Mercurial > repos > gga > chado_organism_get_organisms

annotate organism_get_organisms.xml @ 18:4a4746803b8a draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 170209d14cabe6ce8ab7b9f06df7fbf36af2ba43"
author gga
date Tue, 04 May 2021 12:52:36 +0000
parents 1873b5415ecf
children
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1 <?xml version="1.0"?>
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1873b5415ecf "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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2 <tool id="organism_get_organisms" name="Chado organism get" version="@WRAPPER_VERSION@">
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3 <description></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 <command detect_errors="aggressive"><![CDATA[
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9 @START_PSQL@ &&
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11 chakin organism get_organisms
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13 #if $organism_id:
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14 --organism_id '$organism_id'
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15 #end if
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16 #if $genus:
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17 --genus '$genus'
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18 #end if
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19 #if $species:
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20 --species '$species'
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21 #end if
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22 #if $common:
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23 --common '$common'
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24 #end if
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25 #if $abbr:
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26 --abbr '$abbr'
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27 #end if
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28 #if $comment:
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29 --comment '$comment'
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30 #end if
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31
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32 | jq -S . > '$results'
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34 @STOP_PSQL@
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35 ]]></command>
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36 <inputs>
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37 <expand macro="psql_target"/>
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38 <!-- arguments -->
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39
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40 <!-- options -->
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41 <param name="organism_id" label="Organism Id" argument="--organism_id" type="integer" help="organism_id filter" optional="True" />
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42 <param name="genus" label="Genus" argument="--genus" type="text" help="genus filter" optional="True" />
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43 <param name="species" label="Species" argument="--species" type="text" help="species filter" optional="True" />
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44 <param name="common" label="Common" argument="--common" type="text" help="common filter" optional="True" />
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45 <param name="abbr" label="Abbr" argument="--abbr" type="text" help="abbr filter" optional="True" />
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46 <param name="comment" label="Comment" argument="--comment" type="text" help="comment filter" optional="True" />
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47
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48 </inputs>
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49 <outputs>
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50 <data format="json" name="results"/>
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51 </outputs>
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52 <help>
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53 Get all or some organisms
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54
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55 @HELP@
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56 </help>
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57 </tool>