Mercurial > repos > gga > chado_feature_load_featureprops

annotate feature_load_featureprops.xml @ 15:dbce38cde6a5 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit dc7fe1feecc587f7bc5d09108fbf016b0fd317bc"
author gga
date Mon, 18 Nov 2019 09:56:22 -0500
parents 9db01be25d5b
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1 <?xml version="1.0"?>
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2 <tool id="feature_load_featureprops" name="Chado load feature properties" 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 <code file="chado.py"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 @START_PSQL@ &&
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12 chakin feature load_featureprops
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13 '$tab_file'
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14 '$analysis_id'
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15 '$organism'
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16 '$prop_type'
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18 #if $feature_type:
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19 --feature_type '$feature_type'
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20 #end if
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22 $match_on_name
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24 | jq -S . > '$results'
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26 @ZIP_PSQL@
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27 ]]></command>
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28 <inputs>
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29 <expand macro="psql_target"/>
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30 <!-- arguments -->
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31 <param name="tab_file" label="Tab File" argument="tab_file" type="data" format="tabular" help="Path to the tabular file to load" />
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32 <param argument="analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" />
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33 <param argument="organism" type="select" dynamic_options="list_organisms()" label="Organism" />
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34 <param name="prop_type" label="Property type" argument="prop_type" type="text" help="Type of the feature property (cvterm will be created if it doesn't exist)" />
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36 <!-- options -->
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37 <param name="feature_type" label="Feature type" argument="--feature_type" type="text" help="Type of the target features in sequence ontology (will speed up loading if specified)" optional="true" />
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38 <param name="match_on_name" label="Match on name" argument="--match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match features using their name instead of their uniquename" />
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40 <expand macro="wait_for"/>
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41
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42 </inputs>
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43 <outputs>
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44 <data format="json" name="results"/>
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45 <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} on ${on_string}">
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46 <filter>psql_target['method'] == "pgtools"</filter>
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47 </data>
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48 </outputs>
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49 <help>
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50 Load feature properties from a tabular file (Column1: feature name or uniquename, Column2: property value)
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52 @HELP@
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53 </help>
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54 </tool>