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comparison cofold.xml @ 2:63a559812624 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
author rnateam
date Sun, 18 Sep 2016 06:22:07 -0400
parents 33a17b2a199a
children
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1:33a17b2a199a 2:63a559812624
1 <tool id="cofold" name="Cofold" version="0.0.1"> 1 <tool id="cofold" name="Cofold" version="2.0.4.0">
2 <description>An RNA secondary structure prediction method that takes co-transcriptional folding into account</description> 2 <description>An RNA secondary structure prediction method that takes co-transcriptional folding into account</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.0.1">cofold</requirement> 4 <requirement type="package" version="2.0.4">cofold</requirement>
5 </requirements> 5 </requirements>
6 <version_command>CoFold --version</version_command> 6 <version_command>echo "2.0.4"</version_command>
7 <stdio> 7 <stdio>
8 <exit_code range="1:" /> 8 <exit_code range="1:" />
9 <exit_code range=":-1" /> 9 <exit_code range=":-1" />
10 <regex match="Error:" /> 10 <regex match="Error:" />
11 <regex match="Exception:" /> 11 <regex match="Exception:" />
35 </command> 35 </command>
36 <inputs> 36 <inputs>
37 <param format="fasta" name="infile" type="data" label="FASTA file"/> 37 <param format="fasta" name="infile" type="data" label="FASTA file"/>
38 <param name="distAlpha" type="float" value="0.5" label="temperature [°C]" help="(--distAlpha)"/> 38 <param name="distAlpha" type="float" value="0.5" label="temperature [°C]" help="(--distAlpha)"/>
39 <param name="distTau" type="float" value="640.0" label="temperature [°C]" help="(--distTau)"/> 39 <param name="distTau" type="float" value="640.0" label="temperature [°C]" help="(--distTau)"/>
40 <param name="temperature" size="6" type="float" value="37.0" label="temperature [°C]" help="(-T)"/> 40 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="(-T)"/>
41 <param name="energy_parameter" type="select" label="Thermodynamic energy parameters" help="(-P)"> 41 <param name="energy_parameter" type="select" label="Thermodynamic energy parameters" help="(-P)">
42 <option value="rna_turner1999.par" selected="True">Turner 1999</option> 42 <option value="rna_turner1999.par" selected="True">Turner 1999</option>
43 <option value="rna_turner2004.par">Turner 2004</option> 43 <option value="rna_turner2004.par">Turner 2004</option>
44 <option value="rna_andronescu2007.par">Andronescu 2007</option> 44 <option value="rna_andronescu2007.par">Andronescu 2007</option>
45 </param> 45 </param>
58 <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" 58 <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false"
59 label="Calculate structures subject to constraints" help="(--constraint)"/> 59 label="Calculate structures subject to constraints" help="(--constraint)"/>
60 <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" 60 <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false"
61 label="No conversion" help="Do not convert thymine to uracile (T -> U). (--noconv)"/> 61 label="No conversion" help="Do not convert thymine to uracile (T -> U). (--noconv)"/>
62 <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" 62 <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false"
63 label="No lonely pairs" help="--noLP don't allow lonely pairs. (--noLP)"/> 63 label="No lonely pairs" help="Don't allow lonely pairs. (--noLP)"/>
64 <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" 64 <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false"
65 label="No GU pairing" help="Don't allow pairing of G and U. (--noGU)"/> 65 label="No GU pairing" help="Don't allow pairing of G and U. (--noGU)"/>
66 <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false" 66 <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false"
