Mercurial > repos > yhoogstrate > segmentation_fold

annotate segmentation-fold.xml @ 7:bff6e82064da draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 4a09ba36d8feeea3b61ab5b2b113aac7f34d389f-dirty
author yhoogstrate
date Thu, 10 Mar 2016 03:22:58 -0500
parents fd7f0bf0f5b6
children 8dcf7ca46c72
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1 <tool id="segmentation_fold" name="segmentation-fold" version="1.6.2-0">
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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="1.6.2">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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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[
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184 Segmentation-fold is a bioinformatics application that predicts RNA
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185 2D-structure with an extended version of the Zuker algorithm. This
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186 modification contains a new "structure element" named a segment and is
2
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187 capable of folding a pre-defined substructures with multiple canonical
0
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188 or non-canonical pairings.
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189
2
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190 This allows folding of more complex structures like K-turns, which are
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191 also part of the implemented free energy table. These thermodynamic
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192 parameters (free Gibbs energy) have been estimated using a in silico
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193 approach and therefore lack high resolution.
0
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194 ]]></help>
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195
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196 <citations>
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197 <citation type="bibtex">
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198 @mastersthesis{mastersthesis,
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199 author = {Youri Hoogstrate},
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200 title = {An algorithm for predicting RNA 2D structures including K-turns},
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201 school = {University of Technology Delft, Leiden University},
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202 year = 2012,
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203 address = {},
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204 month = 11,
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205 note = {Research assignment for Master Computer-science},
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206 url = { https://yh-kt-fold.googlecode.com/files/Report.pdf }
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207 }
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208 </citation>
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209 </citations>
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210 </tool>