Mercurial > repos > rnateam > viennarna_rnafold
diff rnafold.xml @ 8:bdb786715d28 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29
| author | rnateam |
|---|---|
| date | Wed, 20 Dec 2017 08:34:54 -0500 |
| parents | 86f517dcfdfb |
| children |
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--- a/rnafold.xml Thu Sep 28 16:24:39 2017 -0400 +++ b/rnafold.xml Wed Dec 20 08:34:54 2017 -0500 @@ -1,4 +1,4 @@ -<tool id="viennarna_rnafold" name="@EXECUTABLE@" version="@VERSION@.3"> +<tool id="viennarna_rnafold" name="@EXECUTABLE@" version="@VERSION@.4"> <description>Calculate minimum free energy secondary structures and partition function of RNAs</description> <macros> <token name="@EXECUTABLE@">RNAfold</token> @@ -31,15 +31,23 @@ #if $layout_type ==0 --layout-type=$general_options.layout_type #end if - #if $mea: - --MEA=$mea + + #if $mea: + #if $meagamma: + --MEA=$meagamma + #else + --MEA + #end if #end if + #if $pf $pf - #if $pfscale: - --pfScale=$pfscale - #end if #end if + + #if $pfscale: + --pfScale=$pfscale + #end if + $advancedOptions.noconversion $advancedOptions.gquad $advancedOptions.nolp @@ -104,7 +112,7 @@ #else "${input_source.fasta_input}" #end if - > '$tabular_file' + > '$dot_bracket_stdout' ]]> </command> @@ -132,9 +140,12 @@ <option value="1" selected="true">Default: Naview layout</option> <option value="0">Simple radial layout</option> </param> - <param argument="--MEA" name="mea" type="float" value="1.0" optional="true" label="Gamma Value" help="Used for the calculation of the Maximum Expected accuracy"/> + + <param name="mea" type="boolean" checked="false" falsevalue="" label="Calculate Maximum Expected accuracy" help="--MEA"/> + <param name="meagamma" type="float" optional="true" label="MEA-Gamma Value"/> + <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/> - <param name="pfscale" type="float" value="1.07" optional="true" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences."/> + <param name="pfscale" type="float" optional="true" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences."/> <section name="advancedOptions" title="Advanced options"> <param name="nops" type="boolean" truevalue="--noPS" falsevalue="" checked="false" label="Do not produce postscript drawing of the mfe structure (reduces run-time)" help="(--noPS)"/> <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/> @@ -279,13 +290,13 @@ </section> </inputs> <outputs> - <data format="dbn" name="tabular_file"/> - <collection name="sequence_outputs" type="list" label="rna_eps outputs"> + <data format="dbn" name="dot_bracket_stdout"/> + <collection name="structure_outputs" type="list" label="rna_strcuture_eps outputs"> <filter>advancedOptions['nops'] is False</filter> <discover_datasets pattern="(?P<designation>.+)_ss\.ps" ext="eps" /> </collection> - <collection name="matrix_outputs" type="list" label="rna_eps outputs"> - <filter>measelect['pf'] is True</filter> + <collection name="matrix_outputs" type="list" label="rna_matrix_eps outputs"> + <filter>pf is True</filter> <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> </collection> </outputs> @@ -293,18 +304,40 @@ <test> <param name="select_fasta" value="true" /> <param name="fasta_input" value="rnafold_input1.fa"/> - <output name="tabular_file" file="rnafold_result1.txt"/> + <output name="dot_bracket_stdout" file="rnafold_result1.txt"/> + </test> + + <test> + <param name="select_fasta" value="true" /> + <param name="mea" value="true" /> + <param name="fasta_input" value="rnafold_input1.fa"/> + <output name="dot_bracket_stdout" file="rnafold_result1_mea.txt"/> </test> <test> <param name="select_fasta" value="true" /> + <param name="pf" value="true" /> + <param name="fasta_input" value="rnafold_input1.fa"/> + <output name="dot_bracket_stdout" file="rnafold_result1_pf.txt"/> + <output_collection name="structure_outputs" type="list"> + <element name="Anolis_caro_chrUn_GL343590.trna2_AlaAGC" file="Anolis_caro_chrUn_GL343590.trna2_AlaAGC_ss.ps" compare="sim_size" /> + <element name="Anolis_caro_chrUn_GL343207.trna3_AlaAGC" file="Anolis_caro_chrUn_GL343207.trna3_AlaAGC_ss.ps" compare="sim_size" /> + </output_collection> + + <output_collection name="matrix_outputs" type="list"> + <element name="Anolis_caro_chrUn_GL343590.trna2_AlaAGC" file="Anolis_caro_chrUn_GL343590.trna2_AlaAGC_dp.ps" compare="sim_size" /> + <element name="Anolis_caro_chrUn_GL343207.trna3_AlaAGC" file="Anolis_caro_chrUn_GL343207.trna3_AlaAGC_dp.ps" compare="sim_size" /> + </output_collection> + </test> + <test> + <param name="select_fasta" value="true" /> <param name="fasta_input" value="rnafold_input2.fa"/> <param name="temperature" value="75"/> - <output name="tabular_file" file="rnafold_result2.txt"/> + <output name="dot_bracket_stdout" file="rnafold_result2.txt"/> </test> <test> <param name="select_fasta" value="false" /> <param name="input_sequence" value="TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA"/> - <output name="tabular_file" file="rnafold_result3.txt"/> + <output name="dot_bracket_stdout" file="rnafold_result3.txt"/> </test> <test> <param name="select_fasta" value="true" /> @@ -313,8 +346,9 @@ <param name="shapeSelector" value="isUsed"/> </conditional> <param name="shapeFile" value="sample_3.react"/> - <output name="tabular_file" file="sample_3_result.txt"/> + <output name="dot_bracket_stdout" file="sample_3_result.txt"/> </test> + </tests> <help> <![CDATA[