Mercurial > repos > gga > chado_expression_add_expression

annotate expression_add_expression.xml @ 8:80444967de58 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bfca9a8c38694bbf04d92a6668e4ea31cf658eb8"
author gga
date Thu, 14 Nov 2019 09:58:15 -0500
parents 126fc4d52d4e
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1 <?xml version="1.0"?>
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2 <tool id="expression_add_expression" name="Chado expression add" 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 expression add_expression
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13 '$organism_id'
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14 '$analysis_id'
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15 '$file_path'
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17 #if $unit:
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18 --unit '$unit'
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19 #end if
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21 --query_type '$query_type'
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23 $match_on_name
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25 #if $re_name:
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26 --re_name '$re_name'
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27 #end if
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29 $skip_missing
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30
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31 > '$results'
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33 @ZIP_PSQL@
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34 ]]></command>
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35 <inputs>
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36 <expand macro="psql_target"/>
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37 <!-- arguments -->
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38 <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
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39 <param argument="analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" />
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40 <param name="file_path" label="Expression matrix" argument="file_path" type="data" format="tabular" help="Tabular file where columns are experimental conditions, and rows are features" />
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41
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42 <param name="unit" label="Unit" argument="--unit" type="text" help="The units associated with the loaded values (ie, FPKM, RPKM, raw counts)" />
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44 <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="mRNA" />
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46 <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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47
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48 <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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49 <expand macro="sanitized"/>
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50 </param>
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52 <param name="skip_missing" label="Skip Missing" argument="--skip_missing" type="boolean" truevalue="--skip_missing" falsevalue="" help="Skip lines with unknown features instead of aborting everything." />
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53
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54 <expand macro="wait_for"/>
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55 </inputs>
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56 <outputs>
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57 <data format="txt" name="results"/>
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58 <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} on ${on_string}">
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59 <filter>psql_target['method'] == "pgtools"</filter>
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60 </data>
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61 </outputs>
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62 <help>
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63 Add an expression matrix file to the database
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65 @HELP@
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66 </help>
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67 </tool>