Mercurial > repos > iuc > query_tabular
annotate query_tabular.xml @ 7:33d61c89fb8d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
| author | iuc |
|---|---|
| date | Tue, 30 Oct 2018 20:19:30 -0400 |
| parents | ad79e7bb1a9e |
| children | 0c95a3f1654f |
| rev | line source |
|---|---|
|
4
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
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changeset
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1 <tool id="query_tabular" name="Query Tabular" version="3.0.0"> |
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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:
diff
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
parents:
diff
changeset
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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
parents:
diff
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:
diff
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:
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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 $save_db: |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
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15 cp '$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' '$workdb' && |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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18 #end if |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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19 #end if |
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4
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
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20 python '$__tool_directory__/query_tabular.py' -d |
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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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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
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29 @RESULT_HEADER@ |
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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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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:
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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
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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
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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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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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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
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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
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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
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0
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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
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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
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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:
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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
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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:
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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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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:
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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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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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changeset
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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:
diff
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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
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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'] = $idx_unique |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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80 #end if |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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81 #if len($idx_non) > 0: |
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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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82 #set $jtbl['index'] = $idx_non |
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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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83 #end if |
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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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84 #set $linefilters = $tbl.input_opts.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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85 @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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86 #if $input_filters: |
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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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87 #set $jtbl['filters'] = $input_filters |
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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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88 #end if |
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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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89 #set $jtbls += [$jtbl] |
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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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90 #end for |
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4
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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91 #set $jstmts = [] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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92 #for $i,$stmt in enumerate($modify_database.sql_stmts): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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93 #set $jstmts += [str($stmt.sqlstmt)] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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94 #end for |
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973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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95 #if len($jstmts) > 0: |
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973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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96 #set $jtbldef['sql_stmts'] = $jstmts |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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97 #end if |
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973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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98 #set $jqueries = [] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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99 #for $i,$query in enumerate($addqueries.queries): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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100 #set $jquery = dict() |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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101 #set $jquery['query'] = str($query.sqlquery) |
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973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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102 #set $jquery['result_file'] = 'results' + str($i) + '.tsv' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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103 #if $query.query_result.header == 'yes': |
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973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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104 #set $header_prefix = '' |
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973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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105 #if $query.query_result.header_prefix: |
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973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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106 #set $header_prefix = chr(int(str($query.query_result.header_prefix))) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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107 #end if |
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973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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108 #set $jquery['header'] = $header_prefix |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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109 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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110 #set $jqueries += [$jquery] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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111 #end for |
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973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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112 #if len($jqueries) > 0: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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113 #set $jtbldef['queries'] = $jqueries |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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114 #end if |
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0
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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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115 #echo $json.dumps($jtbldef) |
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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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116 </configfile> |
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117 </configfiles> |
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118 <inputs> |
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119 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/> |
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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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120 <section name="add_to_database" expanded="false" title="Add tables to an existing database"> |
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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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121 <param name="withdb" type="data" format="sqlite" optional="true" label="Add tables to this Database" |
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122 help="Make sure your added table names are not already in this database"/> |
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123 </section> |
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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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124 <repeat name="tables" title="Database Table" min="0"> |
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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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125 <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/> |
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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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126 <section name="input_opts" expanded="false" title="Filter Dataset Input"> |
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127 <expand macro="macro_line_filters" /> |
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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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128 </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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129 <section name="tbl_opts" expanded="false" title="Table Options"> |
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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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130 <param name="table_name" type="text" value="" optional="true" label="Specify Name for Table"> |
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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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131 <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</help> |
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132 <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator> |
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133 </param> |
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1
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134 <param name="column_names_from_first_line" type="boolean" truevalue="True" falsevalue="False" checked="false" |
