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annotate pg-query.xml @ 0:fa1a61331039 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
author bgruening
date Wed, 24 Apr 2019 06:12:05 -0400
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fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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1 <tool id="pg_query" name="Query" version="@PG_VERSION@">
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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2 <description>postgres database</description>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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3 <macros>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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4 <import>macros.xml</import>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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5 </macros>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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6 <expand macro="requirements" />
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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7 <command detect_errors="aggressive"><![CDATA[
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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8 @UNTAR_INFILE@ &&
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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9 @PG_START@ &&
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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10 ##ls -l ./postgresql &&
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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11 a=" with CSV HEADER DELIMITER ' ';" &&
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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12 echo "COPY ($query) TO STDOUT"\$a | @PSQL@ -L logfile.log > '$outfile' &&
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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13 @PG_STOP@
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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14 &&
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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15 cat logfile.log
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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16 ]]>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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17 </command>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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18 <inputs>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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19 <param name="infile" type="data" format="postgresql" label="Input database" />
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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20 <param name="query" type="text" area="True" size="5x50" label="The query to be issued to the database">
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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21 <sanitizer invalid_char="">
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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22 <valid initial="string.printable">
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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23 <remove value="&apos;" />
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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24 </valid>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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25 <mapping initial="none">
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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26 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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27 </mapping>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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28 </sanitizer>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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29 <validator type="expression" message="Query cannot be empty">value.strip()</validator>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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30 </param>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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31 </inputs>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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32 <outputs>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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33 <data format="txt" name="outfile" />
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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34 </outputs>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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35 <tests>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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36 <test>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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37 <param name="infile" value="pg_import_result1.pg.tar.bz2" ftype="postgresql" />
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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38 <param name="query" value="select version from migrate_version" />
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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39 <output file="pg_query_result1.txt" name="outfile" />
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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40 </test>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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41 <test>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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42 <param name="infile" value="pg_import_result1.pg.tar.bz2" ftype="postgresql" />
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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43 <param name="query" value="select * from galaxy_user" />
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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44 <output file="pg_query_result2.txt" name="outfile" />
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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45 </test>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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46 </tests>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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47 <help>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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48 <![CDATA[
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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49
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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50 @HELP_FOOTER@
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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51
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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52 ]]>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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53 </help>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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54 <expand macro="citations" />
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
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55 </tool>