Mercurial > repos > rnateam > cofold
annotate cofold.xml @ 2:6fed0bc99753 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit 1527e05bcd748a2b3cef22e0e356697066a55635
author | rnateam |
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date | Sat, 11 Nov 2017 15:06:13 -0500 |
parents | 4306e2b9ec40 |
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4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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1 <tool id="cofold" name="Cofold" version="2.0.4.0"> |
0 | 2 <description>An RNA secondary structure prediction method that takes co-transcriptional folding into account</description> |
3 <requirements> | |
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4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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4 <requirement type="package" version="2.0.4">cofold</requirement> |
0 | 5 </requirements> |
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4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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6 <version_command>echo "2.0.4"</version_command> |
0 | 7 <stdio> |
8 <exit_code range="1:" /> | |
9 <exit_code range=":-1" /> | |
10 <regex match="Error:" /> | |
11 <regex match="Exception:" /> | |
12 </stdio> | |
13 <command interpreter="python"> | |
14 <![CDATA[ | |
15 cofold.py | |
16 -i $infile | |
17 -o1 $tabularFile | |
18 --parameters " -T$temperature -d$dangling | |
19 -P $energy_parameter | |
20 --distAlpha $distAlpha | |
21 --distTau $distTau | |
22 #if $advancedOptions.advancedSelector == 'yes': | |
23 $advancedOptions.constraint | |
24 $advancedOptions.noconversion | |
25 $advancedOptions.nolp | |
26 $advancedOptions.nogu | |
27 $advancedOptions.noclosinggu | |
28 $advancedOptions.notetra | |
29 $advancedOptions.circular | |
30 #end if | |
31 "; | |
32 count=`ls -l *.ps | wc -l`; | |
33 echo '#RNA structures: '\$count > $report; | |
34 ]]> | |
35 </command> | |
36 <inputs> | |
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)"/> | |
39 <param name="distTau" type="float" value="640.0" label="temperature [°C]" help="(--distTau)"/> | |
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4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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40 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="(-T)"/> |
0 | 41 <param name="energy_parameter" type="select" label="Thermodynamic energy parameters" help="(-P)"> |
42 <option value="rna_turner1999.par" selected="True">Turner 1999</option> | |
43 <option value="rna_turner2004.par">Turner 2004</option> | |
44 <option value="rna_andronescu2007.par">Andronescu 2007</option> | |
45 </param> | |
46 <param name="dangling" type="select" label="how to treat dangling end energies" help="(-d)"> | |
47 <option value="0">0: ignore dangling ends</option> | |
48 <option value="1">1: unpaired bases participate in one dangling end only</option> | |
49 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option> | |
50 <option value="3">3: allow coaxial stacking</option> | |
51 </param> | |
52 <conditional name="advancedOptions"> | |
53 <param name="advancedSelector" type="select" label="Advanced Options"> | |
54 <option value="no">no</option> | |
55 <option value="yes">yes</option> | |
56 </param> | |
57 <when value="yes"> | |
58 <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" | |
59 label="Calculate structures subject to constraints" help="(--constraint)"/> | |
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)"/> | |
62 <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" | |
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4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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63 label="No lonely pairs" help="Don't allow lonely pairs. (--noLP)"/> |
0 | 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)"/> | |
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)"/> | |
68 <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" | |
69 label="No stabilization for loops, hairpins etc." help="(--noTetra)"/> | |
70 <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" | |
71 label="Assume circular RNA structure" help="(--circ)"/> | |
72 <param name="noPS" type="boolean" truevalue="--noPS" falsevalue="" checked="false" | |
73 label="Don't generate PS files" help="(--noPS)"/> | |
74 </when> | |
75 <when value="no" /> | |
76 </conditional> | |
77 </inputs> | |
78 <outputs> | |
79 <data name="tabularFile" format="tabular" label="Tabular File"/> | |
80 <data name="report" format="txt" label="RNA PS File" hidden="true"> | |
81 <discover_datasets pattern="(?P<designation>.+)\.ps" ext="rna_eps" visible="true"/> | |
82 </data> | |
83 </outputs> | |
84 <tests> | |
85 <test> | |
86 <param name="infile" value="cofold1.fasta" ftype="fasta"/> | |
87 <param name="noPS" value="--noPS"/> | |
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4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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88 <output name="tabularFile" file="cofold_results1.tabular" ftype="tabular" /> |
0 | 89 </test> |
90 <test> | |
91 <param name="infile" value="cofold1.fasta" ftype="fasta"/> | |
92 <param name="noPS" value="--noPS"/> | |
93 <param name="energy_parameter" value="rna_andronescu2007.par"/> | |
94 <param name="dangling" value="1"/> | |
95 <param name="advancedSelector" value="yes"/> | |
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4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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96 <output name="tabularFile" file="cofold_results2.tabular" ftype="tabular" /> |
0 | 97 </test> |
98 <test> | |
99 <param name="infile" value="cofold1.fasta" ftype="fasta"/> | |
100 <param name="noPS" value=""/> | |
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4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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101 <output name="tabularFile" file="cofold_results3.tabular" ftype="tabular" /> |
0 | 102 <output name="report"> |
103 <assert_contents> | |
104 <has_line_matching expression="#RNA structures.*" /> | |
105 </assert_contents> | |
106 <discovered_dataset designation="example1_ss" file="example1_ss.ps" compare="sim_size" delta="100" ftype="rna_eps"/> | |
107 </output> | |
108 </test> | |
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4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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109 <test> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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110 <param name="infile" value="cofold1.fasta" ftype="fasta"/> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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111 <param name="noPS" value="--noPS"/> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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112 <param name="dangling" value="0"/> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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113 <output name="tabularFile" file="cofold_results4.tabular" ftype="tabular" /> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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114 </test> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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115 <test> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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116 <param name="infile" value="cofold1.fasta" ftype="fasta"/> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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117 <param name="noPS" value="--noPS"/> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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118 <param name="dangling" value="3"/> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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119 <output name="tabularFile" file="cofold_results5.tabular" ftype="tabular" /> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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120 </test> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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121 <test> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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122 <param name="infile" value="cofold1.fasta" ftype="fasta"/> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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123 <param name="noPS" value="--noPS"/> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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124 <param name="energy_parameter" value="rna_turner2004.par"/> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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125 <output name="tabularFile" file="cofold_results6.tabular" ftype="tabular" /> |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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126 </test> |
0 | 127 </tests> |
128 <help> | |
129 <![CDATA[ | |
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130 |
4306e2b9ec40
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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131 **What it does** |
0 | 132 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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133 Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. |
0 | 134 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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135 **Input** |
0 | 136 |
137 CoFold requires one input file in FASTA format. | |
138 | |
139 | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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140 **Output** |
0 | 141 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
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142 - Tab-separated file |
0 | 143 - 1st column: header line of FASTA input |
144 - 2nd column: sequence | |
145 - 3rd column: dot-bracket notation | |
146 - 4th column: free energy | |
147 | |
148 ]]> | |
149 </help> | |
150 <citations> | |
151 <citation type="doi">doi:10.1093/nar/gkt174</citation> | |
152 <citation type="doi">doi:10.1093/nar/gks241</citation> | |
153 </citations> | |
154 </tool> |