Mercurial > repos > iuc > query_tabular
annotate query_tabular.xml @ 1:8a33b442ecd9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
| author | iuc |
|---|---|
| date | Fri, 18 Aug 2017 16:48:09 -0400 |
| parents | 3708ff0198b7 |
| children | 973f03d82c86 |
| rev | line source |
|---|---|
|
1
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
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changeset
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1 <tool id="query_tabular" name="Query Tabular" version="2.0.0"> |
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0
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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2 <description>using sqlite sql</description> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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3 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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4 <macros> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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changeset
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5 <import>macros.xml</import> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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6 </macros> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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7 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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8 <requirements> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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9 </requirements> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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10 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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11 <command detect_errors="exit_code"><![CDATA[ |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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12 cat '$query_file' && |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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13 #if $add_to_database.withdb: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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14 #if $save_db: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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15 cp '$add_to_database.withdb' '$sqlitedb' && |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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16 #else: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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17 cp '$add_to_database.withdb' '$workdb' && |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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18 #end if |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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19 #end if |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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20 python '$__tool_directory__/query_tabular.py' |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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21 #if $save_db |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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22 -s '$sqlitedb' |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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23 #else |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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24 -s '$workdb' |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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25 #end if |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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26 -j '$table_json' |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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27 #if $sqlquery: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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28 -Q '$query_file' |
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1
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
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29 @RESULT_HEADER@ |
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0
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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30 -o '$output' |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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31 #end if |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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32 ]]></command> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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33 <configfiles> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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34 <configfile name="query_file"> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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35 $sqlquery |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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36 </configfile> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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37 <configfile name="table_json"> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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38 #import json |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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39 #set $jtbldef = dict() |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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40 #set $jtbls = [] |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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41 #set $jtbldef['tables'] = $jtbls |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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42 #for $i,$tbl in enumerate($tables): |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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43 #set $jtbl = dict() |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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44 #set $jtbl['file_path'] = str($tbl.table) |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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45 #if $tbl.tbl_opts.table_name: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
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46 #set $tname = str($tbl.tbl_opts.table_name) |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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47 #else |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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48 #set $tname = 't' + str($i + 1) |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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49 #end if |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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50 #set $jtbl['table_name'] = $tname |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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51 ## #if $tbl.tbl_opts.sel_cols: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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52 ## #set $jtbl['sel_cols'] = $tbl.tbl_opts.sel_cols el_cols |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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53 ## #end if |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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54 #if $tbl.tbl_opts.pkey_autoincr: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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55 #set $jtbl['pkey_autoincr'] = str($tbl.tbl_opts.pkey_autoincr) |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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56 #end if |
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1
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
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57 #if $tbl.tbl_opts.column_names_from_first_line: |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
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58 #set $jtbl['firstlinenames'] = True |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
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59 #end if |
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0
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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60 #if $tbl.tbl_opts.col_names: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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61 #set $col_names = str($tbl.tbl_opts.col_names) |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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62 #if $tbl.tbl_opts.load_named_columns: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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63 #set $jtbl['load_named_columns'] = True |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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64 #end if |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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65 #else |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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66 #set $col_names = '' |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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67 #end if |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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68 #set $jtbl['column_names'] = $col_names |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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69 #set $idx_unique = [] |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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70 #set $idx_non = [] |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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71 #for $idx in $tbl.tbl_opts.indexes: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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72 #if $idx.unique: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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73 #silent $idx_unique.append(str($idx.index_columns)) |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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74 #else: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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75 #silent $idx_non.append(str($idx.index_columns)) |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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76 #end if |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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77 #end for |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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78 #if len($idx_unique) > 0: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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79 #set $jtbl['unique'] = $idx_unique |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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80 #end if |
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81 #if len($idx_non) > 0: |
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82 #set $jtbl['index'] = $idx_non |
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83 #end if |
