Mercurial > repos > yhoogstrate > segmentation_fold
diff segmentation-fold.xml @ 0:09e921a25c68 draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
| author | yhoogstrate |
|---|---|
| date | Mon, 03 Aug 2015 08:28:39 -0400 |
| parents | |
| children | 27f670a42ba2 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/segmentation-fold.xml Mon Aug 03 08:28:39 2015 -0400 @@ -0,0 +1,210 @@ +<tool id="segmentation_fold" name="segmentation-fold" version="0.2.0"> + <description>RNA-Folding including predefined segments including K-turns</description> + + <requirements> + <requirement type="package" version="1.0.0">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> + + <command><![CDATA[ + segmentation-fold + + #if $input.method == "fasta" + -f $input.input_fasta + #else + -s $input.input_sequence + #end if + + -p $predict_segments + -h $min_hairpin_size + + #if $parameters.settings == "default" + -x "${SEGMENTATION_FOLD_DEFAULT_XML}" + #else + -x $parameters.input_xml + #end if + + -t \${GALAXY_SLOTS:-2} + > $output_dbn + ]]></command> + + <inputs> + + <conditional name="input"> + <param name="method" type="select" label="Energy parameters"> + <option value="fasta" selected="true">As FASTA-file</option> + <option value="text">As text</option> + </param> + <when value="fasta"> + <param name="input_fasta" type="data" format="fasta" label="Fasta file with RNA-sequece (-f)" /> + </when> + <when value="text"> + <param name="input_sequence" type="text" label="RNA-sequece (-s)" /> + </when> + </conditional> + + <param name="predict_segments" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Enable segment prediction functionality (-p)" /> + <param name="min_hairpin_size" type="integer" min="1" value="3" label="Minimum hairpin size (-h)" /> + + <conditional name="parameters"> + <param name="settings" type="select" label="Energy parameters"> + <option value="default" selected="true">Default</option> + <option value="custom">Custom</option> + </param> + <when value="default" /> + <when value="custom"> + <param name="input_xml" type="data" format="xml" multiple="false" label="Use custom 'segments.xml'-syntaxed file (-x)" /> + </when> + </conditional> + </inputs> + + <outputs> + <data format="dot-bracket" name="output_dbn" label="${tool.name} on ${input.input_fasta.hid + ': ' + input.input_fasta.name if $input.method == 'fasta' else $input.input_sequence.upper() }" /> + </outputs> + + <tests> + <test> + <param name="input_fasta" value="test_01.fa" ftype="fasta" /> + <output name="output_dbn" file="test_01.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_02.fa" ftype="fasta" /> + <output name="output_dbn" file="test_02.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_03.fa" ftype="fasta" /> + <output name="output_dbn" file="test_03.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_04.fa" ftype="fasta" /> + <output name="output_dbn" file="test_04.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_05.fa" ftype="fasta" /> + <output name="output_dbn" file="test_05.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_06.fa" ftype="fasta" /> + <output name="output_dbn" file="test_06.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_07.fa" ftype="fasta" /> + <output name="output_dbn" file="test_07.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_08.fa" ftype="fasta" /> + <output name="output_dbn" file="test_08.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_09.fa" ftype="fasta" /> + <output name="output_dbn" file="test_09.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_10.fa" ftype="fasta" /> + <output name="output_dbn" file="test_10.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_11.fa" ftype="fasta" /> + <output name="output_dbn" file="test_11.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_12.fa" ftype="fasta" /> + <output name="output_dbn" file="test_12.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_13.fa" ftype="fasta" /> + <output name="output_dbn" file="test_13.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_14.fa" ftype="fasta" /> + <output name="output_dbn" file="test_14.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_15.fa" ftype="fasta" /> + <output name="output_dbn" file="test_15.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_16.fa" ftype="fasta" /> + <output name="output_dbn" file="test_16.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_17.fa" ftype="fasta" /> + <output name="output_dbn" file="test_17.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_18.fa" ftype="fasta" /> + <output name="output_dbn" file="test_18.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_19.fa" ftype="fasta" /> + <output name="output_dbn" file="test_19.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_20.fa" ftype="fasta" /> + <output name="output_dbn" file="test_20.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_21.fa" ftype="fasta" /> + <output name="output_dbn" file="test_21.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_22.fa" ftype="fasta" /> + <output name="output_dbn" file="test_22.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_23.fa" ftype="fasta" /> + <output name="output_dbn" file="test_23.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_24.fa" ftype="fasta" /> + <output name="output_dbn" file="test_24.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_25.fa" ftype="fasta" /> + <output name="output_dbn" file="test_25.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_26.fa" ftype="fasta" /> + <output name="output_dbn" file="test_26.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_27.fa" ftype="fasta" /> + <output name="output_dbn" file="test_27.dbn" /> + </test> + <test> + <param name="input_fasta" value="test_28.fa" ftype="fasta" /> + <output name="output_dbn" file="test_28.dbn" /> + </test> + </tests> + + <help><![CDATA[ +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 +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. + ]]></help> + + <citations> + <citation type="bibtex"> + @mastersthesis{mastersthesis, + author = {Youri Hoogstrate}, + title = {An algorithm for predicting RNA 2D structures including K-turns}, + school = {University of Technology Delft, Leiden University}, + year = 2012, + address = {}, + month = 11, + note = {Research assignment for Master Computer-science}, + url = { https://yh-kt-fold.googlecode.com/files/Report.pdf } + } + </citation> + </citations> +</tool>