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135 label="Use first line as column names" |
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136 help="The names will be quoted if they are not valid SQLite column names."/> |
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137 <param name="col_names" type="text" value="" optional="true" label="Specify Column Names (comma-separated list)"> |
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138 <help>By default, table columns will be named: c1,c2,c3,...,cn (column names for a table must be unique) |
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3708ff0198b7
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139 You can override the default names by entering a comma -separated list of names, e.g. ',name1,,,name2' would rename the second and fifth columns. |
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140 </help> |
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141 <sanitizer sanitize="False"/> |
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142 <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator> |
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3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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143 </param> |
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144 <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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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145 <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name" |
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146 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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147 <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator> |
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148 </param> |
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149 <repeat name="indexes" title="Table Index"> |
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150 <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/> |
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151 <param name="index_columns" type="text" value="" label="Index on Columns"> |
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1
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152 <help>Create an index on the column names: e.g. for default column names: c1 or c2,c4 ( use the names you gave for columns)</help> |
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0
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153 <validator type="regex" message="Column name, separated by commes if more than one">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator> |
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154 <sanitizer sanitize="False"/> |
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155 </param> |
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156 </repeat> |
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157 </section> |
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158 </repeat> |
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159 <section name="modify_database" expanded="false" title="Modify the database"> |
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160 <repeat name="sql_stmts" title="Database Manipulation SQL Statements" min="0"> |
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161 <param name="sqlstmt" type="text" area="true" size="20x80" value="" optional="true" label="SQL Query to modify the database"> |
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162 <help>These modify the SQLite database</help> |
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163 <sanitizer sanitize="False"/> |
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164 </param> |
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165 </repeat> |
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166 </section> |
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167 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history" |
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168 help="SQLite to tabular tool can run additional queries on this database"/> |
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169 <expand macro="sql_query_input"/> |
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170 <expand macro="result_results_header_line" /> |
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171 <section name="addqueries" expanded="false" title="Additional Queries"> |
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172 <repeat name="queries" title="Database Manipulation SQL Statements" min="0" max="3"> |
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173 <expand macro="sql_query_input"/> |
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174 <expand macro="result_results_header_line" /> |
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175 </repeat> |
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176 </section> |
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177 </inputs> |
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178 <outputs> |
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179 <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}"> |
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180 <filter>save_db</filter> |
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181 </data> |
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182 <data format="tabular" name="output" label="query results on ${on_string}"> |
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183 <filter>not save_db or (sqlquery and len(sqlquery.strip()) > 0)</filter> |
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184 </data> |
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185 <data format="tabular" name="output1" label="query 1 results on ${on_string}" from_work_dir="results0.tsv"> |
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186 <filter>len(addqueries['queries']) > 0</filter> |
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187 </data> |
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188 <data format="tabular" name="output2" label="query 2 results on ${on_string}" from_work_dir="results1.tsv"> |
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189 <filter>len(addqueries['queries']) > 1</filter> |
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190 </data> |
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191 <data format="tabular" name="output3" label="query 3 results on ${on_string}" from_work_dir="results2.tsv"> |
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192 <filter>len(addqueries['queries']) > 2</filter> |
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193 </data> |
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0
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194 </outputs> |
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195 <tests> |
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196 <test> |
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197 <repeat name="tables"> |
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198 <param name="table" ftype="tabular" value="customers.tsv"/> |
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199 <section name="input_opts"> |
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200 <repeat name="linefilters"> |
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201 <conditional name="filter"> |
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202 <param name="filter_type" value="comment"/> |
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203 <param name="comment_char" value="35"/> |
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204 </conditional> |
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205 </repeat> |
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206 </section> |
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207 <section name="tbl_opts"> |
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208 <param name="table_name" value="customers"/> |
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209 <param name="col_names" value="CustomerID,FirstName,LastName,Email,DOB,Phone"/> |
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210 </section> |
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211 </repeat> |
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212 <repeat name="tables"> |
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213 <param name="table" ftype="tabular" value="sales.tsv"/> |
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214 <section name="input_opts"> |
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215 <repeat name="linefilters"> |
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216 <conditional name="filter"> |
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217 <param name="filter_type" value="comment"/> |
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218 <param name="comment_char" value="35"/> |
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219 </conditional> |
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220 </repeat> |
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221 </section> |
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222 <section name="tbl_opts"> |
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223 <param name="table_name" value="sales"/> |
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224 <param name="col_names" value="CustomerID,Date,SaleAmount"/> |
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225 </section> |
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226 </repeat> |
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227 <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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228 <output name="output" file="sales_results.tsv"/> |
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229 </test> |
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230 |
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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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231 <test> |
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232 <repeat name="tables"> |
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233 <param name="table" ftype="tabular" value="customers.tsv"/> |
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234 <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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235 <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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236 <conditional name="filter"> |
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237 <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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238 <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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239 </conditional> |
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240 </repeat> |
|
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241 </section> |
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242 <section name="tbl_opts"> |
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243 <param name="col_names" value=",FirstName,LastName,,DOB,"/> |
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244 </section> |
|
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245 </repeat> |
|
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246 <repeat name="tables"> |
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247 <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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248 <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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249 <repeat name="linefilters"> |
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250 <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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251 <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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252 <param name="skip_lines" value="1"/> |
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253 </conditional> |
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254 </repeat> |
|
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255 </section> |
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256 </repeat> |
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257 <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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258 <output name="output" file="sales_results.tsv"/> |
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259 </test> |
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260 |
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261 <test> |
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262 <repeat name="tables"> |
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263 <param name="table" ftype="tabular" value="customers.tsv"/> |
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264 <section name="input_opts"> |
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265 <repeat name="linefilters"> |
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266 <conditional name="filter"> |
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267 <param name="filter_type" value="skip"/> |
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268 <param name="skip_lines" value="1"/> |
