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/tools/emboss_5/emboss_checktrans.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 93 lines | 73 code | 8 blank | 12 comment | 0 complexity | d134a0b212c8fdf2f43daeeead0b3ca5 MD5 | raw file
 1<tool id="EMBOSS: checktrans9" name="checktrans" version="5.0.0">
 2  <description>Reports STOP codons and ORF statistics of a protein</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>checktrans -sequence $input1 -outfile $out_file1 -outseq $out_file2 -osformat3 $out_format2 -outfeat $out_file3 -offormat4 $out_format3 -orfml $orfml -addlast $addlast -auto</command>
 5  <inputs>
 6    <param format="fasta" name="input1" type="data">
 7      <label>On query</label>
 8    </param>
 9    <param name="orfml" size="4" type="text" value="100">
10      <label>Minimum ORF Length to report</label>
11    </param>
12    <param name="addlast" type="select">
13      <label>An asterisk in the protein sequence indicates the position of a STOP codon. Checktrans assumes that all ORFs end in a STOP codon. Forcing the sequence to end with an asterisk, if there
14      is not one there already, makes checktrans treat the end as a potential ORF. If an asterisk is added, it is not included in the reported count of STOPs</label>
15      <option value="yes">Yes</option>
16      <option value="no">No</option>
17    </param>
18    <param name="out_format2" type="select">
19      <label>Output Sequence File Format</label>
20      <option value="fasta">FASTA (m)</option>
21      <option value="acedb">ACeDB (m)</option>
22      <option value="asn1">ASN.1 (m)</option>
23      <option value="clustal">Clustal (m)</option>
24      <option value="codata">CODATA (m)</option>
25      <option value="embl">EMBL (m)</option>
26      <option value="fitch">Fitch (m)</option>
27      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
28      <option value="genbank">GENBANK (m)</option>
29      <option value="gff">GFF (m)</option>
30      <option value="hennig86">Hennig86 (m)</option>
31      <option value="ig">Intelligenetics (m)</option>
32      <option value="jackknifer">Jackknifer (m)</option>
33      <option value="jackknifernon">Jackknifernon (m)</option>
34      <option value="mega">Mega (m)</option>
35      <option value="meganon">Meganon (m)</option>
36      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
37      <option value="pir">NBRF (PIR) (m)</option>
38      <option value="ncbi">NCBI style FASTA (m)</option>
39      <option value="nexus">Nexus/PAUP (m)</option>
40      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
41      <option value="phylip">PHYLIP interleaved (m)</option>
42      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
43      <option value="selex">SELEX (m)</option>
44      <option value="staden">Staden (s)</option>
45      <option value="strider">DNA strider (m)</option>
46      <option value="swiss">SwisProt entry (m)</option>
47      <option value="text">Plain sequence (s)</option>
48      <option value="treecon">Treecon (m)</option>
49    </param>
50    <param name="out_format3" type="select">
51      <label>Output Feature File Format</label>
52      <option value="gff">GFF</option>
53      <option value="embl">EMBL</option>
54      <option value="swiss">SwissProt</option>
55    </param>
56  </inputs>
57  <outputs>
58    <data format="checktrans" name="out_file1" />
59    <data format="fasta" name="out_file2" />
60    <data format="gff" name="out_file3" />
61  </outputs>
62 <!--   <tests>
63    <test>
64      <param name="input1" value="2.fasta"/>
65      <param name="orfml" value="100"/>
66      <param name="addlast" value="yes"/>
67      <param name="out_format2" value="fasta"/>
68      <param name="out_format3" value="gff"/>
69      <output name="out_file1" file="emboss_checktrans_out1.txt"/>
70      <output name="out_file2" file="emboss_checktrans_out2.fasta"/>
71      <output name="out_file3" file="emboss_checktrans_out3.gff"/>
72    </test>
73  </tests> -->
74  <code file="emboss_format_corrector.py" />
75  <help>
76
77.. class:: warningmark 
78
79The input dataset needs to be sequences. 
80
81----- 
82
83    You can view the original documentation here_.
84    
85    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/checktrans.html
86
87------
88
89**Citation**
90
91If 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;`_
92  </help>
93</tool>