Mercurial > repos > yhoogstrate > segmentation_fold

annotate segmentation-fold.xml @ 10:312edff152eb draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9-dirty
author yhoogstrate
date Thu, 31 Mar 2016 04:20:55 -0400
parents 8e155ad4151a
children 487f438da099
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312edff152eb planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9-dirty
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1 <tool id="segmentation_fold" name="segmentation-fold" version="1.6.3-1">
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2 <description>RNA-Folding including predefined segments including K-turns</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 </requirements>
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8 <stdio></stdio>
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9
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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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12 <command><![CDATA[
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13 segmentation-fold
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15 #if $input.method == "fasta"
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16 -f $input.input_fasta
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17 #else
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18 -s $input.input_sequence
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19 #end if
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21 -p $predict_segments
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22 -h $min_hairpin_size
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24 #if $parameters.settings == "default"
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25 -x "\$SEGMENTATION_FOLD_DEFAULT_XML"
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26 #else
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27 -x "${parameters.input_xml}"
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28 #end if
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29
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30 -t \${GALAXY_SLOTS:-4}
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31 > $output_dbn
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32 ]]></command>
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34 <inputs>
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35 <conditional name="input">
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36 <param name="method" type="select" label="Energy parameters">
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37 <option value="fasta" selected="true">As FASTA-file</option>
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38 <option value="text">As text</option>
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39 </param>
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40 <when value="fasta">
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41 <param name="input_fasta" type="data" format="fasta" label="Fasta file with RNA-sequece (-f)" />
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42 </when>
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43 <when value="text">
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44 <param name="input_sequence" type="text" label="RNA-sequece (-s)" />
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45 </when>
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46 </conditional>
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47
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48 <param name="predict_segments" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Enable segment prediction functionality (-p)" />
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49 <param name="min_hairpin_size" type="integer" min="1" value="3" label="Minimum hairpin size (-h)" />
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50
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51 <conditional name="parameters">
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52 <param name="settings" type="select" label="Energy parameters">
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53 <option value="default" selected="true">Default</option>
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54 <option value="custom">Custom</option>
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55 </param>
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56 <when value="default" />
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57 <when value="custom">
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58 <param name="input_xml" type="data" format="xml" multiple="false" label="Use custom 'segments.xml'-syntaxed file (-x)" />
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59 </when>
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60 </conditional>
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61 </inputs>
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62
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63 <outputs>
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64 <data format="dbn" name="output_dbn" label="segmentation-fold" />
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65 <!--<data format="dot-bracket" name="output_dbn" label="${tool.name} on ${str(input.input_fasta.hid) + ': ' + input.input_fasta.name if $input.method == 'fasta' else $input.input_sequence.upper() }" />-->
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66 </outputs>
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67
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68 <tests>
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69 <test>
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70 <param name="input_fasta" value="test_01.fa" ftype="fasta" />
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71 <output name="output_dbn" file="test_01.dbn" />
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72 </test>
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73 <test>
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74 <param name="input_fasta" value="test_02.fa" ftype="fasta" />
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75 <output name="output_dbn" file="test_02.dbn" />
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76 </test>
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77 <test>
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78 <param name="input_fasta" value="test_03.fa" ftype="fasta" />
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79 <output name="output_dbn" file="test_03.dbn" />
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80 </test>
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81 <test>
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82 <param name="input_fasta" value="test_04.fa" ftype="fasta" />
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83 <output name="output_dbn" file="test_04.dbn" />
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84 </test>
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85 <test>
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86 <param name="input_fasta" value="test_05.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
87 <output name="output_dbn" file="test_05.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
88 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
89 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
90 <param name="input_fasta" value="test_06.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
91 <output name="output_dbn" file="test_06.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
92 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
93 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
94 <param name="input_fasta" value="test_07.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
95 <output name="output_dbn" file="test_07.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
96 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
97 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
98 <param name="input_fasta" value="test_08.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
99 <output name="output_dbn" file="test_08.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
100 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
101 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
102 <param name="input_fasta" value="test_09.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
103 <output name="output_dbn" file="test_09.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
104 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
105 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
106 <param name="input_fasta" value="test_10.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
107 <output name="output_dbn" file="test_10.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
108 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
109 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
110 <param name="input_fasta" value="test_11.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
111 <output name="output_dbn" file="test_11.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
112 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
113 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
114 <param name="input_fasta" value="test_12.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
115 <output name="output_dbn" file="test_12.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
116 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
117 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
118 <param name="input_fasta" value="test_13.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
119 <output name="output_dbn" file="test_13.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
120 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
121 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
122 <param name="input_fasta" value="test_14.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
123 <output name="output_dbn" file="test_14.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
124 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
125 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
126 <param name="input_fasta" value="test_15.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
127 <output name="output_dbn" file="test_15.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
