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comparison emboss_primersearch.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: primersearch81" name="primersearch" version="5.0.0"> 1 <tool id="EMBOSS: primersearch81" name="primersearch" version="5.0.0.1">
2 <description>Searches DNA sequences for matches with primer pairs</description> 2 <description>Searches DNA sequences for matches with primer pairs</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>primersearch -seqall $input1 -infile $input2 -outfile $out_file1 -mismatchpercent $mismatchpercent -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>primersearch -seqall '$input1' -infile '$input2' -outfile '$out_file1' -mismatchpercent $mismatchpercent -auto</command>
5 <inputs> 8 <inputs>
6 <param format="fasta" name="input1" type="data"> 9 <param name="input1" type="data" format="fasta" label="Main sequences" />
7 <label>Main sequences</label> 10 <param name="input2" type="data" format="data" label="Primer file" />
8 </param> 11 <param name="mismatchpercent" type="integer" value="0" label="Allowed percent mismatch" />
9 <param format="data" name="input2" type="data">
10 <label>Primer file</label>
11 </param>
12 <param name="mismatchpercent" type="text" value="0">
13 <label>Allowed percent mismatch</label>
14 </param>
15 </inputs> 12 </inputs>
16 <outputs> 13 <outputs>
17 <data format="primersearch" name="out_file1" /> 14 <data name="out_file1" format="primersearch" />
18 </outputs> 15 </outputs>
19 <tests> 16 <tests>
20 <test> 17 <test>
21 <param name="input1" value="2.fasta"/> 18 <param name="input1" value="2.fasta"/>
22 <param name="input2" value="emboss_primersearch.fasta"/> 19 <param name="input2" value="emboss_primersearch.fasta"/>
23 <param name="mismatchpercent" value="0"/> 20 <param name="mismatchpercent" value="0"/>
24 <output name="out_file1" file="emboss_primersearch_out.primersearch"/> 21 <output name="out_file1" file="emboss_primersearch_out.primersearch"/>
25 </test> 22 </test>
26 </tests> 23 </tests>
27 <help> 24 <help>
25 You can view the original documentation here_.
28 26
29 You can view the original documentation here_. 27 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/primersearch.html
30
31 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/primersearch.html
32
33 ------
34
35 **Citation**
36
37 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;`_
38
39 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;`_
40 </help> 28 </help>
29 <expand macro="citations" />
41 </tool> 30 </tool>