Mercurial > repos > iuc > query_tabular
annotate query_tabular.xml @ 15:09dcef57a945 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit dd35055c76d86fe98985b5825c1751efb8208242
| author | iuc |
|---|---|
| date | Thu, 27 Jun 2024 17:22:43 +0000 |
| parents | 3c54ecaf63b4 |
| children |
| rev | line source |
|---|---|
|
15
09dcef57a945
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit dd35055c76d86fe98985b5825c1751efb8208242
iuc
parents:
14
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changeset
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1 <tool id="query_tabular" name="Query Tabular" version="3.3.2"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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2 <description>using sqlite sql</description> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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3 |
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81ad914a0b08
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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81ad914a0b08
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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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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6 </macros> |
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8
5c3d86bc259c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 1647065a8e6e8d8c98cd0d2194b695fb9425f541"
iuc
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7 <expand macro="requirements"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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8 <command detect_errors="exit_code"><![CDATA[ |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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9 cat '$query_file' && |
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81ad914a0b08
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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10 #if $add_to_database.withdb: |
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81ad914a0b08
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 #if $save_db: |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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12 cp '$add_to_database.withdb' '$sqlitedb' && |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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13 #else: |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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14 cp '$add_to_database.withdb' '$workdb' && |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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15 #end if |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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16 #end if |
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4
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
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17 python '$__tool_directory__/query_tabular.py' -d |
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81ad914a0b08
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 #if $save_db |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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19 -s '$sqlitedb' |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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20 #else |
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81ad914a0b08
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 -s '$workdb' |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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22 #end if |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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23 -j '$table_json' |
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81ad914a0b08
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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24 #if $sqlquery: |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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25 -Q '$query_file' |
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1
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
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26 @RESULT_HEADER@ |
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81ad914a0b08
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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27 -o '$output' |
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81ad914a0b08
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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28 #end if |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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29 ]]></command> |
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81ad914a0b08
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 <configfiles> |
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81ad914a0b08
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 <configfile name="query_file"> |
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81ad914a0b08
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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32 $sqlquery |
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81ad914a0b08
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 </configfile> |
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81ad914a0b08
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="table_json"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
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35 #import json |
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81ad914a0b08
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 #set $jtbldef = dict() |
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81ad914a0b08
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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37 #set $jtbls = [] |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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38 #set $jtbldef['tables'] = $jtbls |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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39 #for $i,$tbl in enumerate($tables): |
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15
09dcef57a945
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit dd35055c76d86fe98985b5825c1751efb8208242
iuc
parents:
14
diff
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40 #set $table = $tbl.table |
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0
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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41 #set $jtbl = dict() |
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81ad914a0b08
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 #set $jtbl['file_path'] = str($tbl.table) |
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81ad914a0b08
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 #if $tbl.tbl_opts.table_name: |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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44 #set $tname = str($tbl.tbl_opts.table_name) |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
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45 #else |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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46 #set $tname = 't' + str($i + 1) |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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47 #end if |
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81ad914a0b08
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 $jtbl['table_name'] = $tname |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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49 ## #if $tbl.tbl_opts.sel_cols: |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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50 ## #set $jtbl['sel_cols'] = $tbl.tbl_opts.sel_cols el_cols |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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51 ## #end if |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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52 #if $tbl.tbl_opts.pkey_autoincr: |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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53 #set $jtbl['pkey_autoincr'] = str($tbl.tbl_opts.pkey_autoincr) |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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54 #end if |
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1
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
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55 #if $tbl.tbl_opts.column_names_from_first_line: |
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53c9f76c0788
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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56 #set $jtbl['firstlinenames'] = True |
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53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
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57 #end if |
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0
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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58 #if $tbl.tbl_opts.col_names: |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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59 #set $col_names = str($tbl.tbl_opts.col_names) |
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81ad914a0b08
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.load_named_columns: |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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61 #set $jtbl['load_named_columns'] = True |
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81ad914a0b08
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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62 #end if |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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63 #else |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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64 #set $col_names = '' |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
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65 #end if |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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changeset
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66 #set $jtbl['column_names'] = $col_names |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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67 #set $idx_unique = [] |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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68 #set $idx_non = [] |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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69 #for $idx in $tbl.tbl_opts.indexes: |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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70 #if $idx.unique: |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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71 #silent $idx_unique.append(str($idx.index_columns)) |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
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72 #else: |
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81ad914a0b08
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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73 #silent $idx_non.append(str($idx.index_columns)) |
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81ad914a0b08
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 #end if |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
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75 #end for |
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81ad914a0b08
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 #if len($idx_unique) > 0: |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
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77 #set $jtbl['unique'] = $idx_unique |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
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78 #end if |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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79 #if len($idx_non) > 0: |
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80 #set $jtbl['index'] = $idx_non |
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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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81 #end if |
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13
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
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82 #set $dataset_name = $tbl.table.element_identifier |
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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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83 #set $linefilters = $tbl.input_opts.linefilters |
