Mercurial > repos > rnateam > viennarna_rnadpdist

comparison rnapdist.xml @ 0:149b7a662bcc draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
author rnateam
date Tue, 06 Dec 2016 12:36:23 -0500
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1 <tool id="viennarna_rnadpdist" name="@EXECUTABLE@" version="@VERSION@.0">
2 <description>Calculate distances between thermodynamic RNA secondary structure ensembles
3 </description>
4
5 <macros>
6 <token name="@EXECUTABLE@">RNApdist</token>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="requirements" />
10 <expand macro="stdio" />
11 <expand macro="version_command" />
12 <command>
13 <![CDATA[
14 RNApdist < '$input' > '$output'
15 --compare=$compare
16 -T$temperature -d$dangling
17 $backtrack
18 #if $varExists('$advancedOptions.nolp')
19 $advancedOptions.noconversion
20 $advancedOptions.nolp
21 $advancedOptions.nogu
22 $advancedOptions.noclosinggu
23 $advancedOptions.notetra
24 #end if
25 #if $backtrack and str($compare)=="m"
26 && cat backtrack.file >> '$outfile'
27 #end if
28
29 ]]>
30 </command>
31
32 <inputs>
33 <param format="fasta" name="input" type="data" label="Fasta file"/>
34 <param name="temperature" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
35 <param name="dangling" type="select" label="How to treat dangling end energies" help="-d">
36 <option value="0">0: ignore dangling ends</option>
37 <option value="1">1: unpaired bases participate in one dangling end only</option>
38 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
39 <option value="3">3: allow coaxial stacking</option>
40 </param>
41 <param name="compare" type="select" label="Comparison Option" help="--compare">
42 <option value="p" selected="True">p: pairwise (1st with 2nd, 3rd with 4th, ...)</option>
43 <option value="m">m: matrix (each with each, output in matrix form)</option>
44 <option value="f" >f: first (1st with 2nd, 1st with 3rd, ...)</option>
45 <option value="c">c: continuous (1st with 2nd, 2nd with 3rd, ...)</option>
46 </param>
47 <param name="backtrack" type="boolean" checked="false" truevalue="--backtrack" falsevalue="" label="Print an alignment" help="--backtrack"/>
48 <conditional name="advancedOptions">
49 <param name="advancedSelector" type="select" label="advanced options">
50 <option value="basic">basic Options</option>
51 <option value="advanced">advanced Options</option>
52 </param>
53 <when value="advanced">
54 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
55 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
56 <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"/>
57 <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)"/>
58 <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/>
59 </when>
60 <when value="basic">
61 </when>
62 </conditional>
63 </inputs>
64 <outputs>
65 <data format="txt" name="output"/>
66 <data format="txt" name="dotplot"/>
67 <collection name="matrix_outputs" type="list" label="rna_eps outputs">
68 <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
69 </collection>
70 </outputs>
71 <tests>
72 <test>
73 <param name="input" value="rnapdist_input1.fa"/>
74 <output name="out_file" file="rnapdist_result1.txt"/>
75 </test>
76 </tests>
77 <help>
78 <![CDATA[
79
80 **RNApdist**
81
82 RNApdist calculates structure distances between the thermodynamic ensembles of the secondary structures of RNA sequences.
83
84 -----
85
86 **Input format**
87
88 RNApdist requires one input file
89 - Fasta file
90
91 ------
92
93 **Outputs**
94
95 - output of alignment scores and alignments (if -B option is selected)
96 - dot plot matrices in postscript format bundled together in a tar file
97
98 ]]>
99 </help>
100 <expand macro="citations" />
101 </tool>