Mercurial > repos > gga > chado_feature_load_go

annotate feature_load_go.xml @ 5:bde9421d7918 draft

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author gga
date Mon, 08 Jul 2019 05:37:40 -0400
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1 <?xml version="1.0"?>
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2 <tool id="feature_load_go" name="Chado load GO annotation" 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 <code file="chado.py"/>
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8 <expand macro="requirements"/>
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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_go
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13 '$input'
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14 '$organism_id'
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15 '$analysis_id'
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17 --query_type '$query_type'
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19 $match_on_name
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21 --name_column '$name_column'
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22 --go_column '$go_column'
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24 #if $re_name:
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25 --re_name '$re_name'
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26 #end if
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28 $skip_missing
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30 > '$results'
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32 && @ZIP_PSQL@
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33 ]]></command>
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34 <inputs>
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35 <expand macro="psql_target"/>
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36 <!-- arguments -->
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37 <param name="input" label="GO annotation" argument="input" type="data" format="tabular" help="Path to the GO annotation file to load" />
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38 <param argument="analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" />
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39 <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
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41 <!-- options -->
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42 <param name="query_type" label="Query type" argument="--query_type" type="text" help="The feature type (e.g. 'gene', 'mRNA', 'polypeptide', 'contig') of the query. It must be a valid Sequence Ontology term." value="polypeptide" />
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43
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44 <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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46 <param name="name_column" label="Identifier column" argument="--name_column" type="integer" value="2" help="Column containing the feature identifiers." />
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47
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48 <param name="go_column" label="GO column" argument="--go_column" type="integer" value="5" help="Column containing the GO id." />
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49
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50 <param name="re_name" label="Name regular expression" argument="--re_name" type="text" help="Regular expression to extract the feature name from the input file (first capturing group will be used)." optional="true">
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51 <expand macro="sanitized"/>
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52 </param>
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53
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54 <param name="skip_missing" label="Skip Missing" argument="--skip_missing" type="boolean" truevalue="--skip_missing" falsevalue="" help="Skip lines with unknown features or GO id instead of aborting everything." />
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56 <expand macro="wait_for"/>
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57 </inputs>
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58 <outputs>
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59 <data format="txt" name="results"/>
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60 <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} on ${on_string}">
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61 <filter>psql_target['method'] == "pgtools"</filter>
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62 </data>
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63 </outputs>
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64 <help>
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65 Load GO annotation from a tabular file
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66
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67 @HELP@
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68 </help>
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69 </tool>