="Single-End output of ${tool.name} on ${on_string}">
71 <filter>(readtype['single_or_paired'] == 'se')</filter> 89 <filter>(readtype['single_or_paired'] == 'se')</filter>
72 </data> 90 </data>
73 91
74 <data format_source="input_paired1" name="output_paired1" label="Paired-End forward strand output of ${tool.name} on ${on_string}"> 92 <data format_source="input_paired1" name="output_paired1" label="Paired-End forward strand output of ${tool.name} on ${on_string}">
75 <filter>(readtype['single_or_paired'] == 'pe')</filter> 93 <filter>(readtype['single_or_paired'] == 'pe' or readtype['single_or_paired'] == 'pe_collection')</filter>
76 </data> 94 </data>
77 95
78 <data format_source="input_paired2" name="output_paired2" label="Paired-End reverse strand output of ${tool.name} on ${on_string}"> 96 <data format_source="input_paired2" name="output_paired2" label="Paired-End reverse strand output of ${tool.name} on ${on_string}">
79 <filter>(readtype['single_or_paired'] == 'pe')</filter> 97 <filter>(readtype['single_or_paired'] == 'pe' or readtype['single_or_paired'] == 'pe_collection')</filter>
80 </data> 98 </data>
81 99
82 <data format_source="input_paired1" name="output_paired_single" label="Singletons from Paired-End output of ${tool.name} on ${on_string}"> 100 <data format_source="input_paired1" name="output_paired_single" label="Singletons from Paired-End output of ${tool.name} on ${on_string}">
83 <filter>(readtype['single_or_paired'] == 'pe')</filter> 101 <filter>(readtype['single_or_paired'] == 'pe' or readtype['single_or_paired'] == 'pe_collection')</filter>
84 </data> 102 </data>
85 </outputs> 103 </outputs>
86 <tests> 104 <tests>
87 <param name="single_or_paired" value="pe"/> 105 <param name="single_or_paired" value="pe"/>
88 <param name="input_paired1" value="test.f.fastq"/> 106 <param name="input_paired1" value="test.f.fastq"/>