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comparison emboss_cpgreport.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: cpgreport16" name="cpgreport" version="5.0.0"> 1 <tool id="EMBOSS: cpgreport16" name="cpgreport" version="5.0.0.1">
2 <description>Reports all CpG rich regions</description> 2 <description>Reports all CpG rich regions</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
4 <command><![CDATA[ 8 <command><![CDATA[
5 cpgreport 9 cpgreport
6 -sequence '$input1' 10 -sequence '$input1'
7 -outfile '$out_file1' 11 -outfile '$out_file1'
8 -outfeat '$out_file2' 12 -outfeat '$out_file2'
9 -offormat3 '$out_format2' 13 -offormat3 $out_format2
10 -score '$score' 14 -score $score
11 -auto 15 -auto
12 ]]> 16 ]]>
13 </command> 17 </command>
14 <inputs> 18 <inputs>
15 <param format="fasta" name="input1" type="data"> 19 <param name="input1" type="data" format="fasta" label="On query" />
16 <label>On query</label> 20 <param name="score" type="integer" min="1" max="200" value="17" label="Score for each CG sequence found" />
17 </param> 21 <param name="out_format2" type="select" label="Output feature file format">
18 <param name="score" type="text" value="17">
19 <label>Score for each CG sequence found (1-200)</label>
20 </param>
21 <param name="out_format2" type="select" label="Output Feature File Format">
22 <option value="gff">GFF</option> 22 <option value="gff">GFF</option>
23 <option value="embl">EMBL</option> 23 <option value="embl">EMBL</option>
24 <option value="swiss">SwissProt</option> 24 <option value="swiss">SwissProt</option>
25 </param> 25 </param>
26 </inputs> 26 </inputs>
27 <outputs> 27 <outputs>
28 <data format="cpgreport" name="out_file1" /> 28 <data name="out_file1" format="cpgreport" />
29 <data format="gff" name="out_file2" /> 29 <data name="out_file2" format="gff" />
30 </outputs> 30 </outputs>
31 <tests> 31 <tests>
32 <test> 32 <test>
33 <param name="input1" value="2.fasta"/> 33 <param name="input1" value="2.fasta"/>
34 <param name="score" value="17"/> 34 <param name="score" value="17"/>
40 <param name="score" value="17"/> 40 <param name="score" value="17"/>
41 <param name="out_format2" value="gff"/> 41 <param name="out_format2" value="gff"/>
42 <output name="out_file1" file="emboss_cpgreport_out1.gff"/> 42 <output name="out_file1" file="emboss_cpgreport_out1.gff"/>
43 </test> --> 43 </test> -->
44 </tests> 44 </tests>
45 <code file="emboss_format_corrector.py" />
46 <help> 45 <help>
47 .. class:: warningmark 46 .. class:: warningmark
48 47
49 The input dataset needs to be sequences. 48 The input dataset needs to be sequences.
50 49
51 ----- 50 -----
52 51
53 You can view the original documentation here_. 52 You can view the original documentation here_.
54
55 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgreport.html
56 53
57 ------ 54 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/cpgreport.html
58
59 **Citation**
60
61 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;`_
62
63 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;`_
64 </help> 55 </help>
56 <expand macro="citations" />
65 </tool> 57 </tool>