Mercurial > repos > rnateam > cofold
diff cofold.xml @ 0:76d9140e8fa5 draft
Imported from capsule None
author | bjoern-gruening |
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date | Fri, 13 Feb 2015 05:33:32 -0500 |
parents | |
children | 4306e2b9ec40 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cofold.xml Fri Feb 13 05:33:32 2015 -0500 @@ -0,0 +1,136 @@ +<tool id="cofold" name="Cofold" version="0.0.1"> + <description>An RNA secondary structure prediction method that takes co-transcriptional folding into account</description> + <requirements> + <requirement type="package" version="0.0.1">cofold</requirement> + </requirements> + <version_command>CoFold --version</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" size="6" 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="--noLP 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="colfold_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="colfold_results2.tabular" ftype="tabular" /> + </test> + <test> + <param name="infile" value="cofold1.fasta" ftype="fasta"/> + <param name="noPS" value=""/> + <output name="tabularFile" file="colfold_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> + </tests> + <help> +<![CDATA[ +**CoFold** + +A tool for prediction of RNA secondary structure that takes co-transcriptional folding into account + +**Input format** + +CoFold requires one input file in FASTA format. + +------ + +**Outputs** + +- Tab-seperated 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>