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comparison emboss_equicktandem.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: equicktandem31" name="equicktandem" version="5.0.0"> 1 <tool id="EMBOSS: equicktandem31" name="equicktandem" version="5.0.0.1">
2 <description>Finds tandem repeats</description> 2 <description>Finds tandem repeats</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>equicktandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>equicktandem -sequence '$input1' -outfile '$out_file1' -origfile '$ofile2' -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto</command>
5 <inputs> 9 <inputs>
6 <param format="fasta" name="input1" type="data"> 10 <param name="input1" type="data" format="fasta" label="Sequence" />
7 <label>Sequence</label> 11 <param name="maxrepeat" type="integer" value="600" label="Maximum repeat size" />
8 </param> 12 <param name="threshold" type="integer" value="20" label="Threshold score" />
9 <param name="maxrepeat" type="text" value="600"> 13 <param name="out_format1" type="select" label="Output report file format">
10 <label>Maximum repeat size</label>
11 </param>
12 <param name="threshold" type="text" value="20">
13 <label>Threshold score</label>
14 </param>
15 <param name="out_format1" type="select">
16 <label>Output Report File Format</label>
17 <option value="table">Table</option> 14 <option value="table">Table</option>
18 <option value="embl">EMBL</option> 15 <option value="embl">EMBL</option>
19 <option value="genbank">GENBANK</option> 16 <option value="genbank">GENBANK</option>
20 <option value="gff">GFF</option> 17 <option value="gff">GFF</option>
21 <option value="pir">PIR</option> 18 <option value="pir">PIR</option>
31 <option value="srs">SRS</option> 28 <option value="srs">SRS</option>
32 <option value="tagseq">TagSeq</option> 29 <option value="tagseq">TagSeq</option>
33 </param> 30 </param>
34 </inputs> 31 </inputs>
35 <outputs> 32 <outputs>
36 <data format="table" name="out_file1" /> 33 <data name="out_file1" format="table" />
37 <data format="equicktandem" name="ofile2" /> 34 <data name="ofile2" format="equicktandem" />
38 </outputs> 35 </outputs>
39 <tests> 36 <tests>
40 <test> 37 <test>
41 <param name="input1" value="1.fasta"/> 38 <param name="input1" value="1.fasta"/>
42 <param name="maxrepeat" value="600"/> 39 <param name="maxrepeat" value="600"/>
43 <param name="threshold" value="20"/> 40 <param name="threshold" value="20"/>
44 <param name="out_format1" value="table"/> 41 <param name="out_format1" value="table"/>
45 <output name="ofile2" file="emboss_equicktandem_out.equicktandem"/> 42 <output name="ofile2" file="emboss_equicktandem_out.equicktandem"/>
46 </test> 43 </test>
47 </tests> 44 </tests>
48 <code file="emboss_format_corrector.py" />
49 <help> 45 <help>
50 .. class:: warningmark 46 .. class:: warningmark
51 47
52 The input dataset needs to be sequences. 48 The input dataset needs to be sequences.
53 49
54 ----- 50 -----
55 51
56 You can view the original documentation here_. 52 You can view the original documentation here_.
57
58 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/equicktandem.html
59 53
60 ------ 54 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/equicktandem.html
61
62 **Citation**
63
64 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;`_
65
66 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;`_
67 </help> 55 </help>
56 <expand macro="citations" />
68 </tool> 57 </tool>