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comparison emboss_dan.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: dan19" name="dan" version="5.0.0"> 1 <tool id="EMBOSS: dan19" name="dan" version="5.0.0.1">
2 <description>Calculates DNA RNA/DNA melting temperature</description> 2 <description>Calculates DNA RNA/DNA melting temperature</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command interpreter="perl">emboss_single_outputfile_wrapper.pl dan -sequence $input1 -windowsize $window -goutfile $out_file1 -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' dan -sequence '$input1' -windowsize $window -goutfile '$out_file1' -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc
5 -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command> 9 -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command>
6 <inputs> 10 <inputs>
7 <param format="data" name="input1" type="data"> 11 <param name="input1" type="data" format="data" label="On query" />
8 <label>On query</label> 12 <param name="window" type="integer" value="20" label="Window size" />
9 </param> 13 <param name="shift" type="integer" value="1" label="Step size (shift increment)" />
10 <param name="window" type="text" value="20"> 14 <param name="dnaconc" type="float" value="50.0" label="DNA Concentration (nM)" />
11 <label>Window Size</label> 15 <param name="saltconc" type="float" value="50.0" label="Salt concentration (mM)" />
12 </param> 16 <param name="thermo" type="select" label="Output the DeltaG, DeltaH and DeltaS values">
13 <param name="shift" type="text" value="1">
14 <label>Step size (shift increment)</label>
15 </param>
16 <param name="dnaconc" type="text" value="50.0">
17 <label>DNA Concentration (nM)</label>
18 </param>
19 <param name="saltconc" type="text" value="50.0">
20 <label>Salt concentration (mM)</label>
21 </param>
22 <param name="thermo" type="select">
23 <label>Output the DeltaG, DeltaH and DeltaS values</label>
24 <option value="yes">Yes</option> 17 <option value="yes">Yes</option>
25 <option value="no">No</option> 18 <option value="no">No</option>
26 </param> 19 </param>
27 <param name="temperature" type="text" value="25 "> 20 <param name="temperature" type="float" value="25.0" label="Temperature at which to calculate the DeltaG, DeltaH and DeltaS values" />
28 <label>Temperature at which to calculate the DeltaG, DeltaH and DeltaS values</label> 21 <param name="rna" type="select" label="Sequence is RNA">
29 </param>
30 <param name="rna" type="select">
31 <label>Sequence is RNA</label>
32 <option value="no">No</option> 22 <option value="no">No</option>
33 <option value="yes">Yes</option> 23 <option value="yes">Yes</option>
34 </param> 24 </param>
35 <param name="product" type="select"> 25 <param name="product" type="select" label="Include percent formamide, percent of mismatches allowed and product length">
36 <label>Include percent formamide, percent of mismatches allowed and product length</label>
37 <option value="no">No</option> 26 <option value="no">No</option>
38 <option value="yes">Yes</option> 27 <option value="yes">Yes</option>
39 </param> 28 </param>
40 <param name="formamide" type="text" value="0 "> 29 <param name="formamide" type="float" value="0.0" label="Formamide concentration (nM)" />
41 <label>Formamide concentration (nM)</label> 30 <param name="mismatch" type="float" value="0.0" label="Percent mismatch to be used in calculations" />
42 </param> 31 <param name="prodlen" type="integer" value="20" label="Product length to be used in calculations" />
43 <param name="mismatch" type="text" value="0 "> 32 <param name="plot1" type="select" label="Create a graph">
44 <label>Percent mismatch to be used in calculations</label>
45 </param>
46 <param name="prodlen" type="text" value="20">
47 <label>Product length to be used in calculations</label>
48 </param>
49 <param name="plot1" type="select">
50 <label>Create a graph</label>
51 <option value="no">No</option> 33 <option value="no">No</option>
52 <option value="yes">Yes</option> 34 <option value="yes">Yes</option>
53 </param> 35 </param>
54 </inputs> 36 </inputs>
55 <outputs> 37 <outputs>
56 <data format="dan" name="out_file1" /> 38 <data name="out_file1" format="dan" />
57 </outputs> 39 </outputs>
58 <!-- 40 <!--
59 <tests> 41 <tests>
60 <test> 42 <test>
61 <param name="input1" value="2.fasta"/> 43 <param name="input1" value="2.fasta"/>
73 <param name="plot1" value="yes"/> 55 <param name="plot1" value="yes"/>
74 <output name="out_file1" file="emboss_dan_out.png"/> 56 <output name="out_file1" file="emboss_dan_out.png"/>
75 </test> 57 </test>
76 </tests> 58 </tests>
77 --> 59 -->
78 <code file="emboss_format_corrector.py" />
79 <help> 60 <help>
80 You can view the original documentation here_. 61 You can view the original documentation here_.
81
82 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dan.html
83 62
84 ------ 63 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/dan.html
85
86 **Citation**
87
88 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;`_
89
90 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;`_
91 </help> 64 </help>
65 <expand macro="citations" />
92 </tool> 66 </tool>