128 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
129 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
130 <param name="input_fasta" value="test_16.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
131 <output name="output_dbn" file="test_16.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
132 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
133 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
134 <param name="input_fasta" value="test_17.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
135 <output name="output_dbn" file="test_17.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
136 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
137 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
138 <param name="input_fasta" value="test_18.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
139 <output name="output_dbn" file="test_18.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
140 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
141 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
142 <param name="input_fasta" value="test_19.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
143 <output name="output_dbn" file="test_19.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
144 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
145 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
146 <param name="input_fasta" value="test_20.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
147 <output name="output_dbn" file="test_20.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
148 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
149 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
150 <param name="input_fasta" value="test_21.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
151 <output name="output_dbn" file="test_21.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
152 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
153 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
154 <param name="input_fasta" value="test_22.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
155 <output name="output_dbn" file="test_22.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
156 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
157 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
158 <param name="input_fasta" value="test_23.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
159 <output name="output_dbn" file="test_23.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
160 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
161 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
162 <param name="input_fasta" value="test_24.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
163 <output name="output_dbn" file="test_24.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
164 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
165 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
166 <param name="input_fasta" value="test_25.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
167 <output name="output_dbn" file="test_25.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
168 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
169 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
170 <param name="input_fasta" value="test_26.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
171 <output name="output_dbn" file="test_26.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
172 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
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173 <test>
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174 <param name="input_fasta" value="test_27.fa" ftype="fasta" />
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175 <output name="output_dbn" file="test_27.dbn" />
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176 </test>
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177 <test>
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178 <param name="input_fasta" value="test_28.fa" ftype="fasta" />
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179 <output name="output_dbn" file="test_28.dbn" />
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180 </test>
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181 </tests>
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182
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183 <help><![CDATA[
9
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184 **What it does**:
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185
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186 Segmentation-fold is a application in the field of bioinformatics that
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187 predicts RNA 2D-structures. The model has an extension with respect to
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188 the classical Zuker algorithm, to allow new "structure elements" named
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189 segments and segmentloops. This makes it capable of folding a
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190 pre-defined substructure with multiple canonical or non-canonical base
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191 pairs, like K-turns and loop-E-motifs. Some of such sturcture elements
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192 are present in the corresponding energy table, although custom tables
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193 can be provided as well.
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194
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195
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196 **Running segmentation-fold**
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197
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198 Segmentation-fold has to be provided with a sequence of which it has to
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199 predict the 2D structure. This can be done using a plain text sequence
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200 (allowed charset: ACTUG) or a FASTA file. A FASTA file has the following
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201 syntax:
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202
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203 >Sequence name and other details
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204
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205 AGUGUAGCUGUGUCGAUCGUAAGUCAG
0
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206
9
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207 As the database of free energy parameters will most likely be updated
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208 over time we have added the possiblity to include this XML file as
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209 additional parameter. The most up to date version of this file can be
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210 found at the following url:
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211
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212 https://github.com/yhoogstrate/segmentation-fold/blob/master/share/segmentation-fold/segments.xml
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213
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214 If you would like to compare the results with a prediction as if the
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215 segment and segmentloop extension were disabled, you can disable it with
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216 the given parameter.
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217
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218 **Output**
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219
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220 The output is in DotBracket format (dbn) and can be visualized with e.g.
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221 DrawRNAjs or VaRNA.
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222
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223 DrawRNAjs can be installed in galaxy by following the instructions at
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224 the following link:
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225
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226 https://github.com/bgruening/galaxytools/tree/master/visualisations/drawrnajs
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227
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228 Details on the dbn-format can be found here:
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229
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230 https://wiki.galaxyproject.org/Learn/Datatypes#Dbn
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231
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232 **Authors**
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233
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234 Youri Hoogstrate (yhoogstrate @ github)
0
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235 ]]></help>
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236
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237 <citations>
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238 <citation type="bibtex">
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239 @mastersthesis{mastersthesis,
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240 author = {Youri Hoogstrate},
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241 title = {An algorithm for predicting RNA 2D structures including K-turns},
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242 school = {University of Technology Delft, Leiden University},
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243 year = 2012,
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244 address = {},
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245 month = 11,
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246 note = {Research assignment for Master Computer-science},
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247 url = { https://yh-kt-fold.googlecode.com/files/Report.pdf }
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248 }
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249 </citation>
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250 </citations>
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251 </tool>