root/galaxy-central/tools/fastx_toolkit/fastx_clipper.xml

リビジョン 2, 3.3 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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  </command>
7 
8  <inputs>
9    <param format="fasta,fastqsolexa" name="input" type="data" label="Library to clip" />
10 
11    <param name="minlength" size="4" type="integer" value="15">
12      <label>Minimum sequence length (after clipping, sequences shorter than this length will be discarded)</label>
13    </param>
14
15        <conditional name="clip_source">
16                <param name="clip_source_list" type="select" label="Source">
17                        <option value="prebuilt" selected="true">Standard (select from the list below)</option>
18                        <option value="user">Enter custom sequence</option>
19                </param>
20
21                <when value="user">
22                        <param name="clip_sequence" size="30" label="Enter custom clipping sequence" type="text" value="AATTGGCC" />
23                </when>
24
25                <when value="prebuilt">
26                        <param name="clip_sequence" type="select" label="Choose Adapter">
27                                <options from_file="fastx_clipper_sequences.txt">
28                                        <column name="name" index="1"/>
29                                        <column name="value" index="0"/>
30                                </options>
31                        </param>
32                </when>
33        </conditional>
34
35        <param name="keepdelta" size="2" type="integer" value="0">
36                <label>enter non-zero value to keep the adapter sequence and x bases that follow it</label>
37                <help>use this for hairpin barcoding. keep at 0 unless you know what you're doing.</help>
38        </param>
39
40        <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases">
41                <option value="">Yes</option>
42                <option value="-n">No</option>
43        </param>
44
45        <param name="DISCARD_OPTIONS" type="select" label="Output options">
46                <option value="-c">Output only clipped sequences (i.e. sequences which contained the adapter)</option>
47                <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option>
48                <option value="">Output both clipped and non-clipped sequences</option>
49        </param>
50
51  </inputs>
52        <!--
53        #functional test with param value starting with - fails.       
54        <tests>
55                <test>
56                        <param name="input" value="fastx_clipper1.fastq" />
57                        <param name="maxmismatches" value="2" />
58                        <param name="minlength" value="15" />
59                        <param name="clip_source_list" value="user" />
60                        <param name="clip_sequence" value="CAATTGGTTAATCCCCCTATATA" />
61                        <param name="keepdelta" value="0" />
62                        <param name="KEEP_N" value="-n" />
63                        <param name="DISCARD_OPTIONS" value="-c" />
64                        <output name="output" file="fastx_clipper1a.out" />
65                </test>
66        </tests>
67        -->
68  <outputs>
69    <data format="input" name="output" metadata_source="input" />
70  </outputs>
71 
72<help>
73**What it does**
74
75This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file.
76
77--------
78
79
80**Clipping Illustration:**
81
82.. image:: ./static/fastx_icons/fastx_clipper_illustration.png
83 
84 
85 
86 
87 
88 
89 
90
91**Clipping Example:**
92
93.. image:: ./static/fastx_icons/fastx_clipper_example.png
94
95
96   
97**In the above example:**
98
99* Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter).
100* Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter).
101
102
103
104   
105</help>
106</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。