Mercurial > repos > rnateam > mea
comparison mea.xml @ 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 |
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| 0:399593f05b4d | 1:9ebd60531aa6 |
|---|---|
| 1 <tool id="mea" name="MEA" version="0.6.4.0"> | 1 <tool id="mea" name="MEA" version="0.6.4.1"> |
| 2 <description>Predict MEA structures and compare structures of RNAs</description> | 2 <description>Predict MEA structures and compare structures of RNAs</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="2.22.6">gengetopt</requirement> | |
| 5 <requirement type="package" version="0.6.4">mea</requirement> | 4 <requirement type="package" version="0.6.4">mea</requirement> |
| 6 </requirements> | 5 </requirements> |
| 7 <stdio> | |
| 8 <exit_code range=":-1"/> | |
| 9 <exit_code range="1:" /> | |
| 10 </stdio> | |
| 11 <version_command>mea --version</version_command> | 6 <version_command>mea --version</version_command> |
| 12 <command><![CDATA[ | 7 <command detect_errors="aggressive"><![CDATA[ |
| 13 mea | 8 mea |
| 14 #if str($predict_mode.predict_selector) == "predict": | 9 #if str($predict_mode.predict_selector) == 'predict': |
| 15 $predict_mode.dotplot | 10 '$predict_mode.dotplot' |
| 16 #if str($predict_mode.mea_parameters.mea_parameters_selector) == "no_default" | 11 #if str($predict_mode.mea_parameters.mea_parameters_selector) == 'no_default' |
| 17 --alpha $predict_mode.mea_parameters.alpha | 12 --alpha $predict_mode.mea_parameters.alpha |
| 18 --beta $predict_mode.mea_parameters.beta | 13 --beta $predict_mode.mea_parameters.beta |
| 19 --gamma $predict_mode.mea_parameters.gamma | 14 --gamma $predict_mode.mea_parameters.gamma |
| 20 --delta $predict_mode.mea_parameters.delta | 15 --delta $predict_mode.mea_parameters.delta |
| 21 #end if | 16 #end if |
| 22 #else | 17 #else |
| 23 --structure `cat $predict_mode.structure` | 18 --structure '$predict_mode.structure' |
| 24 #end if | 19 #end if |
| 25 #if str($compare_mode.compare_selector) == 'compare': | 20 #if str($compare_mode.compare_selector) == 'compare': |
| 26 --reference `cat $compare_mode.reference` | 21 --reference '$compare_mode.reference' |
| 27 $compare_mode.slide_rule | 22 $compare_mode.slide_rule |
| 28 $compare_mode.conflict_rule | 23 $compare_mode.conflict_rule |
| 29 #end if | 24 #end if |
| 30 > $stdout | 25 > $stdout |
| 31 ]]></command> | 26 ]]></command> |
| 59 help="Minimum penalty factor for base pairs. (--delta)" /> | 54 help="Minimum penalty factor for base pairs. (--delta)" /> |
| 60 </when> | 55 </when> |
| 61 </conditional> | 56 </conditional> |
| 62 </when> | 57 </when> |
| 63 <when value="compare"> | 58 <when value="compare"> |
| 64 <param name="structure" format="txt" type="data" label="Structure" optional="False" | 59 <param argument="--structure" type="text" label="Structure" optional="False" |
| 65 help="(Predicted) RNA secondary structure for comparison to a reference structure. (--structure)" /> | 60 help="(Predicted) RNA secondary structure for comparison to a reference structure in dot-bracket format"> |
| 61 <sanitizer> | |
| 62 <valid> | |
| 63 <add value="("/> | |
| 64 <add value=")"/> | |
| 65 <add value="."/> | |
| 66 </valid> | |
| 67 </sanitizer> | |
| 68 </param> | |
| 66 </when> | 69 </when> |
| 67 </conditional> | 70 </conditional> |
| 68 <conditional name="compare_mode"> | 71 <conditional name="compare_mode"> |
| 69 <param name="compare_selector" type="select" label="Compare to a reference structure" | 72 <param name="compare_selector" type="select" label="Compare to a reference structure" |
