Mercurial > repos > xilinxu > xilinxu

comparison fastx_toolkit-0.0.6/galaxy/tools/fastx_toolkit_with_gzip_and_output_label/fastx_clipper.xml @ 3:997f5136985f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xilinxu
date Thu, 14 Aug 2014 04:52:17 -0400
parents
children
comparison
equal deleted inserted replaced
2:dfe9332138cf 3:997f5136985f
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>