annotate tools/emboss_5/emboss_fuzznuc.xml @ 0:9071e359b9a3

Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
1 <tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.1">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
2 <description>Nucleic acid pattern search</description>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
4 <command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
5 <inputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
6 <param format="fasta" name="input1" type="data">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
7 <label>Sequences</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
8 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
9 <param name="pattern" size="5" type="text" value="">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
10 <label>Search pattern</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
11 <sanitizer>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
12 <valid initial="string.printable">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
13 <remove value="&apos;"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
14 </valid>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
15 <mapping initial="none">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
16 <add source="&apos;" target=""/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
17 </mapping>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
18 </sanitizer>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
19 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
20 <param name="mismatch" size="5" type="text" value="0">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
21 <label>Number of mismatches</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
22 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
23 <param name="complement" type="select">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
24 <label>Search complementary strand</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
25 <option value="no">No</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
26 <option value="yes">Yes</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
27 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
28 <param name="out_format1" type="select">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
29 <label>Output Report File Format</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
30 <option value="seqtable">SeqTable</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
31 <option value="embl">EMBL</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
32 <option value="genbank">GENBANK</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
33 <option value="gff">GFF</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
34 <option value="pir">PIR</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
35 <option value="swiss">SwissProt</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
36 <option value="dbmotif">DbMotif</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
37 <option value="diffseq">Diffseq</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
38 <option value="excel">Excel (tab delimited)</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
39 <option value="feattable">FeatTable</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
40 <option value="motif">Motif</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
41 <option value="regions">Regions</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
42 <option value="simple">SRS Simple</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
43 <option value="fuzznuc">Fuzznuc Output File</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
44 <option value="srs">SRS</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
45 <option value="table">Table</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
46 <option value="tagseq">TagSeq</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
47 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
48 </inputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
49 <outputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
50 <data format="fuzznuc" name="out_file1" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
51 </outputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
52 <tests>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
53 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
54 <param name="input1" value="2.fasta"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
55 <param name="pattern" value="AA"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
56 <param name="mismatch" value="0"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
57 <param name="complement" value="no"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
58 <param name="out_format1" value="excel"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
59 <output name="out_file1" file="emboss_fuzznuc_out.tabular"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
60 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
61 </tests>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
62 <code file="emboss_format_corrector.py" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
63 <help>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
64
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
65 .. class:: warningmark
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
66
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
67 The input dataset needs to be sequences.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
68
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
69 -----
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
70
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
71 You can view the original documentation here_.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
72
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
73 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzznuc.html
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
74 </help>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
75 </tool>