Mercurial > repos > gga > chado_analysis_add_analysis

annotate analysis_add_analysis.xml @ 10:21de6e516f97 draft

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author gga
date Mon, 08 Jul 2019 05:39:24 -0400
parents 11b434f48a03
children a2efb5aff729
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1 <?xml version="1.0"?>
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2 <tool id="analysis_add_analysis" name="Chado analysis add" version="@WRAPPER_VERSION@.1">
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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 analysis add_analysis
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12 '$name'
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13 '$program'
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14 '$programversion'
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15 '$sourcename'
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17 #if $algorithm:
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18 --algorithm '$algorithm'
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19 #end if
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20 #if $sourceversion:
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21 --sourceversion '$sourceversion'
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22 #end if
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23 #if $sourceuri:
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24 --sourceuri '$sourceuri'
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25 #end if
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26 #if $description:
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27 --description '$description'
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28 #end if
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29 #if $date_executed:
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30 --date_executed '$date_executed'
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31 #end if
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32
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33 | jq -S . > '$results'
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35 && @ZIP_PSQL@
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36 ]]></command>
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37 <inputs>
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38 <expand macro="psql_target"/>
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39 <!-- arguments -->
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40 <param name="name" label="Name" argument="name" type="text" help="analysis name" />
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41 <param name="program" label="Program" argument="program" type="text" help="analysis program" />
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42 <param name="programversion" label="Programversion" argument="programversion" type="text" help="analysis programversion" />
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43 <param name="sourcename" label="Sourcename" argument="sourcename" type="text" help="analysis sourcename" />
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45 <!-- options -->
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46 <param name="algorithm" label="Algorithm" argument="--algorithm" type="text" help="analysis algorithm" optional="True" />
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47 <param name="sourceversion" label="Sourceversion" argument="--sourceversion" type="text" help="analysis sourceversion" optional="True" />
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48 <param name="sourceuri" label="Sourceuri" argument="--sourceuri" type="text" help="analysis sourceuri" optional="True" />
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49 <param name="description" label="Description" argument="--description" type="text" help="analysis description" optional="True" />
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50 <param name="date_executed" label="Date Executed" argument="--date_executed" type="text" optional="True" help="analysis date_executed (yyyy-mm-dd)">
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51 <validator type="regex" message="Date in YYYY-MM-DD format">^[0-9]{4}-[0-9]{2}-[0-9]{2}$</validator>
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52 </param>
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53
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54 </inputs>
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55 <outputs>
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56 <data format="json" name="results" label="Chado analysis add: ${name}"/>
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57 <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} '${name}' on ${on_string}">
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58 <filter>psql_target['method'] == "pgtools"</filter>
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59 </data>
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60 </outputs>
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61 <help>
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62 Create an analysis
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64 @HELP@
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65 </help>
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66 </tool>