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comparison emboss_palindrome.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: palindrome65" name="palindrome" version="5.0.0"> 1 <tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0.1">
2 <description>Looks for inverted repeats in a nucleotide sequence</description> 2 <description>Looks for inverted repeats in a nucleotide sequence</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>palindrome -sequence $input1 -outfile $out_file1 -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>palindrome -sequence '$input1' -outfile '$out_file1' -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command>
5 <inputs> 8 <inputs>
6 <param format="fasta" name="input1" type="data"> 9 <param name="input1" type="data" format="fasta" label="Sequences" />
7 <label>Sequences</label> 10 <param name="minpallen" type="integer" value="10" label="Minimum length of palindrome" />
8 </param> 11 <param name="maxpallen" type="integer" value="100" label="Maximum length of palindrome" />
9 <param name="minpallen" type="text" value="10"> 12 <param name="gaplimit" type="integer" value="100" label="Maximum gap between repeated regions" />
10 <label>Minimum length of palindrome</label> 13 <param name="nummismatches" type="integer" value="0" label="Number of mismatches allowed" />
11 </param> 14 <param name="overlap" type="select" label="Report overlapping matches">
12 <param name="maxpallen" type="text" value="100">
13 <label>Maximum length of palindrome</label>
14 </param>
15 <param name="gaplimit" type="text" value="100">
16 <label>Maximum gap between repeated regions</label>
17 </param>
18 <param name="nummismatches" type="text" value="0">
19 <label>Number of mismatches allowed</label>
20 </param>
21 <param name="overlap" type="select">
22 <label>Report overlapping matches</label>
23 <option value="yes">Yes</option> 15 <option value="yes">Yes</option>
24 <option value="no">No</option> 16 <option value="no">No</option>
25 </param> 17 </param>
26 </inputs> 18 </inputs>
27 <outputs> 19 <outputs>
28 <data format="palindrome" name="out_file1" /> 20 <data name="out_file1" format="palindrome" />
29 </outputs> 21 </outputs>
30 <tests> 22 <tests>
31 <test> 23 <test>
32 <param name="input1" value="2.fasta"/> 24 <param name="input1" value="2.fasta"/>
33 <param name="minpallen" value="10"/> 25 <param name="minpallen" value="10"/>
37 <param name="overlap" value="yes"/> 29 <param name="overlap" value="yes"/>
38 <output name="out_file1" file="emboss_palindrome_out.palindrome"/> 30 <output name="out_file1" file="emboss_palindrome_out.palindrome"/>
39 </test> 31 </test>
40 </tests> 32 </tests>
41 <help> 33 <help>
42
43 .. class:: warningmark 34 .. class:: warningmark
44 35
45 The input dataset needs to be sequences. 36 The input dataset needs to be sequences.
46 37
47 ----- 38 -----
48 39
49 You can view the original documentation here_. 40 You can view the original documentation here_.
50
51 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/palindrome.html
52 41
53 ------ 42 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/palindrome.html
54
55 **Citation**
56
57 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;`_
58
59 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;`_
60 </help> 43 </help>
44 <expand macro="citations" />
61 </tool> 45 </tool>