67 label="No GU pairing at the ends" help="Don't allow pairing of G and U at the ends of helices. (--noClosingGU)"/> 67 label="No GU pairing at the ends" help="Don't allow pairing of G and U at the ends of helices. (--noClosingGU)"/>
68 <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" 68 <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false"
83 </outputs> 83 </outputs>
84 <tests> 84 <tests>
85 <test> 85 <test>
86 <param name="infile" value="cofold1.fasta" ftype="fasta"/> 86 <param name="infile" value="cofold1.fasta" ftype="fasta"/>
87 <param name="noPS" value="--noPS"/> 87 <param name="noPS" value="--noPS"/>
88 <output name="tabularFile" file="colfold_results1.tabular" ftype="tabular" /> 88 <output name="tabularFile" file="cofold_results1.tabular" ftype="tabular" />
89 </test> 89 </test>
90 <test> 90 <test>
91 <param name="infile" value="cofold1.fasta" ftype="fasta"/> 91 <param name="infile" value="cofold1.fasta" ftype="fasta"/>
92 <param name="noPS" value="--noPS"/> 92 <param name="noPS" value="--noPS"/>
93 <param name="energy_parameter" value="rna_andronescu2007.par"/> 93 <param name="energy_parameter" value="rna_andronescu2007.par"/>
94 <param name="dangling" value="1"/> 94 <param name="dangling" value="1"/>
95 <param name="advancedSelector" value="yes"/> 95 <param name="advancedSelector" value="yes"/>
96 <output name="tabularFile" file="colfold_results2.tabular" ftype="tabular" /> 96 <output name="tabularFile" file="cofold_results2.tabular" ftype="tabular" />
97 </test> 97 </test>
98 <test> 98 <test>
99 <param name="infile" value="cofold1.fasta" ftype="fasta"/> 99 <param name="infile" value="cofold1.fasta" ftype="fasta"/>
100 <param name="noPS" value=""/> 100 <param name="noPS" value=""/>
101 <output name="tabularFile" file="colfold_results3.tabular" ftype="tabular" /> 101 <output name="tabularFile" file="cofold_results3.tabular" ftype="tabular" />
102 <output name="report"> 102 <output name="report">
103 <assert_contents> 103 <assert_contents>
104 <has_line_matching expression="#RNA structures.*" /> 104 <has_line_matching expression="#RNA structures.*" />
105 </assert_contents> 105 </assert_contents>
106 <discovered_dataset designation="example1_ss" file="example1_ss.ps" compare="sim_size" delta="100" ftype="rna_eps"/> 106 <discovered_dataset designation="example1_ss" file="example1_ss.ps" compare="sim_size" delta="100" ftype="rna_eps"/>
107 </output> 107 </output>
108 </test> 108 </test>
109 <test>
110 <param name="infile" value="cofold1.fasta" ftype="fasta"/>
111 <param name="noPS" value="--noPS"/>
112 <param name="dangling" value="0"/>
113 <output name="tabularFile" file="cofold_results4.tabular" ftype="tabular" />
114 </test>
115 <test>
116 <param name="infile" value="cofold1.fasta" ftype="fasta"/>
117 <param name="noPS" value="--noPS"/>
118 <param name="dangling" value="3"/>
119 <output name="tabularFile" file="cofold_results5.tabular" ftype="tabular" />
120 </test>
121 <test>
122 <param name="infile" value="cofold1.fasta" ftype="fasta"/>
123 <param name="noPS" value="--noPS"/>
124 <param name="energy_parameter" value="rna_turner2004.par"/>
125 <output name="tabularFile" file="cofold_results6.tabular" ftype="tabular" />
126 </test>
109 </tests> 127 </tests>
110 <help> 128 <help>
111 <![CDATA[ 129 <![CDATA[
112 **CoFold**
113 130
114 A tool for prediction of RNA secondary structure that takes co-transcriptional folding into account 131 **What it does**
115 132
116 **Input format** 133 Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.
134
135 **Input**
117 136
118 CoFold requires one input file in FASTA format. 137 CoFold requires one input file in FASTA format.
119 138
120 ------
121 139
122 **Outputs** 140 **Output**
123 141
124 - Tab-seperated file 142 - Tab-separated file
125 - 1st column: header line of FASTA input 143 - 1st column: header line of FASTA input
126 - 2nd column: sequence 144 - 2nd column: sequence
127 - 3rd column: dot-bracket notation 145 - 3rd column: dot-bracket notation
128 - 4th column: free energy 146 - 4th column: free energy
129 147