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84 #set $linefilters = $tbl.input_opts.linefilters |
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85 @LINEFILTERS@ |
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86 #if $input_filters: |
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87 #set $jtbl['filters'] = $input_filters |
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88 #end if |
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89 #set $jtbls += [$jtbl] |
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90 #end for |
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91 #echo $json.dumps($jtbldef) |
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92 </configfile> |
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93 </configfiles> |
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94 <inputs> |
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95 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/> |
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96 <section name="add_to_database" expanded="false" title="Add tables to an existing database"> |
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97 <param name="withdb" type="data" format="sqlite" optional="true" label="Add tables to this Database" |
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98 help="Make sure your added table names are not already in this database"/> |
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99 </section> |
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100 <repeat name="tables" title="Database Table" min="0"> |
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101 <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/> |
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102 <section name="input_opts" expanded="false" title="Filter Dataset Input"> |
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103 <expand macro="macro_line_filters" /> |
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104 </section> |
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105 <section name="tbl_opts" expanded="false" title="Table Options"> |
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106 <param name="table_name" type="text" value="" optional="true" label="Specify Name for Table"> |
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107 <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</help> |
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108 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator> |
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109 </param> |
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110 <param name="column_names_from_first_line" type="boolean" truevalue="True" falsevalue="False" checked="false" |
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111 label="Use first line as column names" |
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112 help="The names will be quoted if they are not valid SQLite column names."/> |
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113 <param name="col_names" type="text" value="" optional="true" label="Specify Column Names (comma-separated list)"> |
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114 <help>By default, table columns will be named: c1,c2,c3,...,cn (column names for a table must be unique) |
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115 You can override the default names by entering a comma -separated list of names, e.g. ',name1,,,name2' would rename the second and fifth columns. |
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116 </help> |
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117 <sanitizer sanitize="False"/> |
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118 <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator> |
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119 </param> |
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120 <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load the columns you have named into database"/> |
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121 <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name" |
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122 help="Only creates this additional column when a name is entered. (This can not be the same name as any of the other columns in this table.)"> |
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123 <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator> |
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124 </param> |
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125 <repeat name="indexes" title="Table Index"> |
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126 <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/> |
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127 <param name="index_columns" type="text" value="" label="Index on Columns"> |
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128 <help>Create an index on the column names: e.g. for default column names: c1 or c2,c4 ( use the names you gave for columns)</help> |
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0
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129 <validator type="regex" message="Column name, separated by commes if more than one">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator> |
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1
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130 <sanitizer sanitize="False"/> |
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131 </param> |
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132 </repeat> |
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133 </section> |
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134 </repeat> |
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135 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history" |
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136 help="SQLite to tabular tool can run additional queries on this database"/> |
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137 <param name="sqlquery" type="text" area="true" size="20x80" value="" optional="true" label="SQL Query to generate tabular output"> |
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138 <help>By default: tables are named: t1,t2,...,tn and columns in each table: c1,c2,...,cn</help> |
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139 <sanitizer sanitize="False"/> |
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140 <validator type="regex" message="">^(?ims)\s*select\s+.*\s+from\s+.*$</validator> |
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141 </param> |
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142 <expand macro="result_results_header_line" /> |
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143 </inputs> |
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144 <outputs> |
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145 <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}"> |
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146 <filter>save_db</filter> |
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147 </data> |
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148 <data format="tabular" name="output" label="query results on ${on_string}"> |
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149 <filter>not save_db or (sqlquery and len(sqlquery.strip()) > 0)</filter> |
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150 </data> |
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151 </outputs> |
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152 <tests> |
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153 <test> |
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154 <repeat name="tables"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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155 <param name="table" ftype="tabular" value="customers.tsv"/> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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156 <section name="input_opts"> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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157 <repeat name="linefilters"> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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158 <conditional name="filter"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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159 <param name="filter_type" value="comment"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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160 <param name="comment_char" value="35"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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161 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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162 </repeat> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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163 </section> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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164 <section name="tbl_opts"> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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165 <param name="table_name" value="customers"/> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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166 <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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167 </section> |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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168 </repeat> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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169 <repeat name="tables"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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170 <param name="table" ftype="tabular" value="sales.tsv"/> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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171 <section name="input_opts"> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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172 <repeat name="linefilters"> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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173 <conditional name="filter"> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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174 <param name="filter_type" value="comment"/> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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175 <param name="comment_char" value="35"/> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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176 </conditional> |
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177 </repeat> |
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178 </section> |
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179 <section name="tbl_opts"> |
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180 <param name="table_name" value="sales"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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181 <param name="col_names" value="CustomerID,Date,SaleAmount"/> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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182 </section> |
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183 </repeat> |
