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comparison mea.xml @ 1:9ebd60531aa6 draft default tip

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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
comparison
equal deleted inserted replaced
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 =====