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/tools/emboss_5/emboss_nthseq.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="EMBOSS: nthseq62" name="nthseq" version="5.0.0">
 2  <description>Writes one sequence from a multiple set of sequences</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>nthseq -sequence $input1 -outseq $out_file1 -number $number -osformat2 $out_format1 -auto</command>
 5  <inputs>
 6    <param format="fasta" name="input1" type="data">
 7      <label>Sequences</label>
 8    </param>
 9    <param name="number" size="4" type="text" value="1">
10      <label>Number of the sequence to output</label>
11    </param>
12    <param name="out_format1" type="select">
13      <label>Output Sequence File Format</label>
14      <option value="fasta">FASTA (m)</option>
15      <option value="acedb">ACeDB (m)</option>
16      <option value="asn1">ASN.1 (m)</option>
17      <option value="clustal">Clustal (m)</option>
18      <option value="codata">CODATA (m)</option>
19      <option value="embl">EMBL (m)</option>
20      <option value="fitch">Fitch (m)</option>
21      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
22      <option value="genbank">GENBANK (m)</option>
23      <option value="gff">GFF (m)</option>
24      <option value="hennig86">Hennig86 (m)</option>
25      <option value="ig">Intelligenetics (m)</option>
26      <option value="jackknifer">Jackknifer (m)</option>
27      <option value="jackknifernon">Jackknifernon (m)</option>
28      <option value="mega">Mega (m)</option>
29      <option value="meganon">Meganon (m)</option>
30      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
31      <option value="pir">NBRF (PIR) (m)</option>
32      <option value="ncbi">NCBI style FASTA (m)</option>
33      <option value="nexus">Nexus/PAUP (m)</option>
34      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
35      <option value="phylip">PHYLIP interleaved (m)</option>
36      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
37      <option value="selex">SELEX (m)</option>
38      <option value="staden">Staden (s)</option>
39      <option value="strider">DNA strider (m)</option>
40      <option value="swiss">SwisProt entry (m)</option>
41      <option value="text">Plain sequence (s)</option>
42      <option value="treecon">Treecon (m)</option>
43    </param>
44  </inputs>
45  <outputs>
46    <data format="fasta" name="out_file1" />
47  </outputs>
48  <tests>
49    <test>
50      <param name="input1" value="2.fasta"/>
51      <param name="number" value="1"/>
52      <param name="out_format1" value="fasta"/>
53      <output name="out_file1" file="emboss_nthseq_out.fasta"/>
54    </test>
55  </tests>
56  <code file="emboss_format_corrector.py" />
57  <help>
58
59.. class:: warningmark
60
61The input dataset needs to be sequences.
62
63-----
64
65    You can view the original documentation here_.
66    
67    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/nthseq.html
68
69------
70
71**Citation**
72
73If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
74  </help>
75</tool>