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/tools/emboss_5/emboss_coderet.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 79 lines | 27 code | 4 blank | 48 comment | 0 complexity | e974a2bd8c633aa2b8fbc7102ca118d6 MD5 | raw file
 1<tool id="EMBOSS: coderet13" name="coderet" version="5.0.0">
 2  <description>Extract CDS, mRNA and translations from feature tables</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <!--  <command>coderet -seqall $input1 -outfile $out_file1 -osformat2 $out_format1 -cds $cds -mrna $mrna -translation $translation -auto</command>-->
 5  <command>coderet -seqall $input1 -outfile $out_file1 -auto</command>
 6  <inputs>
 7    <param format="data" name="input1" type="data">
 8      <label>On query</label>
 9    </param>
10    <!--
11    <param name="cds" type="boolean" truevalue="yes" falsevalue="no" checked="true">
12      <label>Extract CDS sequences</label>
13    </param>
14    <param name="mrna" type="select">
15      <label>Extract mRNA sequences</label>
16      <option value="yes">Yes</option>
17      <option value="no">No</option>
18    </param>
19    <param name="translation" type="select">
20      <label>Extract translated sequences</label>
21      <option value="yes">Yes</option>
22      <option value="no">No</option>
23    </param> 
24    <param name="out_format1" type="select">
25      <label>Output Sequence File Format</label>
26      <option value="fasta">FASTA (m)</option>
27      <option value="acedb">ACeDB (m)</option>
28      <option value="asn1">ASN.1 (m)</option>
29      <option value="clustal">Clustal (m)</option>
30      <option value="codata">CODATA (m)</option>
31      <option value="embl">EMBL (m)</option>
32      <option value="fitch">Fitch (m)</option>
33      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
34      <option value="genbank">GENBANK (m)</option>
35      <option value="gff">GFF (m)</option>
36      <option value="hennig86">Hennig86 (m)</option>
37      <option value="ig">Intelligenetics (m)</option>
38      <option value="jackknifer">Jackknifer (m)</option>
39      <option value="jackknifernon">Jackknifernon (m)</option>
40      <option value="mega">Mega (m)</option>
41      <option value="meganon">Meganon (m)</option>
42      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
43      <option value="pir">NBRF (PIR) (m)</option>
44      <option value="ncbi">NCBI style FASTA (m)</option>
45      <option value="nexus">Nexus/PAUP (m)</option>
46      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
47      <option value="phylip">PHYLIP interleaved (m)</option>
48      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
49      <option value="selex">SELEX (m)</option>
50      <option value="staden">Staden (s)</option>
51      <option value="strider">DNA strider (m)</option>
52      <option value="swiss">SwisProt entry (m)</option>
53      <option value="text">Plain sequence (s)</option>
54      <option value="treecon">Treecon (m)</option> 
55    </param> 
56    -->
57  </inputs>
58  <outputs>
59    <data format="coderet" name="out_file1" />
60  </outputs>
61  <tests>
62    <test>
63      <param name="input1" value="2.fasta"/>
64      <output name="out_file1" file="emboss_coderet_out.coderet"/>
65    </test>
66  </tests>
67  <code file="emboss_format_corrector.py" />
68  <help>
69    You can view the original documentation here_.
70    
71    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/coderet.html
72
73------
74
75**Citation**
76
77If 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;`_
78  </help>
79</tool>