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184 <param name="sqlquery" value="SELECT FirstName,LastName,sum(SaleAmount) as "TotalSales" FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC"/> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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185 <output name="output" file="sales_results.tsv"/> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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186 </test> |
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187 |
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188 <test> |
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189 <repeat name="tables"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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190 <param name="table" ftype="tabular" value="customers.tsv"/> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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191 <section name="input_opts"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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192 <repeat name="linefilters"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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193 <conditional name="filter"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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194 <param name="filter_type" value="comment"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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195 <param name="comment_char" value="35"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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196 </conditional> |
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197 </repeat> |
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198 </section> |
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199 <section name="tbl_opts"> |
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200 <param name="col_names" value=",FirstName,LastName,,DOB,"/> |
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201 </section> |
|
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202 </repeat> |
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203 <repeat name="tables"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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204 <param name="table" ftype="tabular" value="sales.tsv"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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205 <section name="input_opts"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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206 <repeat name="linefilters"> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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207 <conditional name="filter"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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208 <param name="filter_type" value="skip"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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209 <param name="skip_lines" value="1"/> |
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210 </conditional> |
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211 </repeat> |
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212 </section> |
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213 </repeat> |
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214 <param name="sqlquery" value="SELECT FirstName,LastName,sum(t2.c3) as "TotalSales" FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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215 <output name="output" file="sales_results.tsv"/> |
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216 </test> |
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217 |
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218 <test> |
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219 <repeat name="tables"> |
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220 <param name="table" ftype="tabular" value="customers.tsv"/> |
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221 <section name="input_opts"> |
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222 <repeat name="linefilters"> |
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223 <conditional name="filter"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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224 <param name="filter_type" value="skip"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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225 <param name="skip_lines" value="1"/> |
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226 </conditional> |
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227 </repeat> |
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228 </section> |
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229 <section name="tbl_opts"> |
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230 <param name="col_names" value=",FirstName,LastName,,BirthDate,"/> |
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231 </section> |
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232 </repeat> |
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233 <param name="sqlquery" value="select FirstName,LastName,re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB" from t1 WHERE re_search('[hp]er',c4)"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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234 <output name="output" file="regex_results.tsv"/> |
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235 </test> |
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236 |
|
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237 <test> |
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238 <repeat name="tables"> |
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239 <param name="table" ftype="tabular" value="IEDB.tsv"/> |
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240 <section name="input_opts"> |
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241 <repeat name="linefilters"> |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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242 <conditional name="filter"> |
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243 <param name="filter_type" value="comment"/> |
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244 <param name="comment_char" value="35"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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245 </conditional> |
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246 </repeat> |
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247 </section> |
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248 <section name="tbl_opts"> |
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249 <param name="table_name" value="iedb"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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250 <param name="col_names" value="ID,allele,seq_num,start,end,length,peptide,method,percentile_rank,ann_ic50,ann_rank,smm_ic50,smm_rank,comblib_sidney2008_score,comblib_sidney2008_rank,netmhcpan_ic50,netmhcpan_rank"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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251 </section> |
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252 </repeat> |
|
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253 <repeat name="tables"> |
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254 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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255 <section name="input_opts"> |
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256 <repeat name="linefilters"> |
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257 <conditional name="filter"> |
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258 <param name="filter_type" value="skip"/> |
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259 <param name="skip_lines" value="1"/> |
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260 </conditional> |
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261 </repeat> |
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262 </section> |
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263 <section name="tbl_opts"> |
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264 <param name="table_name" value="mhc_summary"/> |
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265 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/> |
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266 </section> |
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267 </repeat> |
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268 <param name="sqlquery" value="select iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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269 <output name="output" file="query_results.tsv"/> |
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270 </test> |
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271 |
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272 <test> |
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273 <section name="add_to_database"> |
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274 <param name="withdb" ftype="sqlite" value="testdb.sqlite"/> |
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275 </section> |
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276 <repeat name="tables"> |
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277 <param name="table" ftype="tabular" value="pets.tsv"/> |
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278 <section name="input_opts"> |
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279 <repeat name="linefilters"> |
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280 <conditional name="filter"> |
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281 <param name="filter_type" value="regex"/> |
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282 <param name="regex_pattern" value="^\d+"/> |
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283 <param name="regex_action" value="include_find"/> |
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284 </conditional> |
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285 </repeat> |
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286 <repeat name="linefilters"> |
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287 <conditional name="filter"> |
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288 <param name="filter_type" value="comment"/> |
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289 <param name="comment_char" value="35"/> |
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290 </conditional> |
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291 </repeat> |
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292 <repeat name="linefilters"> |
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293 <conditional name="filter"> |
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294 <param name="filter_type" value="append_line_num"/> |
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295 </conditional> |
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296 </repeat> |
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297 <repeat name="linefilters"> |
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298 <conditional name="filter"> |
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299 <param name="filter_type" value="select_columns"/> |
