Mercurial > repos > yhoogstrate > segmentation_fold

annotate scan-for-segments.xml @ 10:312edff152eb draft

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author yhoogstrate
date Thu, 31 Mar 2016 04:20:55 -0400
parents 8dcf7ca46c72
children
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1 <tool id="scan_for_segments" name="scan-for-segments" version="1.6.3-1">
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2 <description>Scan for the presence of segments in sequences 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:]]*$//'</version_command>
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13 <command><![CDATA[
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14 scan-for-segments
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15 -T \${GALAXY_SLOTS:-4}
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16 -x
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17 #if str($parameters.use_custom_xml) == "true"
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18 "${parameters.input_xml}"
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19 #else
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20 "\$SEGMENTATION_FOLD_DEFAULT_XML"
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21 #end if
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22 -p "in-depth"
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23 "${input_fasta}"
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24
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25 > $output_list
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26 ]]></command>
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27
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28 <inputs>
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29 <param name="input_fasta"
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30 type="data"
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31 format="fasta"
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32 argument="-f"
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33 label="Fasta file with RNA-sequece" />
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34
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35 <conditional name="parameters">
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36 <param name="use_custom_xml"
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37 type="boolean"
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38 truevalue="true"
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39 falsevalue="false"
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40 selected="false"
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41 label="Use segment definition from history" />
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42
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43 <when value="false" />
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44 <when value="true">
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45 <param name="input_xml"
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46 type="data"
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47 format="xml"
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48 multiple="false"
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49 argument="-x"
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50 label="Custom 'segments.xml'-syntaxed file" />
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51 </when>
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52 </conditional>
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53 </inputs>
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54
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55 <outputs>
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56 <data format="text" name="output_list" label="${tool.name} on ${str($input_fasta.hid) + ': ' + $input_fasta.name}" />
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57 </outputs>
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58
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59 <tests>
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60 <test>
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61 <param name="input_fasta" value="SNORD13-revised.fa" ftype="fasta" />
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62 <param name="use_custom_xml" value="false" ftype="fasta" />
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63
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64 <output name="output_list" file="SNORD13-revised.scan-for-segments.txt" />
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65 </test>
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66 <test>
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67 <param name="input_fasta" value="SNORD48-revised.fa" ftype="fasta" />
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68 <param name="use_custom_xml" value="false" ftype="fasta" />
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69
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70 <output name="output_list" file="SNORD48-revised.scan-for-segments.txt" />
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71 </test>
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72 <test>
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73 <param name="input_fasta" value="SNORD114-4-revised.fa" ftype="fasta" />
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74 <param name="use_custom_xml" value="false" ftype="fasta" />
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75
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76 <output name="output_list" file="SNORD114-4-revised.scan-for-segments.txt" />
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77 </test>
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78 <test>
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79 <param name="input_fasta" value="SNORD118-revised.fa" ftype="fasta" />
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80 <param name="use_custom_xml" value="false" ftype="fasta" />
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81
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82 <output name="output_list" file="SNORD118-revised.scan-for-segments.txt" />
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83 </test>
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84 </tests>
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85
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86 <help><![CDATA[
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87 This is an utility of the segmentation-fold package that allows to scan for the presence of certain segments.
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88 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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89 ]]></help>
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90
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91 <citations>
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92 <citation type="bibtex">
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93 @mastersthesis{mastersthesis,
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94 author = {Youri Hoogstrate},
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95 title = {An algorithm for predicting RNA 2D structures including K-turns},
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96 school = {University of Technology Delft, Leiden University},
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97 year = 2012,
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98 address = {},
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99 month = 11,
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100 note = {Research assignment for Master Computer-science},
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101 url = { https://yh-kt-fold.googlecode.com/files/Report.pdf }
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102 }
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103 </citation>
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104 </citations>
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105 </tool>