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comparison fastx_clipper.xml @ 0:78a7d28f2a15 draft

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author idot
date Wed, 10 Jul 2013 06:13:48 -0400
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1 <tool id="cshl_fastx_clipper_ng" name="Clip" version="1.0.1" >
2 <description>adapter sequences</description>
3 <command>
4 cat '$input' |
5 fastx_clipper
6 #if $input.ext == "fastqsanger":
7 -Q 33
8 #elif $input.ext == "fastq":
9 -Q 64
10 #end if
11 -l $minlength -a '$clip_source.clip_sequence' -d $keepdelta -o '$output' -v $KEEP_N $DISCARD_OPTIONS
12 </command>
13
14 <inputs>
15 <param format="fasta,fastq,fastqsanger" name="input" type="data" label="Library to clip" />
16
17 <param name="minlength" size="4" type="integer" value="15">
18 <label>Minimum sequence length (after clipping, sequences shorter than this length will be discarded)</label>
19 </param>
20
21 <conditional name="clip_source">
22 <param name="clip_source_list" type="select" label="Source">
23 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
24 <option value="user">Enter custom sequence</option>
25 </param>
26
27 <when value="user">
28 <param name="clip_sequence" size="30" label="Enter custom clipping sequence" type="text" value="AATTGGCC" />
29 </when>
30
31 <when value="prebuilt">
32 <param name="clip_sequence" type="select" label="Choose Adapter">
33 <options from_file="fastx_clipper_sequences.txt">
34 <column name="name" index="1"/>
35 <column name="value" index="0"/>
36 </options>
37 </param>
38 </when>
39 </conditional>
40
41 <param name="keepdelta" size="2" type="integer" value="0">
42 <label>enter non-zero value to keep the adapter sequence and x bases that follow it</label>
43 <help>use this for hairpin barcoding. keep at 0 unless you know what you're doing.</help>
44 </param>
45
46 <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases">
47 <option value="">Yes</option>
48 <option value="-n">No</option>
49 </param>
50
51 <param name="DISCARD_OPTIONS" type="select" label="Output options">
52 <option value="-c">Output only clipped sequences (i.e. sequences which contained the adapter)</option>
53 <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option>
54 <option value="">Output both clipped and non-clipped sequences</option>
55 </param>
56
57 </inputs>
58 <tests>
59 <test>
60 <param name="input" value="fastx_clipper1.fastq" />
61 <param name="maxmismatches" value="2" />
62 <param name="minlength" value="15" />
63 <param name="clip_source_list" value="user" />
64 <param name="clip_sequence" value="CAATTGGTTAATCCCCCTATATA" />
65 <param name="keepdelta" value="0" />
66 <param name="KEEP_N" value="No" />
67 <param name="DISCARD_OPTIONS" value="Output only clipped sequences (i.e. sequences which contained the adapter)" />
68 <output name="output" file="fastx_clipper1a.out" />
69 </test>
70 </tests>
71
72 <outputs>
73 <data format="input" name="output" metadata_source="input"
74 />
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/fastx_icons/fastx_clipper_illustration.png
88
89
90
91
92
93
94
95
96 **Clipping Example:**
97
98 .. image:: ../static/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 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
111
112 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
113
114 </help>
115 </tool>
116
117 <!-- FASTX-Clipper is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->