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300 <param name="columns" value="7,2,3,4,1"/> |
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301 </conditional> |
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302 </repeat> |
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303 <repeat name="linefilters"> |
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304 <conditional name="filter"> |
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305 <param name="filter_type" value="replace"/> |
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306 <param name="column" value="c4"/> |
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307 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/> |
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308 <param name="regex_replace" value="19\3-\2-\1"/> |
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309 </conditional> |
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310 </repeat> |
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311 </section> |
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312 <section name="tbl_opts"> |
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313 <param name="table_name" value="people"/> |
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314 <param name="col_names" value="id,first,last,dob,pets"/> |
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315 </section> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
316 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
317 <param name="sqlquery" value="SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
318 <output name="output" file="add_to_db_results.tsv"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
319 </test> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
320 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
321 <test> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
322 <repeat name="tables"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
323 <param name="table" ftype="tabular" value="pets.tsv"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
324 <section name="input_opts"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
325 <repeat name="linefilters"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
326 <conditional name="filter"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
327 <param name="filter_type" value="regex"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
328 <param name="regex_pattern" value="^\d+"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
329 <param name="regex_action" value="include_find"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
330 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
331 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
332 <repeat name="linefilters"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
333 <conditional name="filter"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
334 <param name="filter_type" value="comment"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
335 <param name="comment_char" value="35"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
336 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
337 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
338 <repeat name="linefilters"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
339 <conditional name="filter"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
340 <param name="filter_type" value="append_line_num"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
341 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
342 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
343 <repeat name="linefilters"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
344 <conditional name="filter"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
345 <param name="filter_type" value="select_columns"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
346 <param name="columns" value="7,2,3,4,1"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
347 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
348 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
349 <repeat name="linefilters"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
350 <conditional name="filter"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
351 <param name="filter_type" value="replace"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
352 <param name="column" value="c4"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
353 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
354 <param name="regex_replace" value="19\3-\2-\1"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
355 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
356 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
357 </section> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
358 <section name="tbl_opts"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
359 <param name="table_name" value="people"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
360 <param name="col_names" value="id,first,last,dob,pets"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
361 </section> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
362 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
363 <repeat name="tables"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
364 <param name="table" ftype="tabular" value="pets.tsv"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
365 <section name="input_opts"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
366 <repeat name="linefilters"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
367 <conditional name="filter"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
368 <param name="filter_type" value="regex"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
369 <param name="regex_pattern" value="^\d+"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
370 <param name="regex_action" value="include_find"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
371 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
372 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
373 <repeat name="linefilters"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
374 <conditional name="filter"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
375 <param name="filter_type" value="append_line_num"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
376 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
377 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
378 <repeat name="linefilters"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
379 <conditional name="filter"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
380 <param name="filter_type" value="select_columns"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
381 <param name="columns" value="c7,c5,c6"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
382 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
383 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
384 <repeat name="linefilters"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
385 <conditional name="filter"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
386 <param name="filter_type" value="normalize"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
387 <param name="columns" value="c2,c3"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
388 <param name="separator" value=","/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
389 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
390 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
391 </section> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
392 <section name="tbl_opts"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
393 <param name="table_name" value="pet"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
394 <param name="col_names" value="id,name,animal"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
395 </section> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
396 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
397 <param name="sqlquery" value="SELECT people.id,first,last,dob,name,animal,pets FROM people JOIN pet ON people.id = pet.id WHERE animal = 'cat'"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
398 <output name="output" file="pet_normalized_query_results.tsv"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
399 </test> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
400 |
|
1
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
401 <test> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
402 <repeat name="tables"> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
403 <param name="table" ftype="tabular" value="psm_report.tsv"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
404 <section name="input_opts"> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
405 <repeat name="linefilters"> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
406 <conditional name="filter"> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
407 <param name="filter_type" value="select_columns"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
408 <param name="columns" value="1,3,2,6,14,19"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
409 </conditional> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
410 </repeat> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
411 </section> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
412 <section name="tbl_opts"> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
413 <param name="table_name" value="PSMs"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
414 <param name="column_names_from_first_line" value="True"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
415 <param name="col_names" value="Scan"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
416 </section> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
417 </repeat> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
418 <param name="sqlquery" value="SELECT * from PSMs"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
419 <conditional name="query_result"> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
420 <param name="header" value="yes"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
421 <param name="header_prefix" value=""/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
422 </conditional> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
423 <output name="output" file="psm_report_out1.tsv"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
424 </test> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
425 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
426 <test> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
427 <repeat name="tables"> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
428 <param name="table" ftype="tabular" value="psm_report.tsv"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
429 <section name="input_opts"> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
430 <repeat name="linefilters"> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
431 <conditional name="filter"> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
432 <param name="filter_type" value="select_columns"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
433 <param name="columns" value="1,3,2,6,14,19"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
434 </conditional> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
435 </repeat> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
436 </section> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
437 <section name="tbl_opts"> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
