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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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<tool id="cofold" name="Cofold" version="2.0.4.0"> <description>An RNA secondary structure prediction method that takes co-transcriptional folding into account</description> <requirements> <requirement type="package" version="2.0.4">cofold</requirement> </requirements> <version_command>echo "2.0.4"</version_command> <stdio> <exit_code range="1:" /> <exit_code range=":-1" /> <regex match="Error:" /> <regex match="Exception:" /> </stdio> <command interpreter="python"> <![CDATA[ cofold.py -i $infile -o1 $tabularFile --parameters " -T$temperature -d$dangling -P $energy_parameter --distAlpha $distAlpha --distTau $distTau #if $advancedOptions.advancedSelector == 'yes': $advancedOptions.constraint $advancedOptions.noconversion $advancedOptions.nolp $advancedOptions.nogu $advancedOptions.noclosinggu $advancedOptions.notetra $advancedOptions.circular #end if "; count=`ls -l *.ps | wc -l`; echo '#RNA structures: '\$count > $report; ]]> </command> <inputs> <param format="fasta" name="infile" type="data" label="FASTA file"/> <param name="distAlpha" type="float" value="0.5" label="temperature [°C]" help="(--distAlpha)"/> <param name="distTau" type="float" value="640.0" label="temperature [°C]" help="(--distTau)"/> <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="(-T)"/> <param name="energy_parameter" type="select" label="Thermodynamic energy parameters" help="(-P)"> <option value="rna_turner1999.par" selected="True">Turner 1999</option> <option value="rna_turner2004.par">Turner 2004</option> <option value="rna_andronescu2007.par">Andronescu 2007</option> </param> <param name="dangling" type="select" label="how to treat dangling end energies" help="(-d)"> <option value="0">0: ignore dangling ends</option> <option value="1">1: unpaired bases participate in one dangling end only</option> <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option> <option value="3">3: allow coaxial stacking</option> </param> <conditional name="advancedOptions"> <param name="advancedSelector" type="select" label="Advanced Options"> <option value="no">no</option> <option value="yes">yes</option> </param> <when value="yes"> <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate structures subject to constraints" help="(--constraint)"/> <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion" help="Do not convert thymine to uracile (T -> U). (--noconv)"/> <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" label="No lonely pairs" help="Don't allow lonely pairs. (--noLP)"/> <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="Don't allow pairing of G and U. (--noGU)"/> <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false" label="No GU pairing at the ends" help="Don't allow pairing of G and U at the ends of helices. (--noClosingGU)"/> <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="(--noTetra)"/> <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="(--circ)"/> <param name="noPS" type="boolean" truevalue="--noPS" falsevalue="" checked="false" label="Don't generate PS files" help="(--noPS)"/> </when> <when value="no" /> </conditional> </inputs> <outputs> <data name="tabularFile" format="tabular" label="Tabular File"/> <data name="report" format="txt" label="RNA PS File" hidden="true"> <discover_datasets pattern="(?P<designation>.+)\.ps" ext="rna_eps" visible="true"/> </data> </outputs> <tests> <test> <param name="infile" value="cofold1.fasta" ftype="fasta"/> <param name="noPS" value="--noPS"/> <output name="tabularFile" file="cofold_results1.tabular" ftype="tabular" /> </test> <test> <param name="infile" value="cofold1.fasta" ftype="fasta"/> <param name="noPS" value="--noPS"/> <param name="energy_parameter" value="rna_andronescu2007.par"/> <param name="dangling" value="1"/> <param name="advancedSelector" value="yes"/> <output name="tabularFile" file="cofold_results2.tabular" ftype="tabular" /> </test> <test> <param name="infile" value="cofold1.fasta" ftype="fasta"/> <param name="noPS" value=""/> <output name="tabularFile" file="cofold_results3.tabular" ftype="tabular" /> <output name="report"> <assert_contents> <has_line_matching expression="#RNA structures.*" /> </assert_contents> <discovered_dataset designation="example1_ss" file="example1_ss.ps" compare="sim_size" delta="100" ftype="rna_eps"/> </output> </test> <test> <param name="infile" value="cofold1.fasta" ftype="fasta"/> <param name="noPS" value="--noPS"/> <param name="dangling" value="0"/> <output name="tabularFile" file="cofold_results4.tabular" ftype="tabular" /> </test> <test> <param name="infile" value="cofold1.fasta" ftype="fasta"/> <param name="noPS" value="--noPS"/> <param name="dangling" value="3"/> <output name="tabularFile" file="cofold_results5.tabular" ftype="tabular" /> </test> <test> <param name="infile" value="cofold1.fasta" ftype="fasta"/> <param name="noPS" value="--noPS"/> <param name="energy_parameter" value="rna_turner2004.par"/> <output name="tabularFile" file="cofold_results6.tabular" ftype="tabular" /> </test> </tests> <help> <![CDATA[ **What it does** Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. **Input** CoFold requires one input file in FASTA format. **Output** - Tab-separated file - 1st column: header line of FASTA input - 2nd column: sequence - 3rd column: dot-bracket notation - 4th column: free energy ]]> </help> <citations> <citation type="doi">doi:10.1093/nar/gkt174</citation> <citation type="doi">doi:10.1093/nar/gks241</citation> </citations> </tool>