root/galaxy-central/tools/emboss_5/emboss_trimseq.xml @ 3

リビジョン 2, 3.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="EMBOSS: trimseq103" name="trimseq" version="5.0.0">
2  <description>Trim ambiguous bits off the ends of sequences</description>
3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4  <command>trimseq -sequence $input1 -outseq $out_file1 -window "$window" -percent "$percent" -strict $strict -star $star -left $left -right $right -osformat2 $out_format1 -auto</command>
5  <inputs>
6    <param format="fasta" name="input1" type="data">
7      <label>Sequences</label>
8    </param>
9    <param name="window" size="4" type="text" value="1">
10      <label>Window size</label>
11    </param>
12    <param name="percent" size="5" type="text" value="100.0">
13      <label>Threshold of the percentage ambiguity</label>
14    </param>
15    <param name="strict" type="select">
16      <label>Trim all ambiguity codes</label>
17      <option value="no">No</option>
18      <option value="yes">Yes</option>
19    </param>
20    <param name="star" type="select">
21      <label>In protein sequences, trim off not only X's, but also the *'s</label>
22      <option value="no">No</option>
23      <option value="yes">Yes</option>
24    </param>
25    <param name="left" type="select">
26      <label>Trim at the start</label>
27      <option value="yes">Yes</option>
28      <option value="no">No</option>
29    </param>
30    <param name="right" type="select">
31      <label>Trim at the end</label>
32      <option value="yes">Yes</option>
33      <option value="no">No</option>
34    </param>
35    <param name="out_format1" type="select">
36      <label>Output Sequence File Format</label>
37      <option value="fasta">FASTA (m)</option>
38      <option value="acedb">ACeDB (m)</option>
39      <option value="asn1">ASN.1 (m)</option>
40      <option value="clustal">Clustal (m)</option>
41      <option value="codata">CODATA (m)</option>
42      <option value="embl">EMBL (m)</option>
43      <option value="fitch">Fitch (m)</option>
44      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
45      <option value="genbank">GENBANK (m)</option>
46      <option value="gff">GFF (m)</option>
47      <option value="hennig86">Hennig86 (m)</option>
48      <option value="ig">Intelligenetics (m)</option>
49      <option value="jackknifer">Jackknifer (m)</option>
50      <option value="jackknifernon">Jackknifernon (m)</option>
51      <option value="mega">Mega (m)</option>
52      <option value="meganon">Meganon (m)</option>
53      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
54      <option value="pir">NBRF (PIR) (m)</option>
55      <option value="ncbi">NCBI style FASTA (m)</option>
56      <option value="nexus">Nexus/PAUP (m)</option>
57      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
58      <option value="phylip">PHYLIP interleaved (m)</option>
59      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
60      <option value="selex">SELEX (m)</option>
61      <option value="staden">Staden (s)</option>
62      <option value="strider">DNA strider (m)</option>
63      <option value="swiss">SwisProt entry (m)</option>
64      <option value="text">Plain sequence (s)</option>
65      <option value="treecon">Treecon (m)</option>
66    </param>
67  </inputs>
68  <outputs>
69    <data format="fasta" name="out_file1" />
70  </outputs>
71  <tests>
72    <test>
73      <param name="input1" value="2.fasta"/>
74      <param name="window" value="1"/>
75      <param name="percent" value="100.0"/>
76      <param name="strict" value="no"/>
77      <param name="star" value="no"/>
78      <param name="left" value="yes"/>
79      <param name="right" value="yes"/>
80      <param name="out_format1" value="fasta"/>
81      <output name="out_file1" file="emboss_trimseq_out.fasta"/>
82    </test>
83  </tests>
84  <code file="emboss_format_corrector.py" />
85  <help>
86
87.. class:: warningmark
88
89The input dataset needs to be sequences.
90
91-----
92
93    You can view the original documentation here_.
94   
95    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/trimseq.html
96  </help>
97</tool>
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