Mercurial > repos > yhoogstrate > segmentation_fold
changeset 2:eccb5ee89df7 draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36-dirty
| author | yhoogstrate |
|---|---|
| date | Wed, 02 Dec 2015 04:34:50 -0500 |
| parents | 9827a554e52f |
| children | 59ab674be4b5 |
| files | segmentation-fold.xml tool_dependencies.xml |
| diffstat | 2 files changed, 12 insertions(+), 12 deletions(-) [+] |
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--- a/segmentation-fold.xml Sun Aug 02 03:28:30 2015 -0400 +++ b/segmentation-fold.xml Wed Dec 02 04:34:50 2015 -0500 @@ -1,13 +1,13 @@ -<tool id="segmentation_fold" name="segmentation-fold" version="0.2.0"> +<tool id="segmentation_fold" name="segmentation-fold" version="1.1.0_1"> <description>RNA-Folding including predefined segments including K-turns</description> <requirements> - <requirement type="package" version="1.0.0">segmentation-fold</requirement> + <requirement type="package" version="1.1.0">segmentation-fold</requirement> </requirements> <stdio></stdio> - <version_command>segmentation-fold -V | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//'</version_command> + <version_command>segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//'</version_command> <command><![CDATA[ segmentation-fold @@ -15,7 +15,7 @@ #if $input.method == "fasta" -f $input.input_fasta #else - -s $input.input_sequence + -s ${input.input_sequence} #end if -p $predict_segments @@ -27,7 +27,7 @@ -x $parameters.input_xml #end if - -t \${GALAXY_SLOTS:-2} + -t \${GALAXY_SLOTS:-4} > $output_dbn ]]></command> @@ -184,13 +184,13 @@ Segmentation-fold is a bioinformatics application that predicts RNA 2D-structure with an extended version of the Zuker algorithm. This modification contains a new "structure element" named a segment and is -capable of folding a pre-defined substructure with multiple canonical +capable of folding a pre-defined substructures with multiple canonical or non-canonical pairings. -This allows folding of more complex structures like the K-turns, which -are also part of the implemented free energy tables. These thermodynamic -parameters (free Gibbs energy levels) have been estimated using a -computational approach and therefore lack accuracy. +This allows folding of more complex structures like K-turns, which are +also part of the implemented free energy table. These thermodynamic +parameters (free Gibbs energy) have been estimated using a in silico +approach and therefore lack high resolution. ]]></help> <citations>
--- a/tool_dependencies.xml Sun Aug 02 03:28:30 2015 -0400 +++ b/tool_dependencies.xml Wed Dec 02 04:34:50 2015 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="segmentation-fold" version="1.0.0"> - <repository changeset_revision="73c1fc0ae03f" name="package_segmentation_fold_1_0_0" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="segmentation-fold" version="1.1.0"> + <repository changeset_revision="fba0d6f9dd67" name="package_segmentation_fold_1_1_0" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>