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comparison emboss_checktrans.xml @ 10:d49956b87f7e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
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children 8992d258e42f
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9:511429456d3c 10:d49956b87f7e
1 <tool id="EMBOSS: checktrans9" name="checktrans" version="5.0.0.1">
2 <description>Reports STOP codons and ORF statistics of a protein</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <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>
9 <inputs>
10 <param name="input1" type="data" format="fasta" label="On query" />
11 <param name="orfml" type="integer" value="100" label="Minimum ORF length to report" />
12 <param name="addlast" type="select" label="An asterisk in the protein sequence indicates the position of a STOP codon" help="Checktrans assumes that all ORFs end in a STOP codon. Forcing the sequence to end with an asterisk, if there 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">
13 <option value="yes">Yes</option>
14 <option value="no">No</option>
15 </param>
16 <param name="out_format2" type="select" label="Output sequence file format">
17 <option value="fasta">FASTA (m)</option>
18 <option value="acedb">ACeDB (m)</option>
19 <option value="asn1">ASN.1 (m)</option>
20 <option value="clustal">Clustal (m)</option>
21 <option value="codata">CODATA (m)</option>
22 <option value="embl">EMBL (m)</option>
23 <option value="fitch">Fitch (m)</option>
24 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
25 <option value="genbank">GENBANK (m)</option>
26 <option value="gff">GFF (m)</option>
27 <option value="hennig86">Hennig86 (m)</option>
28 <option value="ig">Intelligenetics (m)</option>
29 <option value="jackknifer">Jackknifer (m)</option>
30 <option value="jackknifernon">Jackknifernon (m)</option>
31 <option value="mega">Mega (m)</option>
32 <option value="meganon">Meganon (m)</option>
33 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
34 <option value="pir">NBRF (PIR) (m)</option>
35 <option value="ncbi">NCBI style FASTA (m)</option>
36 <option value="nexus">Nexus/PAUP (m)</option>
37 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
38 <option value="phylip">PHYLIP interleaved (m)</option>
39 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
40 <option value="selex">SELEX (m)</option>
41 <option value="staden">Staden (s)</option>
42 <option value="strider">DNA strider (m)</option>
43 <option value="swiss">SwisProt entry (m)</option>
44 <option value="text">Plain sequence (s)</option>
45 <option value="treecon">Treecon (m)</option>
46 </param>
47 <param name="out_format3" type="select" label="Output feature file format">
48 <option value="gff">GFF</option>
49 <option value="embl">EMBL</option>
50 <option value="swiss">SwissProt</option>
51 </param>
52 </inputs>
53 <outputs>
54 <data name="out_file1" format="checktrans" />
55 <data name="out_file2" format="fasta" />
56 <data name="out_file3" format="gff" />
57 </outputs>
58 <!-- <tests>
59 <test>
60 <param name="input1" value="2.fasta"/>
61 <param name="orfml" value="100"/>
62 <param name="addlast" value="yes"/>
63 <param name="out_format2" value="fasta"/>
64 <param name="out_format3" value="gff"/>
65 <output name="out_file1" file="emboss_checktrans_out1.txt"/>
66 <output name="out_file2" file="emboss_checktrans_out2.fasta"/>
67 <output name="out_file3" file="emboss_checktrans_out3.gff"/>
68 </test>
69 </tests> -->
70 <help>
71 .. class:: warningmark
72
73 The input dataset needs to be sequences.
74
75 -----
76
77 You can view the original documentation here_.
78
79 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/checktrans.html
80 </help>
81 <expand macro="citations" />
82 </tool>