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comparison emboss_cpgreport.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: cpgreport16" name="cpgreport" version="5.0.0.1">
2 <description>Reports all CpG rich regions</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command><![CDATA[
9 cpgreport
10 -sequence '$input1'
11 -outfile '$out_file1'
12 -outfeat '$out_file2'
13 -offormat3 $out_format2
14 -score $score
15 -auto
16 ]]>
17 </command>
18 <inputs>
19 <param name="input1" type="data" format="fasta" label="On query" />
20 <param name="score" type="integer" min="1" max="200" value="17" label="Score for each CG sequence found" />
21 <param name="out_format2" type="select" label="Output feature file format">
22 <option value="gff">GFF</option>
23 <option value="embl">EMBL</option>
24 <option value="swiss">SwissProt</option>
25 </param>
26 </inputs>
27 <outputs>
28 <data name="out_file1" format="cpgreport" />
29 <data name="out_file2" format="gff" />
30 </outputs>
31 <tests>
32 <test>
33 <param name="input1" value="2.fasta"/>
34 <param name="score" value="17"/>
35 <param name="out_format2" value="embl"/>
36 <output name="out_file1" file="emboss_cpgreport_out2.cpgreport"/>
37 </test>
38 <!-- <test>
39 <param name="input1" value="2.fasta"/>
40 <param name="score" value="17"/>
41 <param name="out_format2" value="gff"/>
42 <output name="out_file1" file="emboss_cpgreport_out1.gff"/>
43 </test> -->
44 </tests>
45 <help>
46 .. class:: warningmark
47
48 The input dataset needs to be sequences.
49
50 -----
51
52 You can view the original documentation here_.
53
54 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/cpgreport.html
55 </help>
56 <expand macro="citations" />
57 </tool>