Mercurial > repos > yhoogstrate > segmentation_fold

annotate energy-estimation-utility.xml @ 9:8e155ad4151a draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
author yhoogstrate
date Thu, 31 Mar 2016 04:12:13 -0400
parents 8dcf7ca46c72
children 312edff152eb
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1 <tool id="energy_estimation_utility" name="energy-estimation-utility" version="1.6.3-0">
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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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4 <requirements>
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5 <requirement type="package" version="1.6.3">segmentation-fold</requirement>
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6 <requirement type="package" version="2.7.10">python</requirement>
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7 </requirements>
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8
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9 <stdio></stdio>
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11 <version_command>segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//'</version_command>
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13 <command><![CDATA[
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14 energy-estimation-utility
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15 #if $parameters.use_custom_xml == "true"
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16 -x "${parameters.input_xml}"
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17 #else
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18 -x "\$SEGMENTATION_FOLD_DEFAULT_XML"
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19 #end if
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21 -r ${randomization.shuffle_n_times}
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22 > "${output_list}"
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23 ]]></command>
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24
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25 <inputs>
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26 <conditional name="parameters">
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27 <param name="use_custom_xml"
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28 type="boolean"
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29 truevalue="true"
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30 falsevalue="false"
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31 selected="false"
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32 label="Use segment definition from history" />
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33
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34 <when value="false" />
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35 <when value="true">
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36 <param name="input_xml"
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37 type="data"
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38 format="xml"
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39 multiple="false"
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40 argument="-x"
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41 label="Custom 'segments.xml'-syntaxed file" />
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42 </when>
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43 </conditional>
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44
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45 <conditional name="randomization">
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46 <param name="do_randomization"
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47 type="boolean"
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48 truevalue="true"
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49 falsevalue="false"
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50 selected="false"
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51 label="Randomly shuffle the sequence(s) instead"
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52 help="This can be helpful in determining a baseline of observing an energy parameter by chance" />
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53
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54 <when value="false">
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55 <param name="shuffle_n_times"
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56 type="hidden"
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57 value="0"/>
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58 </when>
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59 <when value="true">
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60 <param name="shuffle_n_times"
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61 type="integer"
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62 min="0"
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63 value="10"
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64 argument="-r"
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65 label="Number of times the sequences have to be shuffled and energy parameters have to be estimated on" />
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66 </when>
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67 </conditional>
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68 </inputs>
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69
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70 <outputs>
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71 <data format="text" name="output_list" label="${tool.name}" />
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72 </outputs>
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73
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74 <tests>
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75 <test>
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76 <param name="use_custom_xml" value="true" />
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77 <param name="input_xml" value="segments_truncated.xml" ftype="xml" />
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78 <param name="do_randomization" value="false" />
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79 <param name="shuffle_n_times" value="0" />
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80
4
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81 <output name="output_list" file="segments_truncated.out.txt" lines_diff="2" /><!-- Accept rounding errors by diff CPU's etc. -->
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82 </test>
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83 <test>
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84 <param name="use_custom_xml" value="true" />
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85 <param name="input_xml" value="segments_truncated.xml" ftype="xml" />
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86 <param name="do_randomization" value="false" />
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87 <param name="shuffle_n_times" value="1" />
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88
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89 <output name="output_list" file="segments_truncated.2.out.txt" lines_diff="10" />
3
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90 </test>
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91 </tests>
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92
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93 <help><![CDATA[
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94 The tool uses the sequences from the xml file.
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95 ]]></help>
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96
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97 <citations>
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98 <citation type="bibtex">
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99 @mastersthesis{mastersthesis,
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100 author = {Youri Hoogstrate},
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101 title = {An algorithm for predicting RNA 2D structures including K-turns},
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102 school = {University of Technology Delft, Leiden University},
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103 year = 2012,
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104 address = {},
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105 month = 11,
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106 note = {Research assignment for Master Computer-science},
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107 url = { https://yh-kt-fold.googlecode.com/files/Report.pdf }
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108 }
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109 </citation>
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110 </citations>
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111 </tool>