Mercurial > repos > rnateam > viennarna_rnaheat
comparison rnaheat.xml @ 0:b885d4fab5d4 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
author | rnateam |
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date | Tue, 06 Dec 2016 12:31:31 -0500 |
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-1:000000000000 | 0:b885d4fab5d4 |
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1 <tool id="viennarna_rnaheat" name="@EXECUTABLE@" version="@VERSION@.0"> | |
2 <description>Calculate energies of RNA in a temperature range</description> | |
3 <macros> | |
4 <token name="@EXECUTABLE@">RNAheat</token> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <expand macro="stdio" /> | |
9 <expand macro="version_command" /> | |
10 <command> | |
11 <![CDATA[ | |
12 RNAheat < '$input' > '$output' | |
13 --Tmin $tmin --Tmax $tmax -d$dangling --stepsize=$stepsize --ipoints=$ipoints | |
14 #if $varExists('$advancedOptions.noconversion') | |
15 $advancedOptions.noconversion | |
16 $advancedOptions.nolp | |
17 $advancedOptions.nogu | |
18 $advancedOptions.noclosinggu | |
19 $advancedOptions.notetra | |
20 #if $advancedOptions.nsp | |
21 --nsp='$advancedOptions.nsp' | |
22 #end if | |
23 #end if | |
24 ]]> | |
25 </command> | |
26 | |
27 <inputs> | |
28 <param format="fasta" name="input" type="data" label="Input file"/> | |
29 <param name="tmin" type="float" value="0.0" label="minimal temperature [°C]" help="--Tmin"/> | |
30 <param name="tmax" type="float" value="100.0" label="maximal temperature [°C]" help="--Tmax"/> | |
31 <param name="stepsize" type="float" value="1.0" label="stepsize [°C]" help="--stepsize"/> | |
32 <param name="ipoints" type="integer" value="2" label="data points to fit parabola to: 2*value+1" help="--ipoints"/> | |
33 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d"> | |
34 <option value="0">0: ignore dangling ends</option> | |
35 <option value="1">1: unpaired bases participate in one dangling end only</option> | |
36 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option> | |
37 <option value="3">3: allow coaxial stacking</option> | |
38 </param> | |
39 <conditional name="advancedOptions"> | |
40 <param name="advancedSelector" type="select" label="advanced options"> | |
41 <option value="basic">basic Options</option> | |
42 <option value="advanced">advanced Options</option> | |
43 </param> | |
44 <when value="advanced"> | |
45 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/> | |
46 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/> | |
47 <param name="noclosinggu" type="boolean" truevalue="" falsevalue="--noClosingGU" checked="true" label="Allow GU pairing at the ends" help="Allow pairing of G and U at the ends of helices. --noClosingGU"/> | |
48 <param name="notetra" type="boolean" truevalue="" falsevalue="--noTetra" checked="true" label="Allow stabilization for loops, hairpins etc." help=" Include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (--noTetra)"/> | |
49 <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/> | |
50 <param argument="--nsp" type="text" value="" label="Allow other pairs in addition to the usual AU,GC,and GU pairs." | |
51 help="Its argument is a comma separated list of additionally allowed pairs. If the first character is '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy." /> | |
52 </when> | |
53 <when value="basic"> | |
54 </when> | |
55 </conditional> | |
56 </inputs> | |
57 <outputs> | |
58 <data format="txt" name="output"/> | |
59 </outputs> | |
60 <tests> | |
61 <test> | |
62 <param name="input" value="rnaheat_input1.fa"/> | |
63 <output name="out_file" file="rnaheat_result1.txt"/> | |
64 </test> | |
65 </tests> | |
66 <help> | |
67 <![CDATA[ | |
68 **RNAheat** | |
69 | |
70 Calculates the specific heat of RNA sequences in the temperature range t1 to t2, from the partition function by numeric differentiation. The program fits a parabola to 2*ipoints+1 data points to calculate 2nd derivatives. Increasing this parameter produces a smoother curve. | |
71 | |
72 | |
73 ----- | |
74 | |
75 **Input format** | |
76 | |
77 RNAheat requires one input file Fasta format. | |
78 | |
79 | |
80 ------ | |
81 | |
82 **Outputs** | |
83 | |
84 The result is written as a list of pairs of temperature in C and specific heat in Kcal/(Mol*K) for each sequence in the input file. | |
85 | |
86 | |
87 ]]> | |
88 </help> | |
89 <expand macro="citations" /> | |
90 </tool> |