| 70 help="Whether to compare the predicted (or specified) structure to a reference structure."> | 73 help="Whether to compare the predicted (or specified) structure to a reference structure."> |
| 71 <option value="dont_compare">Do not compare</option> | 74 <option value="dont_compare">Do not compare</option> |
| 72 <option value="compare">Compare to reference structure</option> | 75 <option value="compare">Compare to reference structure</option> |
| 73 </param> | 76 </param> |
| 74 <when value="dont_compare" /> | 77 <when value="dont_compare" /> |
| 75 <when value="compare"> | 78 <when value="compare"> |
| 76 <param name="reference" | 79 <param name="reference" optional="false" type="text" label="Reference" |
| 77 optional="false" | 80 help="Reference structure in dot-bracket format"> |
| 78 format="txt" type="data" | 81 <sanitizer> |
| 79 label="Reference" | 82 <valid> |
| 80 help="Reference structure in dot-bracket format"/> | 83 <add value="("/> |
| 84 <add value=")"/> | |
| 85 <add value="."/> | |
| 86 </valid> | |
| 87 </sanitizer> | |
| 88 </param> | |
| 81 <param name="slide_rule" label="Slide Rule" type="boolean" | 89 <param name="slide_rule" label="Slide Rule" type="boolean" |
| 82 optional="False" checked="True" falsevalue="--no-slide-rule" truevalue="" help="Use slide rule. (--no-slide-rule)" /> | 90 optional="False" checked="True" falsevalue="--no-slide-rule" truevalue="" help="Use slide rule. (--no-slide-rule)" /> |
| 83 <param name="conflict_rule" label="Conflict Rule" type="boolean" | 91 <param name="conflict_rule" label="Conflict Rule" type="boolean" |
| 84 optional="False" checked="True" falsevalue="--no-conflict-rule" truevalue="" help="Use onflict rule. (--no-conflict-rule)"/> | 92 optional="False" checked="True" falsevalue="--no-conflict-rule" truevalue="" help="Use onflict rule. (--no-conflict-rule)"/> |
| 85 </when> | 93 </when> |
| 92 <test> | 100 <test> |
| 93 <param name="mea_parameter_selector" value="default" /> | 101 <param name="mea_parameter_selector" value="default" /> |
| 94 <param name="predict_selector" value="predict" /> | 102 <param name="predict_selector" value="predict" /> |
| 95 <param name="compare_selector" value="compare" /> | 103 <param name="compare_selector" value="compare" /> |
| 96 <param name="dotplot" value="test_dp.ps" /> | 104 <param name="dotplot" value="test_dp.ps" /> |
| 97 <param name="reference" value="test_reference.txt" /> | 105 <param name="reference" value=".....(((.((((((..((......))....)))))).)))...((((((((.(((..(((....))).............))).))).)))))" /> |
| 98 <output name="stdout" file="test_predict.out" /> | 106 <output name="stdout" file="test_predict.out" /> |
| 99 </test> | 107 </test> |
| 100 <test> | 108 <test> |
| 101 <param name="mea_parameter_selector" value="default" /> | 109 <param name="mea_parameter_selector" value="default" /> |
| 102 <param name="predict_selector" value="compare" /> | 110 <param name="predict_selector" value="compare" /> |
| 103 <param name="compare_selector" value="compare" /> | 111 <param name="compare_selector" value="compare" /> |
| 104 <param name="structure" value="test_structure.txt" /> | 112 <param name="structure" value=".....(((.((((((..((......))....)))))).)))......(((((.(((.....(((....))).........).)).))).))..." /> |
| 105 <param name="reference" value="test_reference.txt" /> | 113 <param name="reference" value=".....(((.((((((..((......))....)))))).)))...((((((((.(((..(((....))).............))).))).)))))" /> |
| 106 <output name="stdout" file="test_compare.out" /> | 114 <output name="stdout" file="test_compare.out" /> |
| 107 </test> | 115 </test> |
| 108 </tests> | 116 </tests> |
| 109 <help><![CDATA[ | 117 <help><![CDATA[ |
| 110 ===== | 118 ===== |