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/tools/emboss_5/emboss_degapseq.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 64 lines | 60 code | 4 blank | 0 comment | 0 complexity | 8b2972e65cf8618e50a4d3ca07d0022d MD5 | raw file
 1<tool id="EMBOSS: degapseq20" name="degapseq" version="5.0.0">
 2  <description>Removes gap characters from sequences</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>degapseq -sequence $input1 -outseq $out_file1 -osformat2 $out_format1 -auto</command>
 5  <inputs>
 6    <param format="data" name="input1" type="data">
 7      <label>On query</label>
 8    </param>
 9    <param name="out_format1" type="select">
10      <label>Output Sequence File Format</label>
11      <option value="fasta">FASTA (m)</option>
12      <option value="acedb">ACeDB (m)</option>
13      <option value="asn1">ASN.1 (m)</option>
14      <option value="clustal">Clustal (m)</option>
15      <option value="codata">CODATA (m)</option>
16      <option value="embl">EMBL (m)</option>
17      <option value="fitch">Fitch (m)</option>
18      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
19      <option value="genbank">GENBANK (m)</option>
20      <option value="gff">GFF (m)</option>
21      <option value="hennig86">Hennig86 (m)</option>
22      <option value="ig">Intelligenetics (m)</option>
23      <option value="jackknifer">Jackknifer (m)</option>
24      <option value="jackknifernon">Jackknifernon (m)</option>
25      <option value="mega">Mega (m)</option>
26      <option value="meganon">Meganon (m)</option>
27      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
28      <option value="pir">NBRF (PIR) (m)</option>
29      <option value="ncbi">NCBI style FASTA (m)</option>
30      <option value="nexus">Nexus/PAUP (m)</option>
31      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
32      <option value="phylip">PHYLIP interleaved (m)</option>
33      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
34      <option value="selex">SELEX (m)</option>
35      <option value="staden">Staden (s)</option>
36      <option value="strider">DNA strider (m)</option>
37      <option value="swiss">SwisProt entry (m)</option>
38      <option value="text">Plain sequence (s)</option>
39      <option value="treecon">Treecon (m)</option>
40    </param>
41  </inputs>
42  <outputs>
43    <data format="fasta" name="out_file1" />
44  </outputs>
45  <tests>
46    <test>
47      <param name="input1" value="2.fasta"/>
48      <param name="out_format1" value="fasta"/>
49      <output name="out_file1" file="emboss_degapseq_out.fasta"/>
50    </test>
51  </tests>
52  <code file="emboss_format_corrector.py" />
53  <help>
54    You can view the original documentation here_.
55    
56    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/degapseq.html
57
58------
59
60**Citation**
61
62If 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;`_
63  </help>
64</tool>