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comparison fastx_clipper.xml @ 0:2fe2d2b9e8e4 draft

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author devteam
date Wed, 25 Sep 2013 11:07:38 -0400
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1 <tool id="cshl_fastx_clipper" name="Clip" version="1.0.1" >
2 <description>adapter sequences</description>
3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements>
6 <command>
7 zcat -f $input | fastx_clipper -l $minlength -a $clip_source.clip_sequence -d $keepdelta -o $output -v $KEEP_N $DISCARD_OPTIONS
8 #if $input.ext == "fastqsanger":
9 -Q 33
10 #end if
11 </command>
12
13 <inputs>
14 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to clip" />
15
16 <param name="minlength" size="4" type="integer" value="15">
17 <label>Minimum sequence length (after clipping, sequences shorter than this length will be discarded)</label>
18 </param>
19
20 <conditional name="clip_source">
21 <param name="clip_source_list" type="select" label="Source">
22 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
23 <option value="user">Enter custom sequence</option>
24 </param>
25
26 <when value="user">
27 <param name="clip_sequence" size="30" label="Enter custom clipping sequence" type="text" value="AATTGGCC" />
28 </when>
29
30 <when value="prebuilt">
31 <param name="clip_sequence" type="select" label="Choose Adapter">
32 <options from_file="fastx_clipper_sequences.txt">
33 <column name="name" index="1"/>
34 <column name="value" index="0"/>
35 </options>
36 </param>
37 </when>
38 </conditional>
39
40 <param name="keepdelta" size="2" type="integer" value="0">
41 <label>enter non-zero value to keep the adapter sequence and x bases that follow it</label>
42 <help>use this for hairpin barcoding. keep at 0 unless you know what you're doing.</help>
43 </param>
44
45 <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases">
46 <option value="">Yes</option>
47 <option value="-n">No</option>
48 </param>
49
50 <param name="DISCARD_OPTIONS" type="select" label="Output options">
51 <option value="-c">Output only clipped sequences (i.e. sequences which contained the adapter)</option>
52 <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option>
53 <option value="">Output both clipped and non-clipped sequences</option>
54 </param>
55
56 </inputs>
57 <!--
58 #functional test with param value starting with - fails.
59 -->
60 <tests>
61 <test>
62 <param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/>
63 <param name="maxmismatches" value="2" />
64 <param name="minlength" value="15" />
65 <param name="clip_source_list" value="user" />
66 <param name="clip_sequence" value="CAATTGGTTAATCCCCCTATATA" />
67 <param name="keepdelta" value="0" />
68 <param name="KEEP_N" value="+-n" />
69 <param name="DISCARD_OPTIONS" value="+-c" />
70 <output name="output" file="fastx_clipper1a.out" />
71 </test>
72 </tests>
73 <outputs>
74 <data format="input" name="output" metadata_source="input" />
75 </outputs>
76
77 <help>
78 **What it does**
79
80 This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file.
81
82 --------
83
84
85 **Clipping Illustration:**
86
87 .. image:: ${static_path}/fastx_icons/fastx_clipper_illustration.png
88
89
90
91
92
93
94
95
96 **Clipping Example:**
97
98 .. image:: ${static_path}/fastx_icons/fastx_clipper_example.png
99
100
101
102 **In the above example:**
103
104 * Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter).
105 * Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter).
106
107
108
109
110 ------
111
112 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
113
114 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
115
116 </help>
117 </tool>