Mercurial > repos > xuebing > sharplabtool

comparison tools/fastx_toolkit/fastx_clipper.xml @ 0:9071e359b9a3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:9071e359b9a3
1 <tool id="cshl_fastx_clipper" name="Clip" version="1.0.1" >
2 <description>adapter sequences</description>
3 <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
4 <command>
5 zcat -f $input | fastx_clipper -l $minlength -a $clip_source.clip_sequence -d $keepdelta -o $output -v $KEEP_N $DISCARD_OPTIONS
6 #if $input.ext == "fastqsanger":
7 -Q 33
8 #end if
9 </command>
10
11 <inputs>
12 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to clip" />
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 sequences (i.e. sequences which contained the adapter)</option>
50 <option value="-C">Output only non-clipped sequences (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 </inputs>
55 <!--
56 #functional test with param value starting with - fails.
57 <tests>
58 <test>
59 <param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/>
60 <param name="maxmismatches" value="2" />
61 <param name="minlength" value="15" />
62 <param name="clip_source_list" value="user" />
63 <param name="clip_sequence" value="CAATTGGTTAATCCCCCTATATA" />
64 <param name="keepdelta" value="0" />
65 <param name="KEEP_N" value="-n" />
66 <param name="DISCARD_OPTIONS" value="-c" />
67 <output name="output" file="fastx_clipper1a.out" />
68 </test>
69 </tests>
70 -->
71 <outputs>
72 <data format="input" name="output" metadata_source="input" />
73 </outputs>
74
75 <help>
76 **What it does**
77
78 This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file.
79
80 --------
81
82
83 **Clipping Illustration:**
84
85 .. image:: ./static/fastx_icons/fastx_clipper_illustration.png
86
87
88
89
90
91
92
93
94 **Clipping Example:**
95
96 .. image:: ./static/fastx_icons/fastx_clipper_example.png
97
98
99
100 **In the above example:**
101
102 * Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter).
103 * Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter).
104
105
106
107
108 </help>
109 </tool>