Mercurial > repos > rnateam > mea
changeset 1:9ebd60531aa6 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea commit 6767a5ffb02052c844e9d862c79912f998f39d8e
| author | rnateam |
|---|---|
| date | Mon, 20 Nov 2017 05:04:03 -0500 |
| parents | 399593f05b4d |
| children | |
| files | mea.xml test-data/test_reference.txt test-data/test_structure.txt tool_dependencies.xml |
| diffstat | 4 files changed, 30 insertions(+), 51 deletions(-) [+] |
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--- a/mea.xml Sat Aug 01 04:46:19 2015 -0400 +++ b/mea.xml Mon Nov 20 05:04:03 2017 -0500 @@ -1,29 +1,24 @@ -<tool id="mea" name="MEA" version="0.6.4.0"> +<tool id="mea" name="MEA" version="0.6.4.1"> <description>Predict MEA structures and compare structures of RNAs</description> <requirements> - <requirement type="package" version="2.22.6">gengetopt</requirement> <requirement type="package" version="0.6.4">mea</requirement> </requirements> - <stdio> - <exit_code range=":-1"/> - <exit_code range="1:" /> - </stdio> <version_command>mea --version</version_command> - <command><![CDATA[ + <command detect_errors="aggressive"><![CDATA[ mea - #if str($predict_mode.predict_selector) == "predict": - $predict_mode.dotplot - #if str($predict_mode.mea_parameters.mea_parameters_selector) == "no_default" + #if str($predict_mode.predict_selector) == 'predict': + '$predict_mode.dotplot' + #if str($predict_mode.mea_parameters.mea_parameters_selector) == 'no_default' --alpha $predict_mode.mea_parameters.alpha --beta $predict_mode.mea_parameters.beta --gamma $predict_mode.mea_parameters.gamma --delta $predict_mode.mea_parameters.delta #end if #else - --structure `cat $predict_mode.structure` + --structure '$predict_mode.structure' #end if #if str($compare_mode.compare_selector) == 'compare': - --reference `cat $compare_mode.reference` + --reference '$compare_mode.reference' $compare_mode.slide_rule $compare_mode.conflict_rule #end if @@ -61,8 +56,16 @@ </conditional> </when> <when value="compare"> - <param name="structure" format="txt" type="data" label="Structure" optional="False" - help="(Predicted) RNA secondary structure for comparison to a reference structure. (--structure)" /> + <param argument="--structure" type="text" label="Structure" optional="False" + help="(Predicted) RNA secondary structure for comparison to a reference structure in dot-bracket format"> + <sanitizer> + <valid> + <add value="("/> + <add value=")"/> + <add value="."/> + </valid> + </sanitizer> + </param> </when> </conditional> <conditional name="compare_mode"> @@ -73,11 +76,16 @@ </param> <when value="dont_compare" /> <when value="compare"> - <param name="reference" - optional="false" - format="txt" type="data" - label="Reference" - help="Reference structure in dot-bracket format"/> + <param name="reference" optional="false" type="text" label="Reference" + help="Reference structure in dot-bracket format"> + <sanitizer> + <valid> + <add value="("/> + <add value=")"/> + <add value="."/> + </valid> + </sanitizer> + </param> <param name="slide_rule" label="Slide Rule" type="boolean" optional="False" checked="True" falsevalue="--no-slide-rule" truevalue="" help="Use slide rule. (--no-slide-rule)" /> <param name="conflict_rule" label="Conflict Rule" type="boolean" @@ -94,15 +102,15 @@ <param name="predict_selector" value="predict" /> <param name="compare_selector" value="compare" /> <param name="dotplot" value="test_dp.ps" /> - <param name="reference" value="test_reference.txt" /> + <param name="reference" value=".....(((.((((((..((......))....)))))).)))...((((((((.(((..(((....))).............))).))).)))))" /> <output name="stdout" file="test_predict.out" /> </test> <test> <param name="mea_parameter_selector" value="default" /> <param name="predict_selector" value="compare" /> <param name="compare_selector" value="compare" /> - <param name="structure" value="test_structure.txt" /> - <param name="reference" value="test_reference.txt" /> + <param name="structure" value=".....(((.((((((..((......))....)))))).)))......(((((.(((.....(((....))).........).)).))).))..." /> + <param name="reference" value=".....(((.((((((..((......))....)))))).)))...((((((((.(((..(((....))).............))).))).)))))" /> <output name="stdout" file="test_compare.out" /> </test> </tests>
--- a/test-data/test_reference.txt Sat Aug 01 04:46:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -.....(((.((((((..((......))....)))))).)))...((((((((.(((..(((....))).............))).))).)))))
--- a/test-data/test_structure.txt Sat Aug 01 04:46:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -.....(((.((((((..((......))....)))))).)))......(((((.(((.....(((....))).........).)).))).))... -
--- a/tool_dependencies.xml Sat Aug 01 04:46:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="gengetopt" version="2.22.6"> - <repository changeset_revision="6071205c5cd3" name="package_gengetopt_2_22_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="mea" version="0.6.4"> - <install version="1.0"> - <actions> - <action type="download_by_url"> - http://www.bioinf.uni-leipzig.de/Software/mea/mea-0.6.4.tar.gz - </action> - <action type="set_environment_for_install"> - <repository changeset_revision="6071205c5cd3" name="package_gengetopt_2_22_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="gengetopt" version="2.22.6" /> - </repository> - </action> - <action type="autoconf" /> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="set_to" name="MEA_ROOT_PATH">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme>Compiling MEA requires a C++ compiler (usually g++)</readme> - </package> -</tool_dependency>