Mercurial > repos > gga > tripal_organism_sync

annotate organism_sync.xml @ 0:98e917aa6819 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:54:11 -0400
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98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 <?xml version="1.0"?>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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2 <tool id="organism_sync" profile="16.04" name="Synchronize an organism" 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>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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6 </macros>
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7 <expand macro="requirements"/>
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8 <code file="tripal.py"/>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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9 <expand macro="stdio"/>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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10 <command><![CDATA[
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11
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12 @AUTH@
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98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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14 tripaille organism sync
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16 --organism_id '${organism_id}'
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17
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18 &&
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19
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20 echo "Data loaded" > $results
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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21 ]]></command>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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22 <inputs>
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23 <param argument="--organism_id"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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24 type="select"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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25 dynamic_options="list_organisms()"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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26 label="Organism" />
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27 </inputs>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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28 <outputs>
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29 <data format="txt" name="results" label="Synchronize Organism into Tripal" />
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30 </outputs>
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31 <tests>
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32 <test expect_failure="true">
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33 <param name="organism_id" value="Testus testus" />
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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34
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35 <expand macro="test_result" />
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39 @HELP_OVERVIEW@
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40
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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41 **Synchronize Organism**
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42
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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43 With this tool, you can synchronize an organism from the Chado database into the Tripal instance.
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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44 A corresponding Drupal node will be created.
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45
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46 @HELP@
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47 ]]></help>
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48 <expand macro="citation"/>
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49 </tool>