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269 </conditional> |
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270 </repeat> |
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271 </section> |
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272 <section name="tbl_opts"> |
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273 <param name="col_names" value=",FirstName,LastName,,BirthDate,"/> |
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274 </section> |
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275 </repeat> |
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276 <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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277 <output name="output" file="regex_results.tsv"/> |
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278 </test> |
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279 |
|
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280 <test> |
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281 <repeat name="tables"> |
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282 <param name="table" ftype="tabular" value="IEDB.tsv"/> |
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283 <section name="input_opts"> |
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284 <repeat name="linefilters"> |
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285 <conditional name="filter"> |
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286 <param name="filter_type" value="comment"/> |
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287 <param name="comment_char" value="35"/> |
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288 </conditional> |
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289 </repeat> |
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290 </section> |
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291 <section name="tbl_opts"> |
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292 <param name="table_name" value="iedb"/> |
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293 <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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294 </section> |
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295 </repeat> |
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296 <repeat name="tables"> |
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297 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/> |
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298 <section name="input_opts"> |
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299 <repeat name="linefilters"> |
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300 <conditional name="filter"> |
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301 <param name="filter_type" value="skip"/> |
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302 <param name="skip_lines" value="1"/> |
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303 </conditional> |
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304 </repeat> |
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305 </section> |
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306 <section name="tbl_opts"> |
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307 <param name="table_name" value="mhc_summary"/> |
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308 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/> |
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309 </section> |
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310 </repeat> |
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311 <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"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
312 <output name="output" file="query_results.tsv"/> |
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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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diff
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|
313 </test> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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314 |
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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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diff
changeset
|
315 <test> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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diff
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316 <section name="add_to_database"> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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diff
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|
317 <param name="withdb" ftype="sqlite" value="testdb.sqlite"/> |
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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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318 </section> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
319 <repeat name="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
|
320 <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
|
321 <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
|
322 <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
|
323 <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
|
324 <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
|
325 <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
|
326 <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
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327 </conditional> |
|
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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328 </repeat> |
|
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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329 <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
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330 <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
|
331 <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
|
332 <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
|
333 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
334 </repeat> |
|
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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335 <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
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336 <conditional name="filter"> |
|
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
|
337 <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
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338 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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339 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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diff
changeset
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340 <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
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341 <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
iuc
parents:
diff
changeset
|
342 <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
|
343 <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:
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344 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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345 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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diff
changeset
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346 <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
iuc
parents:
diff
changeset
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347 <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
iuc
parents:
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changeset
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348 <param name="filter_type" value="replace"/> |
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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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349 <param name="column" value="c4"/> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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diff
changeset
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350 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/> |
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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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351 <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:
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changeset
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352 </conditional> |
|
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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353 </repeat> |
|
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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354 </section> |
|
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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355 <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
iuc
parents:
diff
changeset
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356 <param name="table_name" value="people"/> |
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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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357 <param name="col_names" value="id,first,last,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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358 </section> |
|
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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359 </repeat> |
|
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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360 <param name="sqlquery" value="SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_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
|
361 <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
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362 </test> |
|
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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363 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
364 <test> |
|
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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365 <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
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366 <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
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367 <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
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368 <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
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369 <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
iuc
parents:
diff
changeset
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370 <param name="filter_type" value="regex"/> |
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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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371 <param name="regex_pattern" value="^\d+"/> |
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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
|
372 <param name="regex_action" value="include_find"/> |
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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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diff
changeset
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373 </conditional> |
|
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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374 </repeat> |
|
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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375 <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
|
376 <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
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377 <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
|
378 <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
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379 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
380 </repeat> |
|
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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381 <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
|
382 <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
|
383 <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
|
384 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
385 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
386 <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
|
387 <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
|
388 <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
|
389 <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
|
390 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
391 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
392 <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
|
393 <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
|
394 <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
|
395 <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
|
396 <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
|
397 <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
|
398 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
399 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
