|
3
|
1 <tool id="cshl_fastx_clipper" name="Clip" version="1.0.1" >
|
|
|
2 <description>adapter sequences</description>
|
|
|
3 <command>
|
|
|
4 zcat -f $input | fastx_clipper $GZIPOUT -s $maxmismatches -l $minlength -a $clip_source.clip_sequence -d $keepdelta -o $output -v $KEEP_N $DISCARD_OPTIONS
|
|
|
5 </command>
|
|
|
6
|
|
|
7 <inputs>
|
|
|
8 <param format="fasta,fastqsolexa" name="input" type="data" label="Library to clip" />
|
|
|
9
|
|
|
10 <param name="maxmismatches" size="4" type="integer" value="2">
|
|
|
11 <label>Maximum number of mismatches allowed (when matching the adapter sequence)</label>
|
|
|
12 </param>
|
|
|
13
|
|
|
14 <param name="minlength" size="4" type="integer" value="15">
|
|
|
15 <label>Minimum sequence length (after clipping, sequences shorter than this length will be discarded)</label>
|
|
|
16 </param>
|
|
|
17
|
|
|
18 <conditional name="clip_source">
|
|
|
19 <param name="clip_source_list" type="select" label="Source">
|
|
|
20 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
|
|
|
21 <option value="user">Enter custom sequence</option>
|
|
|
22 </param>
|
|
|
23
|
|
|
24 <when value="user">
|
|
|
25 <param name="clip_sequence" size="30" label="Enter custom clipping sequence" type="text" value="AATTGGCC" />
|
|
|
26 </when>
|
|
|
27
|
|
|
28 <when value="prebuilt">
|
|
|
29 <param name="clip_sequence" type="select" label="Choose Adapter">
|
|
|
30 <options from_file="fastx_clipper_sequences.txt">
|
|
|
31 <column name="name" index="1"/>
|
|
|
32 <column name="value" index="0"/>
|
|
|
33 </options>
|
|
|
34 </param>
|
|
|
35 </when>
|
|
|
36 </conditional>
|
|
|
37
|
|
|
38 <param name="keepdelta" size="2" type="integer" value="0">
|
|
|
39 <label>enter non-zero value to keep the adapter sequence and x bases that follow it</label>
|
|
|
40 <help>use this for hairpin barcoding. keep at 0 unless you know what you're doing.</help>
|
|
|
41 </param>
|
|
|
42
|
|
|
43 <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases">
|
|
|
44 <option value="">Yes</option>
|
|
|
45 <option value="-n">No</option>
|
|
|
46 </param>
|
|
|
47
|
|
|
48 <param name="DISCARD_OPTIONS" type="select" label="Output options">
|
|
|
49 <option value="-c">Output only clipped seqeunces (i.e. sequences which contained the adapter)</option>
|
|
|
50 <option value="-C">Output only non-clipped seqeunces (i.e. sequences which did not contained the adapter)</option>
|
|
|
51 <option value="">Output both clipped and non-clipped sequences</option>
|
|
|
52 </param>
|
|
|
53
|
|
|
54 <param name="GZIPOUT" type="select" label="Compress output file (using GZIP) ">
|
|
|
55 <option value="-z">yes</option>
|
|
|
56 <option value="">no</option>
|
|
|
57 </param>
|
|
|
58
|
|
|
59
|
|
|
60 </inputs>
|
|
|
61
|
|
|
62 <tests>
|
|
|
63 <test>
|
|
|
64 <!-- Clip a FASTQ file -->
|
|
|
65 <param name="input" value="fastx_clipper1.fastq" />
|
|
|
66 <param name="maxmismatches" value="2" />
|
|
|
67 <param name="minlength" value="15" />
|
|
|
68 <param name="clip_source.clip_source_list" value="user" />
|
|
|
69 <param name="clip_source.clip_sequence" value="CAATTGGTTAATCCCCCTATATA" />
|
|
|
70 <param name="keepdelta" value="0" />
|
|
|
71 <param name="KEEP_N" value="-n" />
|
|
|
72 <param name="DISCARD_OPTIONS" value="-c" />
|
|
|
73 <param name="GZIPOUT" value=""/>
|
|
|
74 <output name="output" file="fastx_clipper1a.out" />
|
|
|
75 </test>
|
|
|
76 </tests>
|
|
|
77
|
|
|
78 <outputs>
|
|
|
79 <data format="input" name="output" label="$input.tag clipped" metadata_source="input" />
|
|
|
80 </outputs>
|
|
|
81
|
|
|
82 <help>
|
|
|
83 **What it does**
|
|
|
84
|
|
|
85 This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file.
|
|
|
86
|
|
|
87 --------
|
|
|
88
|
|
|
89
|
|
|
90 **Clipping Illustration:**
|
|
|
91
|
|
|
92 .. image:: ../static/fastx_icons/fastx_clipper_illustration.png
|
|
|
93
|
|
|
94
|
|
|
95
|
|
|
96
|
|
|
97
|
|
|
98
|
|
|
99
|
|
|
100
|
|
|
101 **Clipping Example:**
|
|
|
102
|
|
|
103 .. image:: ../static/fastx_icons/fastx_clipper_example.png
|
|
|
104
|
|
|
105
|
|
|
106
|
|
|
107 **In the above example:**
|
|
|
108
|
|
|
109 * Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter).
|
|
|
110 * Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter).
|
|
|
111
|
|
|
112
|
|
|
113
|
|
|
114
|
|
|
115 </help>
|
|
|
116 </tool>
|
