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comparison emboss_epestfind.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: epestfind29" name="epestfind" version="5.0.0"> 1 <tool id="EMBOSS: epestfind29" name="epestfind" version="5.0.0.1">
2 <description>Finds PEST motifs as potential proteolytic cleavage sites</description> 2 <description>Finds PEST motifs as potential proteolytic cleavage sites</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' epestfind -sequence '$input1' -goutfile '$ofile2' -outfile '$ofile1' -window $window -order $order -potential $potential -poor $poor
5 -invalid $invalid -map $map -graph png -auto</command> 8 -invalid $invalid -map $map -graph png -auto</command>
6 <inputs> 9 <inputs>
7 <param format="data" name="input1" type="data"> 10 <param name="input1" type="data" format="data" label="Sequence" />
8 <label>Sequence</label> 11 <param name="window" type="integer" value="10" label="Minimal distance between positively charged amino acids" />
9 </param> 12 <param name="order" type="select" label="Sort by">
10 <param name="window" type="text" value="10">
11 <label>Minimal distance between positively charged amino acids</label>
12 </param>
13 <param name="order" type="select">
14 <label>Sort by</label>
15 <option value="3">Score</option> 13 <option value="3">Score</option>
16 <option value="1">Length</option> 14 <option value="1">Length</option>
17 <option value="2">Position</option> 15 <option value="2">Position</option>
18 </param> 16 </param>
19 <param name="threshold" type="text" value="5.0"> 17 <param name="threshold" type="float" value="5.0" label="Threshold value to discriminate weak from potential PEST motifs" />
20 <label>Threshold value to discriminate weak from potential PEST motifs.</label> 18 <param name="potential" type="select" label="Decide whether potential PEST motifs should be printed">
21 </param>
22 <param name="potential" type="select">
23 <label>Decide whether potential PEST motifs should be printed</label>
24 <option value="yes">Yes</option> 19 <option value="yes">Yes</option>
25 <option value="no">No</option> 20 <option value="no">No</option>
26 </param> 21 </param>
27 <param name="poor" type="select"> 22 <param name="poor" type="select" label="Decide whether poor PEST motifs should be printed">
28 <label>Decide whether poor PEST motifs should be printed</label>
29 <option value="yes">Yes</option> 23 <option value="yes">Yes</option>
30 <option value="no">No</option> 24 <option value="no">No</option>
31 </param> 25 </param>
32 <param name="invalid" type="select"> 26 <param name="invalid" type="select" label="Decide whether invalid PEST motifs should be printed">
33 <label>Decide whether invalid PEST motifs should be printed</label>
34 <option value="no">No</option> 27 <option value="no">No</option>
35 <option value="yes">Yes</option> 28 <option value="yes">Yes</option>
36 </param> 29 </param>
37 <param name="map" type="select"> 30 <param name="map" type="select" label="Decide whether PEST motifs should be mapped to sequence">
38 <label>Decide whether PEST motifs should be mapped to sequence</label>
39 <option value="yes">Yes</option> 31 <option value="yes">Yes</option>
40 <option value="no">No</option> 32 <option value="no">No</option>
41 </param> 33 </param>
42 </inputs> 34 </inputs>
43 <outputs> 35 <outputs>
44 <data format="png" name="ofile2" /> 36 <data name="ofile2" format="png" />
45 <data format="epestfind" name="ofile1" /> 37 <data name="ofile1" format="epestfind" />
46 </outputs> 38 </outputs>
47 <!-- <tests> 39 <!-- <tests>
48 <test> 40 <test>
49 <param name="input1" value="2.fasta"/> 41 <param name="input1" value="2.fasta"/>
50 <param name="window" value="10"/> 42 <param name="window" value="10"/>
57 <output name="ofile1" file="emboss_epestfind_out.epestfind"/> 49 <output name="ofile1" file="emboss_epestfind_out.epestfind"/>
58 </test> 50 </test>
59 </tests> output file contains file location info --> 51 </tests> output file contains file location info -->
60 <help> 52 <help>
61 You can view the original documentation here_. 53 You can view the original documentation here_.
62
63 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/epestfind.html
64 54
65 ------ 55 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/epestfind.html
66
67 **Citation**
68
69 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;`_
70
71 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;`_
72 </help> 56 </help>
57 <expand macro="citations" />
73 </tool> 58 </tool>