400 </section> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
401 <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
|
402 <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
|
403 <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
|
404 </section> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
405 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
406 <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
|
407 <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
|
408 <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
|
409 <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
|
410 <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
|
411 <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
|
412 <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
|
413 <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
|
414 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
415 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
416 <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
|
417 <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
|
418 <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
|
419 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
420 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
421 <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
|
422 <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
|
423 <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
|
424 <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
|
425 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
426 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
427 <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
|
428 <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
|
429 <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
|
430 <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
|
431 <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
|
432 </conditional> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
433 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
434 </section> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
435 <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
|
436 <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
|
437 <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
|
438 </section> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
439 </repeat> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
440 <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
|
441 <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
|
442 </test> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
443 |
|
1
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
444 <test> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
445 <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
|
446 <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
|
447 <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
|
448 <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
|
449 <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
|
450 <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
|
451 <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
|
452 </conditional> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
453 </repeat> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
454 </section> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
455 <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
|
456 <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
|
457 <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
|
458 <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
|
459 </section> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
460 </repeat> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
461 <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
|
462 <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
|
463 <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
|
464 <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
|
465 </conditional> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
466 <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
|
467 </test> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
468 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
469 <test> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
470 <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
|
471 <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
|
472 <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
|
473 <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
|
474 <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
|
475 <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
|
476 <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
|
477 </conditional> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
478 </repeat> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
479 </section> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
480 <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
|
481 <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
|
482 <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
|
483 <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
|
484 </section> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
485 </repeat> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
486 <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
|
487 <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
|
488 <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
|
489 <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
|
490 </conditional> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
491 <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
|
492 </test> |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
493 |
|
4
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
494 <test> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
495 <repeat name="tables"> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
496 <param name="table" ftype="tabular" value="psm_report.tsv"/> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
497 <section name="input_opts"> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
498 <repeat name="linefilters"> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
499 <conditional name="filter"> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
500 <param name="filter_type" value="select_columns"/> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
501 <param name="columns" value="1,3,2,6,14,19,23"/> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
502 </conditional> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
503 </repeat> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
504 </section> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
505 <section name="tbl_opts"> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
506 <param name="table_name" value="PSMs"/> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
507 <param name="column_names_from_first_line" value="True"/> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
508 <param name="col_names" value="scan,,,,,,confidence"/> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
509 </section> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
510 </repeat> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
511 <section name="modify_database"> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
512 <repeat name="sql_stmts"> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
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513 <param name="sqlstmt" value="UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0"/> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
514 </repeat> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
515 </section> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
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diff
changeset
|
516 <param name="sqlquery" value="SELECT scan,"m/z", "Precursor m/z Error [ppm]", Sequence, "Protein(s)", confidence FROM PSMs WHERE NOT re_search(', ',"Protein(s)")"/> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
517 <conditional name="query_result"> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
518 <param name="header" value="yes"/> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
519 <param name="header_prefix" value="#"/> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
520 </conditional> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
521 <section name="addqueries"> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
522 <repeat name="queries"> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
523 <param name="sqlquery" value="SELECT * FROM psms WHERE confidence > 97.0"/> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
524 <conditional name="query_result"> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
525 <param name="header" value="yes"/> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
526 <param name="header_prefix" value=""/> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
527 </conditional> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
528 </repeat> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
529 </section> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
530 <output name="output" file="psm_dbmod_output.tsv"/> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
531 <output name="output1" file="psm_dbmod_output1.tsv"/> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
532 </test> |
|
973f03d82c86
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
533 |
|
0
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
534 </tests> |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
535 <help><![CDATA[ |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
536 ============= |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
537 Query Tabular |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
538 ============= |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
539 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
540 **Inputs** |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
541 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
542 Loads tabular datasets into a SQLite_ data base. |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
543 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
544 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
|
545 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
546 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
547 @LINEFILTERS_HELP@ |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
548 |
|
1
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
549 **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
|
550 |
|
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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551 Specify Name for Table: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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552 |
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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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553 - By default tables will be named: t1, t2, t3, 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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|
554 |
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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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|
555 - **Specify Name for 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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diff
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556 You can provide your own name for a database table, the name should begin with a letter and only contain letters, digits, or underscores. |
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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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557 The name should not be a SQLite key word: https://sqlite.org/lang_keywords.html |
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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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|
558 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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|
559 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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560 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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561 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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562 - 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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563 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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564 - 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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565 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
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566 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
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567 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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568 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
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parents:
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569 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