438 <param name="table_name" value="PSMs"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
439 <param name="column_names_from_first_line" value="True"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
440 <param name="col_names" value="Scan"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
441 </section> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
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diff
changeset
|
442 </repeat> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
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diff
changeset
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443 <param name="sqlquery" value="SELECT Scan,"m/z", "Precursor m/z Error [ppm]", Sequence, "Protein(s)" FROM PSMs WHERE NOT re_search(', ',"Protein(s)")"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
444 <conditional name="query_result"> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
445 <param name="header" value="yes"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
446 <param name="header_prefix" value=""/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
447 </conditional> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
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diff
changeset
|
448 <output name="output" file="psm_report_out2.tsv"/> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
449 </test> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
450 |
|
0
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
451 </tests> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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452 <help><![CDATA[ |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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453 ============= |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
454 Query Tabular |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
455 ============= |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
456 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
457 **Inputs** |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
458 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
459 Loads tabular datasets into a SQLite_ data base. |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
460 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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461 An existing SQLite_ data base can be used as input, and any selected tabular datasets will be added as new tables in that data base. |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
462 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
463 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
464 @LINEFILTERS_HELP@ |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
465 |
|
1
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
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diff
changeset
|
466 **Table Options** |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
467 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
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diff
changeset
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468 Specify Name for Table: |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
469 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
470 - By default tables will be named: t1, t2, t3, etc. |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
471 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
472 - **Specify Name for Table** |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
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diff
changeset
|
473 You can provide your own name for a database table, the name should begin with a letter and only contain letters, digits, or underscores. |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
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diff
changeset
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474 The name should not be a SQLite key word: https://sqlite.org/lang_keywords.html |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
475 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
476 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
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477 There are several ways to name columns in a table: |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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478 |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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479 - By default table columns will be named: c1, c2, c3, etc. |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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|
480 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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481 - If **Use first line as column names** is selected, the first line is interpreted as column names, and not loaded into the table as a data row. |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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482 Any missing column name will be assigned cn where *n* is the ordinal position of the column, |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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483 e.g. a blank header for the second column would be named: c2. |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
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changeset
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484 The column names will be quoted is they are not valid identifiers, |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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changeset
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485 e.g. if they are SQLite keywords, or start with a non letter character, or contain a character other than a letter, digit, or underscore. |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
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changeset
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486 The precedent for quoting is to enclose the identifier in double quotes, |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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487 else if it contains a double quote enclose in square brackets, |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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488 else if it contains a square bracket enclose in grave accents. |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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489 **NOTE:** that this is the first line after line filtering has been applied. |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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490 If a line filter *prepend a line number column* had been used, the name of the first column would be "1". |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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491 You could rename that column using **Specify Column Names** |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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492 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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493 - **Specify Column Names** (comma-separated list) |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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494 This will override any previously assigned column names. |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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495 You can also choose to only load those columns for which you provided a name, |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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496 but that is better accomplished with the line filter: *select columns*. |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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|
497 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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changeset
|
498 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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|
499 **Table Index** |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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|
500 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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changeset
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501 Queries on larger tables can be much faster if indexes are specified. |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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502 In general, specifiy an index for table columns used in joins with other tables, |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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503 or on columns used in SQL query WHERE clauses or in GROUP BY clauses. |
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8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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504 |
|
0
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
505 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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506 **Outputs** |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
507 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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508 The results of a SQL query are output to the history as a tabular file. |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
509 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
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510 The SQLite_ data base can also be saved and output as a dataset in the history. |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
511 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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512 *(The* **SQLite to tabular** *tool can run additional queries on this database.)* |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
513 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
514 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
515 @QUERY_HELP@ |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
516 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
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517 @LINEFILTERS_HELP_EXAMPLE@ |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
518 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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parents:
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changeset
|
519 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
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520 Table name: pets |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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parents:
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changeset
|
521 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
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522 Table columns: Pets,FirstName,LastName,Birthdate,PetNames,PetType,line_num,entry_num,row_num |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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parents:
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changeset
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523 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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changeset
