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
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> |