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570 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
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571 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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572 **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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573 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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574 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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575 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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576 - **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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577 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
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578 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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579 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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580 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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581 |
|
8a33b442ecd9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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582 **Table Index** |
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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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583 |
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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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584 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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585 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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586 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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587 |
|
0
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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588 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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589 **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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590 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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591 The results of a SQL query are output to the history as a tabular file. |
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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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592 |
|
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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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593 The SQLite_ data base can also be saved and output as a dataset in the history. |
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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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594 |
|
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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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595 *(The* **SQLite to tabular** *tool can run additional queries on this database.)* |
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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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596 |
|
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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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597 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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598 @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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599 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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600 @LINEFILTERS_HELP_EXAMPLE@ |
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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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601 |
|
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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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|
602 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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603 Table name: pets |
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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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604 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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605 Table columns: Pets,FirstName,LastName,Birthdate,PetNames,PetType,line_num,entry_num,row_num |
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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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606 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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607 Query: SELECT * FROM pets |
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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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|
608 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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609 Result: |
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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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610 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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611 ====== ========== ======== ========== ========= ======== ========= ========== ======== |
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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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612 #Pets FirstName LastName BirthDate PetNames PetType line_num entry_num row_num |
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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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613 ====== ========== ======== ========== ========= ======== ========= ========== ======== |
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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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614 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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615 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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616 1 Steven Jones 1974-04-04 Allie cat 4 2 3 |
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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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617 0 Jane Doe 1978-05-24 5 3 4 |
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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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618 1 James Smith 1980-10-20 Spot 6 4 5 |
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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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619 ====== ========== ======== ========== ========= ======== ========= ========== ======== |
|
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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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620 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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621 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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622 **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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623 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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624 *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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625 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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626 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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627 In this example we create 2 tables, one for single-valued fields and a second with list-valued fields normalized. |
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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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628 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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629 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
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630 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
631 *People Table* |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
632 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
633 :: |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
634 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
635 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
|
636 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:
diff
changeset
|
637 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
|
638 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:
diff
changeset
|
639 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
640 Table: People |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
641 Columns: id,FirstName,LastName,DOB,Pets |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
642 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
643 == ========= ======== ========== ==== |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
644 id FirstName LastName DOB Pets |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
645 == ========= ======== ========== ==== |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
646 1 Paula Brown 1978-05-24 2 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
647 2 Steven Jones 1974-04-04 1 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
648 3 Jane Doe 1978-05-24 0 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
649 4 James Smith 1980-10-20 1 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
650 == ========= ======== ========== ==== |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
651 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
652 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
653 *Pet Table* |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
654 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
655 :: |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
656 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
657 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
|
658 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:
diff
changeset
|
659 Filter 3 - by regex expression matching [exclude]: '^0\t' (exclude lines with no pets) |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
660 Filter 4 - normalize list columns[5,6]: |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
661 Filter 5 - select columns 7,5,6 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
662 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
663 Table: Pet |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
664 Columns: id,PetName,PetType |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
665 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
666 == ======== ======== |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
667 id PetName PetType |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
668 == ======== ======== |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
669 1 Rex dog |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
670 1 Fluff cat |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
671 2 Allie cat |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
672 4 Spot |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
673 == ======== ======== |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
674 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
675 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
676 Query: SELECT FirstName,LastName,PetName FROM People JOIN Pet ON People.id = Pet.id WHERE PetType = 'cat'; |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
677 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
678 Result: |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
679 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
680 ========= ======== ======== |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
681 FirstName LastName PetName |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
682 ========= ======== ======== |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
683 Paula Brown Fluff |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
684 Steven Jones Allie |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
685 ========= ======== ======== |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
686 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
687 |
|
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
688 ]]></help> |
|
6
ad79e7bb1a9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 43d0f694b024cf9b1f0e26d803d3f19f38c95ee9-dirty
iuc
parents:
4
diff
changeset
|
689 <expand macro="citations" /> |
|
0
3708ff0198b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
690 </tool> |