Mercurial > repos > gga > tripal_organism_get_organisms

annotate organism_get_organisms.xml @ 6:5127a6fdbf7c draft default tip

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit ea279e5b47cf3d5767328d17b0e40e57b0238ea1"
author gga
date Wed, 14 Aug 2019 10:04:40 -0400
parents 8f6e896ac034
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1 <?xml version="1.0"?>
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2 <tool id="organism_get_organisms" profile="16.04" name="Get organisms" version="@WRAPPER_VERSION@.0">
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3 <description>from 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 <requirement type="package" version="1.5">jq</requirement>
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9 </expand>
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10 <expand macro="stdio"/>
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11 <command><![CDATA[
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12
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13 @AUTH@
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791692de64d6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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15 tripaille organism get_organisms
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16
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17 #if $organism_id:
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18 --organism_id "$organism_id"
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19 #end if
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20 #if $genus:
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21 --genus "$genus"
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22 #end if
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23 #if $species:
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24 --species "$species"
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25 #end if
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26 #if $common:
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27 --common "$common"
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28 #end if
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29 #if $abbr:
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30 --abbr "$abbr"
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31 #end if
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32 #if $comment:
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33 --comment "$comment"
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34 #end if
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35
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36 | jq -S . > '$results'
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37 ]]></command>
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38 <inputs>
4
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39 <param name="organism_id" label="Organism Id" argument="organism_id" type="text" optional="true" help="An organism ID" />
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40 <param name="genus" label="Genus" argument="genus" type="text" optional="true" help="The genus of the organism" />
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41 <param name="species" label="Species" argument="species" type="text" optional="true" help="The species of the organism" />
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42 <param name="common" label="Common" argument="common" type="text" optional="true" help="The common name of the organism" />
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43 <param name="abbr" label="Abbr" argument="abbr" type="text" optional="true" help="The abbreviation of the organism" />
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44 <param name="comment" label="Comment" argument="comment" type="text" optional="true" help="A comment / description" />
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45 </inputs>
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46 <outputs>
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47 <data format="json" name="results" label="Tripal organisms" />
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48 </outputs>
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49 <tests>
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50 <test expect_failure="true">
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51 <expand macro="test_result" />
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52 </test>
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53 </tests>
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54 <help><![CDATA[
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55 @HELP_OVERVIEW@
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56
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57 **Get Organisms**
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58
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59 With this tool, you can list organisms from the Tripal/Chado database
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60
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61 @HELP@
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62 ]]></help>
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63 <expand macro="citation"/>
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64 </tool>