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comparison emboss_extractfeat.xml @ 10:d49956b87f7e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
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children 8992d258e42f
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9:511429456d3c 10:d49956b87f7e
1 <tool id="EMBOSS: extractfeat34" name="extractfeat" version="5.0.0.1">
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 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <code file="emboss_format_corrector.py" />
9 <command>extractfeat -sequence '$input1' -outseq '$out_file1' -before $before -after $after -source '$source' -type '$type' -sense $sense -minscore $minscore -maxscore $maxscore -tag '$tag' -value
10 '$value' -join $join -featinname $featinname -describe '$describe' -osformat2 $out_format1 -auto</command>
11 <inputs>
12 <param name="input1" type="data" format="data" label="Sequences" />
13 <param name="before" type="integer" value="0" label="Number of bases or residues before the feature to include in the extracted sequence" />
14 <param name="after" type="integer" value="0" label="Number of bases or residues after the feature to include in the extracted sequence" />
15 <param name="source" type="text" value="*" label="Feature source" />
16 <param name="type" type="text" value="*" label="Feature type" />
17 <param name="sense" type="select" label="Feature sense">
18 <option value="0">Any sense</option>
19 <option value="1">Forward sense</option>
20 <option value="-1">Reverse sense</option>
21 </param>
22 <param name="minscore" type="float" value="0.0" label="Minimum score" />
23 <param name="maxscore" type="float" value="0.0" label="Maximum score" />
24 <param name="tag" type="text" value="*" label="Feature tags" />
25 <param name="value" type="text" value="*" label="Tag values" />
26 <param name="join" type="select" label="Join features">
27 <option value="no">No</option>
28 <option value="yes">Yes</option>
29 </param>
30 <param name="featinname" type="select" label="Put feature type in sequence name">
31 <option value="no">No</option>
32 <option value="yes">Yes</option>
33 </param>
34 <param name="describe" type="text" value="" label="Specify one or more tag names that should be added to the output sequence Description text" />
35 <param name="out_format1" type="select" label="Output sequence file format">
36 <option value="fasta">FASTA (m)</option>
37 <option value="acedb">ACeDB (m)</option>
38 <option value="asn1">ASN.1 (m)</option>
39 <option value="clustal">Clustal (m)</option>
40 <option value="codata">CODATA (m)</option>
41 <option value="embl">EMBL (m)</option>
42 <option value="fitch">Fitch (m)</option>
43 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
44 <option value="genbank">GENBANK (m)</option>
45 <option value="gff">GFF (m)</option>
46 <option value="hennig86">Hennig86 (m)</option>
47 <option value="ig">Intelligenetics (m)</option>
48 <option value="jackknifer">Jackknifer (m)</option>
49 <option value="jackknifernon">Jackknifernon (m)</option>
50 <option value="mega">Mega (m)</option>
51 <option value="meganon">Meganon (m)</option>
52 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
53 <option value="pir">NBRF (PIR) (m)</option>
54 <option value="ncbi">NCBI style FASTA (m)</option>
55 <option value="nexus">Nexus/PAUP (m)</option>
56 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
57 <option value="phylip">PHYLIP interleaved (m)</option>
58 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
59 <option value="selex">SELEX (m)</option>
60 <option value="staden">Staden (s)</option>
61 <option value="strider">DNA strider (m)</option>
62 <option value="swiss">SwisProt entry (m)</option>
63 <option value="text">Plain sequence (s)</option>
64 <option value="treecon">Treecon (m)</option>
65 </param>
66 </inputs>
67 <outputs>
68 <data name="out_file1" format="fasta" />
69 </outputs>
70 <help>
71 You can view the original documentation here_.
72
73 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/extractfeat.html
74 </help>
75 <expand macro="citations" />
76 </tool>