Mercurial > repos > yhoogstrate > segmentation_fold

annotate energy-estimation-utility.xml @ 4:21e619c46cb5 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 61ba605ef9eb63914a248fe389860daa2249af69
author yhoogstrate
date Wed, 02 Mar 2016 05:47:07 -0500
parents 59ab674be4b5
children fd7f0bf0f5b6
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1 <tool id="energy_estimation_utility" name="energy-estimation-utility" version="1.6.0">
3
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2 <description>Estimate the maximal energy a segment needs to assign to become part of the optimal structure using segmentation-fold</description>
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3
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4 <requirements>
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5 <requirement type="package" version="1.1.0">segmentation-fold</requirement>
3
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6 </requirements>
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8 <stdio></stdio>
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10 <version_command>segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//'</version_command>
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11
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12 <command><![CDATA[
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13 energy-estimation-utility
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14 #if $parameters.use_custom_xml == "true"
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15 -x "${parameters.input_xml}"
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16 #else
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17 -x "\$SEGMENTATION_FOLD_DEFAULT_XML"
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18 #end if
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19
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20 -r ${randomization.shuffle_n_times}
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21 > "${output_list}"
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22 ]]></command>
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23
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24 <inputs>
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25 <conditional name="parameters">
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26 <param name="use_custom_xml"
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27 type="boolean"
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28 truevalue="true"
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29 falsevalue="false"
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30 selected="false"
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31 label="Use segment definition from history" />
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32
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33 <when value="false" />
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34 <when value="true">
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35 <param name="input_xml"
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36 type="data"
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37 format="xml"
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38 multiple="false"
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39 argument="-x"
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40 label="Custom 'segments.xml'-syntaxed file" />
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41 </when>
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42 </conditional>
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43
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44 <conditional name="randomization">
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45 <param name="do_randomization"
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46 type="boolean"
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47 truevalue="true"
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48 falsevalue="false"
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49 selected="false"
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50 label="Randomly shuffle the sequence(s) instead"
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51 help="This can be helpful in determining a baseline of observing an energy parameter by chance" />
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52
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53 <when value="false">
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54 <param name="shuffle_n_times"
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55 type="hidden"
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56 value="0"/>
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57 </when>
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58 <when value="true">
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59 <param name="shuffle_n_times"
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60 type="integer"
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61 min="0"
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62 value="10"
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63 argument="-r"
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64 label="Number of times the sequences have to be shuffled and energy parameters have to be estimated on" />
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65 </when>
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66 </conditional>
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67 </inputs>
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68
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69 <outputs>
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70 <data format="text" name="output_list" label="${tool.name}" />
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71 </outputs>
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72
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73 <tests>
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74 <test>
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75 <param name="use_custom_xml" value="true" />
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76 <param name="input_xml" value="segments_truncated.xml" ftype="xml" />
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77 <param name="do_randomization" value="false" />
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78 <param name="shuffle_n_times" value="0" />
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79
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80 <output name="output_list" file="segments_truncated.out.txt" lines_diff="2" /><!-- Accept rounding errors by diff CPU's etc. -->
3
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81 </test>
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82 <test>
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83 <param name="use_custom_xml" value="true" />
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84 <param name="input_xml" value="segments_truncated.xml" ftype="xml" />
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85 <param name="do_randomization" value="false" />
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86 <param name="shuffle_n_times" value="1" />
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87
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88 <output name="output_list" file="segments_truncated.2.out.txt" lines_diff="10" />
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89 </test>
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90 </tests>
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91
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92 <help><![CDATA[
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93 The tool uses the sequences from the xml file.
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94 ]]></help>
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95
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96 <citations>
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97 <citation type="bibtex">
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98 @mastersthesis{mastersthesis,
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99 author = {Youri Hoogstrate},
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100 title = {An algorithm for predicting RNA 2D structures including K-turns},
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101 school = {University of Technology Delft, Leiden University},
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102 year = 2012,
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103 address = {},
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104 month = 11,
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105 note = {Research assignment for Master Computer-science},
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106 url = { https://yh-kt-fold.googlecode.com/files/Report.pdf }
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107 }
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108 </citation>
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109 </citations>
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110 </tool>