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comparison emboss_coderet.xml @ 11:0e2484b6829b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author iuc
date Mon, 30 Jan 2017 13:27:40 -0500
parents 9b98d3d903c6
children 27c43fb015f0
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10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: coderet13" name="coderet" version="5.0.0"> 1 <tool id="EMBOSS: coderet13" name="coderet" version="5.0.0">
2 <description>Extract CDS, mRNA and translations from feature tables</description> 2 <description>Extract CDS, mRNA and translations from feature tables</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <!-- <command>coderet -seqall $input1 -outfile $out_file1 -osformat2 $out_format1 -cds $cds -mrna $mrna -translation $translation -auto</command>--> 4 <import>macros.xml</import>
5 <command>coderet -seqall $input1 -outfile $out_file1 -auto</command> 5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <!-- <command>coderet -seqall '$input1' -outfile '$out_file1' -osformat2 $out_format1 -cds $cds -mrna $mrna -translation $translation -auto</command>-->
9 <command>coderet -seqall '$input1' -outfile '$out_file1' -auto</command>
6 <inputs> 10 <inputs>
7 <param format="data" name="input1" type="data"> 11 <param name="input1" type="data" format="data" label="On query" />
8 <label>On query</label>
9 </param>
10 <!-- 12 <!--
11 <param name="cds" type="boolean" truevalue="yes" falsevalue="no" checked="true"> 13 <param name="cds" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Extract CDS sequences" />
12 <label>Extract CDS sequences</label> 14 <param name="mrna" type="select" label="Extract mRNA sequences">
13 </param>
14 <param name="mrna" type="select">
15 <label>Extract mRNA sequences</label>
16 <option value="yes">Yes</option> 15 <option value="yes">Yes</option>
17 <option value="no">No</option> 16 <option value="no">No</option>
18 </param> 17 </param>
19 <param name="translation" type="select"> 18 <param name="translation" type="select" label="Extract translated sequences">
20 <label>Extract translated sequences</label>
21 <option value="yes">Yes</option> 19 <option value="yes">Yes</option>
22 <option value="no">No</option> 20 <option value="no">No</option>
23 </param> 21 </param>
24 <param name="out_format1" type="select"> 22 <param name="out_format1" type="select" label="Output sequence file format">
25 <label>Output Sequence File Format</label>
26 <option value="fasta">FASTA (m)</option> 23 <option value="fasta">FASTA (m)</option>
27 <option value="acedb">ACeDB (m)</option> 24 <option value="acedb">ACeDB (m)</option>
28 <option value="asn1">ASN.1 (m)</option> 25 <option value="asn1">ASN.1 (m)</option>
29 <option value="clustal">Clustal (m)</option> 26 <option value="clustal">Clustal (m)</option>
30 <option value="codata">CODATA (m)</option> 27 <option value="codata">CODATA (m)</option>
49 <option value="selex">SELEX (m)</option> 46 <option value="selex">SELEX (m)</option>
50 <option value="staden">Staden (s)</option> 47 <option value="staden">Staden (s)</option>
51 <option value="strider">DNA strider (m)</option> 48 <option value="strider">DNA strider (m)</option>
52 <option value="swiss">SwisProt entry (m)</option> 49 <option value="swiss">SwisProt entry (m)</option>
53 <option value="text">Plain sequence (s)</option> 50 <option value="text">Plain sequence (s)</option>
54 <option value="treecon">Treecon (m)</option> 51 <option value="treecon">Treecon (m)</option>
55 </param> 52 </param>
56 --> 53 -->
57 </inputs> 54 </inputs>
58 <outputs> 55 <outputs>
59 <data format="coderet" name="out_file1" /> 56 <data name="out_file1" format="coderet" />
60 </outputs> 57 </outputs>
61 <tests> 58 <tests>
62 <test> 59 <test>
63 <param name="input1" value="2.fasta"/> 60 <param name="input1" value="2.fasta"/>
64 <output name="out_file1" file="emboss_coderet_out.coderet"/> 61 <output name="out_file1" file="emboss_coderet_out.coderet"/>
65 </test> 62 </test>
66 </tests> 63 </tests>
67 <code file="emboss_format_corrector.py" />
68 <help> 64 <help>
69 You can view the original documentation here_. 65 You can view the original documentation here_.
70
71 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/coderet.html
72 66
73 ------ 67 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/coderet.html
74
75 **Citation**
76
77 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
78
79 If 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;`_
80 </help> 68 </help>
69 <expand macro="citations" />
81 </tool> 70 </tool>