annotate feature_load_featureprops.xml @ 0:b5d8e6e26d01 draft

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date Thu, 21 Jun 2018 08:44:44 -0400
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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@.0">
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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 @AUTH@
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11
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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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17
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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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21 #if $match_on_name:
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22 $match_on_name
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23 #end if
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24
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25 | jq -S . > $results
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26 ]]></command>
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27 <inputs>
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28 <!-- arguments -->
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29 <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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30 <param argument="--analysis_id"
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31 type="select"
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32 dynamic_options="list_analyses()"
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33 label="Analysis" />
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34 <param argument="--organism"
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35 type="select"
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36 dynamic_options="list_organisms()"
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37 label="Organism" />
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38 <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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39
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40 <!-- options -->
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41 <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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42 <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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43
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44 <expand macro="wait_for"/>
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45
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46 </inputs>
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47 <outputs>
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48 <data format="json" name="results"/>
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49 </outputs>
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50 <help>
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51 Load feature properties from a tabular file (Column1: feature name or uniquename, Column2: property value)
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52
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53 @HELP@
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54 </help>
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55 </tool>