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comparison emboss_garnier.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: garnier40" name="garnier" version="5.0.0"> 1 <tool id="EMBOSS: garnier40" name="garnier" version="5.0.0">
2 <description>Predicts protein secondary structure</description> 2 <description>Predicts protein secondary structure</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>garnier -sequence $input1 -outfile $out_file1 -idc $idc -rformat2 $out_format1 -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>garnier -sequence '$input1' -outfile '$out_file1' -idc $idc -rformat2 $out_format1 -auto</command>
5 <inputs> 9 <inputs>
6 <param format="data" name="input1" type="data"> 10 <param name="input1" type="data" format="data" label="Sequences" />
7 <label>Sequences</label> 11 <param name="idc" type="select" label="idc" help="In their paper, GOR mention that if you know something about the secondary structure content of the protein you are analyzing, you can do better in prediction. 'idc' is an index into a set of arrays, dharr[] and dsarr[], which provide 'decision constants' (dch, dcs), which are offsets that are applied to the weights for the helix and sheet (extend) terms. So, idc=0 says don't use the decision constant offsets, and idc=1 to 6 indicates that various combinations of dch,dcs offsets should be used">
8 </param>
9 <param name="idc" type="select">
10 <label>In their paper, GOR mention that if you know something about the secondary structure content of the protein you are analyzing, you can do better in prediction. 'idc' is an index into a
11 set of arrays, dharr[] and dsarr[], which provide 'decision constants' (dch, dcs), which are offsets that are applied to the weights for the helix and sheet (extend) terms. So, idc=0 says don't
12 use the decision constant offsets, and idc=1 to 6 indicates that various combinations of dch,dcs offsets should be used</label>
13 <option value="0">idc 0</option> 12 <option value="0">idc 0</option>
14 <option value="1">idc 1</option> 13 <option value="1">idc 1</option>
15 <option value="2">idc 2</option> 14 <option value="2">idc 2</option>
16 <option value="3">idc 3</option> 15 <option value="3">idc 3</option>
17 <option value="4">idc 4</option> 16 <option value="4">idc 4</option>
18 <option value="5">idc 5</option> 17 <option value="5">idc 5</option>
19 <option value="6">idc 6</option> 18 <option value="6">idc 6</option>
20 </param> 19 </param>
21 <param name="out_format1" type="select"> 20 <param name="out_format1" type="select" label="Output report file format">
22 <label>Output Report File Format</label>
23 <option value="tagseq">TagSeq</option> 21 <option value="tagseq">TagSeq</option>
24 <option value="embl">EMBL</option> 22 <option value="embl">EMBL</option>
25 <option value="genbank">GENBANK</option> 23 <option value="genbank">GENBANK</option>
26 <option value="gff">GFF</option> 24 <option value="gff">GFF</option>
27 <option value="pir">PIR</option> 25 <option value="pir">PIR</option>
37 <option value="srs">SRS</option> 35 <option value="srs">SRS</option>
38 <option value="table">Table</option> 36 <option value="table">Table</option>
39 </param> 37 </param>
40 </inputs> 38 </inputs>
41 <outputs> 39 <outputs>
42 <data format="garnier" name="out_file1" /> 40 <data name="out_file1" format="garnier" />
43 </outputs> 41 </outputs>
44 <tests> 42 <tests>
45 <test> 43 <test>
46 <param name="input1" value="2.fasta"/> 44 <param name="input1" value="2.fasta"/>
47 <param name="idc" value="0"/> 45 <param name="idc" value="0"/>
48 <param name="out_format1" value="excel"/> 46 <param name="out_format1" value="excel"/>
49 <output name="out_file1" file="emboss_garnier_out.tabular"/> 47 <output name="out_file1" file="emboss_garnier_out.tabular"/>
50 </test> 48 </test>
51 </tests> 49 </tests>
52 <code file="emboss_format_corrector.py" />
53 <help> 50 <help>
54 You can view the original documentation here_. 51 You can view the original documentation here_.
55
56 .. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/garnier.html
57 52
58 ------ 53 .. _here: https://galaxy-iuc.github.io/emboss-5.0-docs/garnier.html
59
60 **Citation**
61
62 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;`_
63
64 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;`_
65 </help> 54 </help>
55 <expand macro="citations" />
66 </tool> 56 </tool>