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

リビジョン 2, 4.4 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="EMBOSS: extractfeat34" name="extractfeat" version="5.0.0">
2  <!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences --> 
3  <description>Extract features from a sequence</description>
4  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
5  <command>extractfeat -sequence $input1 -outseq $out_file1 -before $before -after $after -source "$source" -type "$type" -sense $sense -minscore $minscore -maxscore $maxscore -tag "$tag" -value
6  "$value" -join $join -featinname $featinname -describe "$describe" -osformat2 $out_format1 -auto</command>
7  <inputs>
8    <param format="data" name="input1" type="data">
9      <label>Sequences</label>
10    </param>
11    <param name="before" size="4" type="text" value="0">
12      <label>Number of bases or residues before the feature to include in the extracted sequence</label>
13    </param>
14    <param name="after" size="4" type="text" value="0">
15      <label>Number of bases or residues after the feature to include in the extracted sequence</label>
16    </param>
17    <param name="source" size="4" type="text" value="*">
18      <label>Feature source</label>
19    </param>
20    <param name="type" size="4" type="text" value="*">
21      <label>Feature type</label>
22    </param>
23    <param name="sense" type="select">
24      <label>Feature sense</label>
25      <option value="0">Any sense</option>
26      <option value="1">Forward sense</option>
27      <option value="-1">Reverse sense</option>
28    </param>
29    <param name="minscore" size="4" type="text" value="0.0">
30      <label>Minimum score</label>
31    </param>
32    <param name="maxscore" size="4" type="text" value="0.0">
33      <label>Maximum score</label>
34    </param>
35    <param name="tag" size="4" type="text" value="*">
36      <label>Feature tags</label>
37    </param>
38    <param name="value" size="4" type="text" value="*">
39      <label>Tag values</label>
40    </param>
41    <param name="join" type="select">
42      <label>Join features</label>
43      <option value="no">No</option>
44      <option value="yes">Yes</option>
45    </param>
46    <param name="featinname" type="select">
47      <label>Put feature type in sequence name</label>
48      <option value="no">No</option>
49      <option value="yes">Yes</option>
50    </param>
51    <param name="describe" size="4" type="text" value="">
52      <label>Specify one or more tag names that should be added to the output sequence Description text</label>
53    </param>
54    <param name="out_format1" type="select">
55      <label>Output Sequence File Format</label>
56      <option value="fasta">FASTA (m)</option>
57      <option value="acedb">ACeDB (m)</option>
58      <option value="asn1">ASN.1 (m)</option>
59      <option value="clustal">Clustal (m)</option>
60      <option value="codata">CODATA (m)</option>
61      <option value="embl">EMBL (m)</option>
62      <option value="fitch">Fitch (m)</option>
63      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
64      <option value="genbank">GENBANK (m)</option>
65      <option value="gff">GFF (m)</option>
66      <option value="hennig86">Hennig86 (m)</option>
67      <option value="ig">Intelligenetics (m)</option>
68      <option value="jackknifer">Jackknifer (m)</option>
69      <option value="jackknifernon">Jackknifernon (m)</option>
70      <option value="mega">Mega (m)</option>
71      <option value="meganon">Meganon (m)</option>
72      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
73      <option value="pir">NBRF (PIR) (m)</option>
74      <option value="ncbi">NCBI style FASTA (m)</option>
75      <option value="nexus">Nexus/PAUP (m)</option>
76      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
77      <option value="phylip">PHYLIP interleaved (m)</option>
78      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
79      <option value="selex">SELEX (m)</option>
80      <option value="staden">Staden (s)</option>
81      <option value="strider">DNA strider (m)</option>
82      <option value="swiss">SwisProt entry (m)</option>
83      <option value="text">Plain sequence (s)</option>
84      <option value="treecon">Treecon (m)</option>
85    </param>
86  </inputs>
87  <outputs>
88    <data format="fasta" name="out_file1" />
89  </outputs>
90  <code file="emboss_format_corrector.py" />
91  <help>
92    You can view the original documentation here_.
93   
94    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractfeat.html
95  </help>
96</tool>
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