| Previous changeset 2:84aad99aca1f (2017-05-16) Next changeset 4:0fb2770103f3 (2017-07-12) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 04c9cc19a39fea2e20986ca27d364f86f65184fd |
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modified:
rnafold.xml |
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| diff -r 84aad99aca1f -r fcf2463f85c1 rnafold.xml --- a/rnafold.xml Tue May 16 16:30:38 2017 -0400 +++ b/rnafold.xml Mon May 29 17:24:36 2017 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="viennarna_rnafold" name="@EXECUTABLE@" version="@VERSION@.1"> +<tool id="viennarna_rnafold" name="@EXECUTABLE@" version="@VERSION@.2"> <description>Calculate minimum free energy secondary structures and partition function of RNAs</description> <macros> <token name="@EXECUTABLE@">RNAfold</token> @@ -45,6 +45,7 @@ $advancedOptions.noconversion $advancedOptions.gquad $advancedOptions.nolp + $advancedOptions.nops $advancedOptions.nogu $advancedOptions.noclosinggu $advancedOptions.notetra @@ -148,6 +149,7 @@ </when> </conditional> <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)"/> <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/> <param name="noclosinggu" type="boolean" truevalue="" falsevalue="--noClosingGU" checked="true" label="Allow GU pairing at the ends" help="Allow pairing of G and U at the ends of helices. --noClosingGU"/> @@ -214,7 +216,7 @@ <option value="notUsed" selected="true">Don't use shape reactivity data</option> </param> <when value ="isUsed"> - <param type="data" name="shapeFile" format="shape,*" label="Shape file" argument="--shape"/> + <param type="data" name="shapeFile" format="txt" label="Shape file" argument="--shape"/> <conditional name="shapeMethod"> <param name="methodSelector" type="select" label="Shape reactivity data" argument="--shapeMethod"> <option value="D" selected="true">D: Convert by using a linear equation according to Deigan et al 2009</option> @@ -287,6 +289,7 @@ <outputs> <data format="dbn" name="tabular_file"/> <collection name="sequence_outputs" type="list" label="rna_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"> |