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/tools/emboss_5/emboss_newseq.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 78 lines | 74 code | 4 blank | 0 comment | 0 complexity | dfc536b361c3629f86c44f431d4480f5 MD5 | raw file
 1<tool id="EMBOSS: newseq59" name="newseq" version="5.0.0">
 2  <description>Type in a short new sequence</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>newseq -outseq $out_file1 -name "$seqname" -description "$description" -type $type -sequence "$sequence" -osformat5 $out_format1 -auto</command>
 5  <inputs>
 6    <param name="seqname" size="10" type="text" value="">
 7      <label>Name of of the sequence</label>
 8    </param>
 9    <param name="description" size="10" type="text" value="">
10      <label>Description of the sequence</label>
11    </param>
12    <param name="type" type="select">
13      <label>Type of sequence</label>
14      <option value="N">Nucleic</option>
15      <option value="P">Protein</option>
16    </param>
17    <param name="sequence" size="50" type="text" value="">
18      <label>The sequence itself</label>
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="seqname" value="cytoc"/>
59      <param name="description" value="fragment of cytochrome c"/>
60      <param name="type" value="N"/>
61      <param name="sequence" value="KKKEERADLIAY"/>
62      <param name="out_format1" value="fasta"/>
63      <output name="out_file1" file="emboss_newseq_out.fasta"/>
64    </test>
65  </tests>
66  <code file="emboss_format_corrector.py" />
67  <help>
68    You can view the original documentation here_.
69    
70    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newseq.html
71
72------
73
74**Citation**
75
76If 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;`_
77  </help>
78</tool>