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comparison emboss_iep.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 d5c3794bd246
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10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: iep45" name="iep" version="5.0.0"> 1 <tool id="EMBOSS: iep45" name="iep" version="5.0.0.1">
2 <description>Calculates the isoelectric point of a protein</description> 2 <description>Calculates the isoelectric point of a protein</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>iep -sequence $input1 -outfile $out_file1 -step $step -amino $amino -graph png -termini $termini -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>iep -sequence '$input1' -outfile '$out_file1' -step $step -amino $amino -graph png -termini $termini -auto</command>
5 <inputs> 8 <inputs>
6 <param format="data" name="input1" type="data"> 9 <param name="input1" type="data" format="data" label="Sequences" />
7 <label>Sequences</label> 10 <param name="step" type="float" value="0.5" label="Step value for pH" />
8 </param> 11 <param name="amino" type="integer" value="1" label="Number of N-termini" />
9 <param name="step" type="text" value=".5"> 12 <param name="termini" type="select" label="Include charge at N and C terminus">
10 <label>Step value for pH</label>
11 </param>
12 <param name="amino" type="text" value="1">
13 <label>Number of N-termini</label>
14 </param>
15 <param name="termini" type="select">
16 <label>Include charge at N and C terminus</label>
17 <option value="yes">Yes</option> 13 <option value="yes">Yes</option>
18 <option value="no">No</option> 14 <option value="no">No</option>
19 </param> 15 </param>
20 </inputs> 16 </inputs>
21 <outputs> 17 <outputs>
22 <data format="iep" name="out_file1" /> 18 <data name="out_file1" format="iep" />
23 </outputs> 19 </outputs>
24 <tests> 20 <tests>
25 <test> 21 <test>
26 <param name="input1" value="2.fasta"/> 22 <param name="input1" value="2.fasta"/>
27 <param name="step" value="0.5"/> 23 <param name="step" value="0.5"/>
30 <output name="out_file1" file="emboss_iep_out.iep"/> 26 <output name="out_file1" file="emboss_iep_out.iep"/>
31 </test> 27 </test>
32 </tests> 28 </tests>
33 <help> 29 <help>
34 You can view the original documentation here_. 30 You can view the original documentation here_.
35
36 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/iep.html
37 31
38 ------ 32 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/iep.html
39
40 **Citation**
41
42 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;`_
43
44 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;`_
45 </help> 33 </help>
34 <expand macro="citations" />
46 </tool> 35 </tool>