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/tools/emboss_5/emboss_splitter.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="EMBOSS: splitter92" name="splitter" version="5.0.0">
 2  <description>Split a sequence into (overlapping) smaller sequences</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>splitter -sequence $input1 -outseq $out_file1 -size "$size" -overlap "$overlap" -addoverlap $addoverlap -osformat2 $out_format1 -auto</command>
 5  <inputs>
 6    <param format="fasta" name="input1" type="data">
 7      <label>Sequences</label>
 8    </param>
 9    <param name="size" size="10" type="text" value="10000">
10      <label>Size to split at</label>
11    </param>
12    <param name="overlap" size="4" type="text" value="0">
13      <label>Overlap between split sequences</label>
14    </param>
15    <param name="addoverlap" type="select">
16      <label>Add overlap to size</label>
17      <option value="no">No</option>
18      <option value="yes">Yes</option>
19    </param>
20    <param name="out_format1" type="select">
21      <label>Output Sequence File Format</label>
22      <option value="fasta">FASTA (m)</option>
23      <option value="acedb">ACeDB (m)</option>
24      <option value="asn1">ASN.1 (m)</option>
25      <option value="clustal">Clustal (m)</option>
26      <option value="codata">CODATA (m)</option>
27      <option value="embl">EMBL (m)</option>
28      <option value="fitch">Fitch (m)</option>
29      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
30      <option value="genbank">GENBANK (m)</option>
31      <option value="gff">GFF (m)</option>
32      <option value="hennig86">Hennig86 (m)</option>
33      <option value="ig">Intelligenetics (m)</option>
34      <option value="jackknifer">Jackknifer (m)</option>
35      <option value="jackknifernon">Jackknifernon (m)</option>
36      <option value="mega">Mega (m)</option>
37      <option value="meganon">Meganon (m)</option>
38      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
39      <option value="pir">NBRF (PIR) (m)</option>
40      <option value="ncbi">NCBI style FASTA (m)</option>
41      <option value="nexus">Nexus/PAUP (m)</option>
42      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
43      <option value="phylip">PHYLIP interleaved (m)</option>
44      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
45      <option value="selex">SELEX (m)</option>
46      <option value="staden">Staden (s)</option>
47      <option value="strider">DNA strider (m)</option>
48      <option value="swiss">SwisProt entry (m)</option>
49      <option value="text">Plain sequence (s)</option>
50      <option value="treecon">Treecon (m)</option>
51    </param>
52  </inputs>
53  <outputs>
54    <data format="fasta" name="out_file1" />
55  </outputs>
56  <tests>
57    <test>
58      <param name="input1" value="2.fasta"/>
59      <param name="size" value="10000"/>
60      <param name="overlap" value="0"/>
61      <param name="addoverlap" value="no"/>
62      <param name="out_format1" value="fasta"/>
63      <output name="out_file1" file="emboss_splitter_out.fasta"/>
64    </test>
65  </tests>
66  <code file="emboss_format_corrector.py" />
67  <help>
68
69.. class:: warningmark
70
71The input dataset needs to be sequences.
72
73-----
74
75    You can view the original documentation here_.
76    
77    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/splitter.html
78
79------
80
81**Citation**
82
83If 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;`_
84  </help>
85</tool>