Mercurial > repos > yhoogstrate > segmentation_fold

annotate scan-for-segments.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="scan_for_segments" name="scan-for-segments" version="1.6.0">
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2 <description>Scan for the presence of segments in sequences 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>
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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 scan-for-segments
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14 -T \${GALAXY_SLOTS:-4}
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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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20 -p "in-depth"
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21 "${input_fasta}"
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22
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23 > $output_list
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24 ]]></command>
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25
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26 <inputs>
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27 <param name="input_fasta"
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28 type="data"
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29 format="fasta"
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30 argument="-f"
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31 label="Fasta file with RNA-sequece" />
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32
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33 <conditional name="parameters">
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34 <param name="use_custom_xml"
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35 type="boolean"
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36 truevalue="true"
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37 falsevalue="false"
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38 selected="false"
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39 label="Use segment definition from history" />
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40
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41 <when value="false" />
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42 <when value="true">
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43 <param name="input_xml"
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44 type="data"
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45 format="xml"
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46 multiple="false"
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47 argument="-x"
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48 label="Custom 'segments.xml'-syntaxed file" />
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49 </when>
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50 </conditional>
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51 </inputs>
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52
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53 <outputs>
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54 <data format="text" name="output_list" label="${tool.name} on ${str($input_fasta.hid) + ': ' + $input_fasta.name}" />
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55 </outputs>
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56
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57 <tests>
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58 <test>
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59 <param name="input_fasta" value="SNORD13-revised.fa" ftype="fasta" />
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60 <param name="use_custom_xml" value="false" ftype="fasta" />
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61
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62 <output name="output_list" file="SNORD13-revised.scan-for-segments.txt" />
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63 </test>
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64 <test>
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65 <param name="input_fasta" value="SNORD48-revised.fa" ftype="fasta" />
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66 <param name="use_custom_xml" value="false" ftype="fasta" />
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67
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68 <output name="output_list" file="SNORD48-revised.scan-for-segments.txt" />
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69 </test>
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70 <test>
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71 <param name="input_fasta" value="SNORD114-4-revised.fa" ftype="fasta" />
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72 <param name="use_custom_xml" value="false" ftype="fasta" />
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73
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74 <output name="output_list" file="SNORD114-4-revised.scan-for-segments.txt" />
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75 </test>
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76 <test>
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77 <param name="input_fasta" value="SNORD118-revised.fa" ftype="fasta" />
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78 <param name="use_custom_xml" value="false" ftype="fasta" />
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79
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80 <output name="output_list" file="SNORD118-revised.scan-for-segments.txt" />
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81 </test>
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82 </tests>
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83
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84 <help><![CDATA[
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85 This is an utility of the segmentation-fold package that allows to scan for the presence of certain segments.
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86 If present, it will also scan for the Gibbs free energy necessairy the segment has to provide to contribute to the optimal structure.
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87 ]]></help>
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88
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89 <citations>
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90 <citation type="bibtex">
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91 @mastersthesis{mastersthesis,
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92 author = {Youri Hoogstrate},
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93 title = {An algorithm for predicting RNA 2D structures including K-turns},
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94 school = {University of Technology Delft, Leiden University},
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95 year = 2012,
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96 address = {},
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97 month = 11,
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98 note = {Research assignment for Master Computer-science},
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99 url = { https://yh-kt-fold.googlecode.com/files/Report.pdf }
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100 }
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101 </citation>
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102 </citations>
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103 </tool>