Mercurial > repos > gga > tripal_feature_sync

annotate feature_sync.xml @ 1:52a9ee230029 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
author gga
date Tue, 19 Sep 2017 12:26:23 -0400
parents c01c63c043f0
children e621d1187d73
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1 <?xml version="1.0"?>
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2 <tool id="feature_sync" profile="16.04" name="Synchronize features" version="@WRAPPER_VERSION@.0">
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3 <description>from Chado to Tripal</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <code file="tripal.py"/>
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9 <expand macro="stdio"/>
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10 <command><![CDATA[
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12 @AUTH@
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14 tripaille feature sync
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16 #for $rep in $repeat_types:
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17 --types '${rep.types}'
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18 #end for
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20 #for $rep in $repeat_ids:
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21 --ids '${rep.ids}'
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22 #end for
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24 --organism_id '${organism_id}'
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25
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26 &&
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27
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28 echo "Data loaded" > $results
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29 ]]></command>
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30 <inputs>
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31 <param argument="--organism_id"
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32 type="select"
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33 dynamic_options="list_organisms()"
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34 label="Organism" />
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35
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36 <repeat name="repeat_types" title="Feature types">
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37 <param name="types"
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38 argument="--types"
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39 type="text"
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40 optional="true"
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41 label="Feature type to synchronize"
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42 help="Type of records to be synced (e.g. 'gene' or 'mRNA')" />
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43 </repeat>
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44
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45 <repeat name="repeat_ids" title="Feature ids">
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46 <param name="ids"
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47 argument="--ids"
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48 type="text"
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49 optional="true"
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50 label="Feature to synchronize"
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51 help="Name of a feature to be synced (e.g. 'gene0001')" />
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52 </repeat>
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53 </inputs>
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54 <outputs>
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55 <data format="txt" name="results" label="Synchronize features into Tripal" />
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56 </outputs>
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57 <tests>
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58 <test expect_failure="true">
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59 <param name="organism" value="Testus testus" />
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60 <param name="types" value="gene mRNA" />
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61 <param name="types" value="gene0001 gene0002" />
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62
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63 <expand macro="test_result" />
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67 @HELP_OVERVIEW@
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68
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69 **Synchronize Features**
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70
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71 With this tool, you can synchronize some features from the Chado database into the Tripal instance.
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72 A corresponding Drupal node will be created for each feature.
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73
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74 @HELP@
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75 ]]></help>
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76 <expand macro="citation"/>
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77 </tool>