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524 Query: SELECT * FROM pets |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
525 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
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526 Result: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
527 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
|
528 ====== ========== ======== ========== ========= ======== ========= ========== ======== |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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529 #Pets FirstName LastName BirthDate PetNames PetType line_num entry_num row_num |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
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530 ====== ========== ======== ========== ========= ======== ========= ========== ======== |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
531 2 Paula Brown 1978-05-24 Rex dog 3 1 1 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
532 2 Paula Brown 1978-05-24 Fluff cat 3 1 2 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
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533 1 Steven Jones 1974-04-04 Allie cat 4 2 3 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
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534 0 Jane Doe 1978-05-24 5 3 4 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
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535 1 James Smith 1980-10-20 Spot 6 4 5 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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parents:
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changeset
|
536 ====== ========== ======== ========== ========= ======== ========= ========== ======== |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
537 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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parents:
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changeset
|
538 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
539 **Normalizing by Line Filtering into 2 Tables** |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
540 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
541 *Relational database opertions work with single-valued column entries. |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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542 To apply relational operations to tabular files that contain fields with lists of values, |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
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543 we need to "normalize" those fields, duplicating lines for each item in the list. |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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parents:
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changeset
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544 In this example we create 2 tables, one for single-valued fields and a second with list-valued fields normalized. |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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parents:
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changeset
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545 Becauce we add a line number first for each table, we can join the 2 tables on the line number column.* |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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changeset
|
546 https://en.wikipedia.org/wiki/First_normal_form |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
|
547 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
|
548 *People Table* |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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parents:
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changeset
|
549 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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parents:
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changeset
|
550 :: |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
|
551 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
|
552 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number) |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
553 Filter 2 - append a line number column: |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
|
554 Filter 3 - regex replace value in column[4]: '(\d+)/(\d+)/(\d+)' '19\3-\2-\1' (convert dates to sqlite format) |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
555 Filter 4 - select columns 7,2,3,4,1 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
|
556 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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changeset
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557 Table: People |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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changeset
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558 Columns: id,FirstName,LastName,DOB,Pets |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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559 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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changeset
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560 == ========= ======== ========== ==== |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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561 id FirstName LastName DOB Pets |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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562 == ========= ======== ========== ==== |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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563 1 Paula Brown 1978-05-24 2 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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564 2 Steven Jones 1974-04-04 1 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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changeset
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565 3 Jane Doe 1978-05-24 0 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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changeset
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566 4 James Smith 1980-10-20 1 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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567 == ========= ======== ========== ==== |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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568 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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569 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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570 *Pet Table* |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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571 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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572 :: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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573 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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changeset
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574 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number) |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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575 Filter 2 - append a line number column: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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576 Filter 3 - by regex expression matching [exclude]: '^0\t' (exclude lines with no pets) |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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577 Filter 4 - normalize list columns[5,6]: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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578 Filter 5 - select columns 7,5,6 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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579 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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580 Table: Pet |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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581 Columns: id,PetName,PetType |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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582 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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583 == ======== ======== |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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584 id PetName PetType |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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585 == ======== ======== |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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586 1 Rex dog |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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587 1 Fluff cat |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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588 2 Allie cat |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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589 4 Spot |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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590 == ======== ======== |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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591 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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592 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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593 Query: SELECT FirstName,LastName,PetName FROM People JOIN Pet ON People.id = Pet.id WHERE PetType = 'cat'; |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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594 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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595 Result: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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596 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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597 ========= ======== ======== |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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598 FirstName LastName PetName |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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599 ========= ======== ======== |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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600 Paula Brown Fluff |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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601 Steven Jones Allie |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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602 ========= ======== ======== |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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603 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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604 |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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605 ]]></help> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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606 </tool> |