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comparison emboss_dan.xml @ 10:d49956b87f7e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
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children 8992d258e42f
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9:511429456d3c 10:d49956b87f7e
1 <tool id="EMBOSS: dan19" name="dan" version="5.0.0.1">
2 <description>Calculates DNA RNA/DNA melting temperature</description>
3 <macros>
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
9 -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command>
10 <inputs>
11 <param name="input1" type="data" format="data" label="On query" />
12 <param name="window" type="integer" value="20" label="Window size" />
13 <param name="shift" type="integer" value="1" label="Step size (shift increment)" />
14 <param name="dnaconc" type="float" value="50.0" label="DNA Concentration (nM)" />
15 <param name="saltconc" type="float" value="50.0" label="Salt concentration (mM)" />
16 <param name="thermo" type="select" label="Output the DeltaG, DeltaH and DeltaS values">
17 <option value="yes">Yes</option>
18 <option value="no">No</option>
19 </param>
20 <param name="temperature" type="float" value="25.0" label="Temperature at which to calculate the DeltaG, DeltaH and DeltaS values" />
21 <param name="rna" type="select" label="Sequence is RNA">
22 <option value="no">No</option>
23 <option value="yes">Yes</option>
24 </param>
25 <param name="product" type="select" label="Include percent formamide, percent of mismatches allowed and product length">
26 <option value="no">No</option>
27 <option value="yes">Yes</option>
28 </param>
29 <param name="formamide" type="float" value="0.0" label="Formamide concentration (nM)" />
30 <param name="mismatch" type="float" value="0.0" label="Percent mismatch to be used in calculations" />
31 <param name="prodlen" type="integer" value="20" label="Product length to be used in calculations" />
32 <param name="plot1" type="select" label="Create a graph">
33 <option value="no">No</option>
34 <option value="yes">Yes</option>
35 </param>
36 </inputs>
37 <outputs>
38 <data name="out_file1" format="dan" />
39 </outputs>
40 <!--
41 <tests>
42 <test>
43 <param name="input1" value="2.fasta"/>
44 <param name="window" value="20"/>
45 <param name="shift" value="1"/>
46 <param name="dnaconc" value="50"/>
47 <param name="saltconc" value="50"/>
48 <param name="thermo" value="yes"/>
49 <param name="temperature" value="25"/>
50 <param name="rna" value="no"/>
51 <param name="product" value="no"/>
52 <param name="formamide" value="0"/>
53 <param name="mismatch" value="0"/>
54 <param name="prodlen" value="20"/>
55 <param name="plot1" value="yes"/>
56 <output name="out_file1" file="emboss_dan_out.png"/>
57 </test>
58 </tests>
59 -->
60 <help>
61 You can view the original documentation here_.
62
63 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/dan.html
64 </help>
65 <expand macro="citations" />
66 </tool>