comparison rnacofold.xml @ 0:78d673470d45 draft

Imported from capsule None
author rnateam
date Wed, 04 Feb 2015 12:05:27 -0500
parents
children 5e58cbf27a05
comparison
equal deleted inserted replaced
-1:000000000000 0:78d673470d45
1 <tool id="rnacofold" name="RNAcofold" version="2.1.6.0">
2 <description>Calculate secondary structures of two RNAs with dimerization</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <expand macro="stdio" />
6 <macros>
7 <token name="@EXECUTABLE@">RNAcofold</token>
8 <import>macros.xml</import>
9 </macros>
10 <command>
11 <![CDATA[
12 RNAcofold < $input > $tabularFile
13 -T$temperature -d$dangling
14 $pf
15 $allpf
16 #if $varExists('$advancedOptions.noconversion')
17 $advancedOptions.constraint
18 $advancedOptions.noconversion
19 $advancedOptions.gquad
20 $advancedOptions.nolp
21 $advancedOptions.nogu
22 $advancedOptions.noclosinggu
23 $advancedOptions.notetra
24 #end if
25 ]]>
26 </command>
27 <inputs>
28 <param format="fasta" name="input" type="data" label="Fasta file"/>
29 <param name="temperature" size="6" type="float" value="37.0" label="temperature [°C]" help="-T"/>
30 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
31 <option value="0">0: ignore dangling ends</option>
32 <option value="1">1: unpaired bases participate in one dangling end only</option>
33 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
34 <option value="3">3: allow coaxial stacking</option>
35 </param>
36 <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
37 <param name="allpf" type="boolean" checked="false" truevalue="--all_pf" falsevalue="" label="Calculate homo-dimers" help="--all_pf"/>
38 <conditional name="advancedOptions">
39 <param name="advancedSelector" type="select" label="advanced options">
40 <option value="basic">basic Options</option>
41 <option value="advanced">advanced Options</option>
42 </param>
43 <when value="advanced">
44 <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate structure subject to constraints" help="--constraint"/>
45 <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion T->U" help="--noconv"/>
46 <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="-g take into account G Quadruplex formation"/>
47 <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" label="No lonely pairs" help="--noLP don't allow lonely pairs."/>
48 <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="--noGU don't allow pairing of G and U."/>
49 <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false" label="No GU pairing at the ends" help="--noClosingGU don't allow pairing of G and U at the ends of helices."/>
50 <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
51 </when>
52 </conditional>
53 </inputs>
54 <outputs>
55 <data format="txt" name="tabularFile"/>
56 <collection name="sequence_outputs" type="list" label="rna_eps outputs">
57 <discover_datasets pattern="(?P&lt;designation&gt;.+)_ss\.ps" ext="eps" />
58 </collection>
59 <collection name="matrix_outputs" type="list" label="rna_eps outputs">
60 <filter>pf is True</filter>
61 <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
62 </collection>
63 </outputs>
64 <tests>
65 </tests>
66 <help>
67 <![CDATA[
68 **RNAcofold**
69
70
71 -----
72
73 **Input format**
74
75 RNAcofold requires one input file:
76
77 - Fasta file
78
79 Two different RNA sequences can be specified concatenated with the '&' character. The folding of the two sequences with each other will be calculated.
80
81
82 ------
83
84 **Outputs**
85
86 - Energies of the RNA sequences and the dimers
87 - Structure images
88 - Dot Plot Matrix images (if --partfunc is used)
89
90 ]]>
91 </help>
92 <expand macro="requirements" />
93 </tool>