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84 @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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85 #if $input_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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86 #set $jtbl['filters'] = $input_filters |
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87 #end if |
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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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88 #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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89 #end for |
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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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90 #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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91 #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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92 #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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93 #end for |
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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 #if len($jstmts) > 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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95 #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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96 #end if |
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97 #set $jqueries = [] |
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98 #for $i,$query in enumerate($addqueries.queries): |
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99 #set $jquery = dict() |
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100 #set $jquery['query'] = str($query.sqlquery) |
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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 $jquery['result_file'] = 'results' + str($i) + '.tsv' |
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102 #if $query.query_result.header == 'yes': |
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103 #set $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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104 #if $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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105 #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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106 #end if |
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107 #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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108 #end if |
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109 #set $jqueries += [$jquery] |
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110 #end for |
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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 #if len($jqueries) > 0: |
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112 #set $jtbldef['queries'] = $jqueries |
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113 #end if |
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114 #echo $json.dumps($jtbldef) |
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115 </configfile> |
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116 </configfiles> |
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117 <inputs> |
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118 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/> |
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119 <section name="add_to_database" expanded="false" title="Add tables to an existing database"> |
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120 <param name="withdb" type="data" format="sqlite" optional="true" label="Add tables to this Database" |
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121 help="Make sure your added table names are not already in this database"/> |
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122 </section> |
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123 <repeat name="tables" title="Database Table" min="0"> |
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124 <param name="table" type="data" format="tabular" label="Tabular Dataset for Table"/> |
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125 <section name="input_opts" expanded="false" title="Filter Dataset Input"> |
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126 <expand macro="macro_line_filters" /> |
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127 </section> |
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128 <section name="tbl_opts" expanded="false" title="Table Options"> |
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129 <param name="table_name" type="text" value="" optional="true" label="Specify Name for Table"> |
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130 <help>By default, tables will be named: t1,t2,...,tn (table names must be unique)</help> |
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131 <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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132 </param> |
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133 <param name="column_names_from_first_line" type="boolean" truevalue="True" falsevalue="False" checked="false" |
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134 label="Use first line as column names" |
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135 help="The names will be quoted if they are not valid SQLite column names."/> |
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136 <param name="col_names" type="text" value="" optional="true" label="Specify Column Names (comma-separated list)"> |
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137 <help>By default, table columns will be named: c1,c2,c3,...,cn (column names for a table must be unique) |
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138 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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139 </help> |
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140 <sanitizer sanitize="False"/> |
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141 <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+[^,`]*`|\[\S+[^,"]*\])?)*$</validator> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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142 </param> |
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143 <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load the columns you have named into database"/> |
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144 <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name" |
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145 help="Only creates this additional column when a name is entered. (This can not be the same name as any of the other columns in this table.)"> |
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146 <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator> |
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147 </param> |
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148 <repeat name="indexes" title="Table Index"> |
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149 <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/> |
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81ad914a0b08
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150 <param name="index_columns" type="text" value="" label="Index on Columns"> |
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151 <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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152 <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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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153 <sanitizer sanitize="False"/> |
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154 </param> |
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155 </repeat> |
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156 </section> |
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157 </repeat> |
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158 <section name="modify_database" expanded="false" title="Modify the database"> |
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159 <repeat name="sql_stmts" title="Database Manipulation SQL Statements" min="0"> |
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160 <param name="sqlstmt" type="text" area="true" size="20x80" value="" optional="true" label="SQL Query to modify the database"> |
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161 <help>These modify the SQLite database</help> |
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162 <sanitizer sanitize="False"/> |
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163 </param> |
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164 </repeat> |
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165 </section> |
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166 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history" |
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167 help="SQLite to tabular tool can run additional queries on this database"/> |
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168 <expand macro="sql_query_input"/> |
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169 <expand macro="result_results_header_line" /> |
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170 <section name="addqueries" expanded="false" title="Additional Queries"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
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171 <repeat name="queries" title="SQL Query" min="0" max="3"> |
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172 <expand macro="sql_query_input"/> |
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173 <expand macro="result_results_header_line" /> |
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174 </repeat> |
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175 </section> |
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176 </inputs> |
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177 <outputs> |
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178 <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}"> |
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179 <filter>save_db</filter> |
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180 </data> |
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181 <data format="tabular" name="output" label="query results on ${on_string}"> |
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182 <filter>not save_db or (sqlquery and len(sqlquery.strip()) > 0)</filter> |
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183 </data> |
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184 <data format="tabular" name="output1" label="query 1 results on ${on_string}" from_work_dir="results0.tsv"> |
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185 <filter>len(addqueries['queries']) > 0</filter> |
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186 </data> |
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187 <data format="tabular" name="output2" label="query 2 results on ${on_string}" from_work_dir="results1.tsv"> |
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188 <filter>len(addqueries['queries']) > 1</filter> |
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189 </data> |
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190 <data format="tabular" name="output3" label="query 3 results on ${on_string}" from_work_dir="results2.tsv"> |
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191 <filter>len(addqueries['queries']) > 2</filter> |
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192 </data> |
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0
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193 </outputs> |
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194 <tests> |
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195 <!-- Test 1 --> |
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196 <test expect_num_outputs="1"> |
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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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13
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
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231 <!-- Test 2 --> |
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232 <test expect_num_outputs="1"> |
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233 <repeat name="tables"> |
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234 <param name="table" ftype="tabular" value="customers.tsv"/> |
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235 <section name="input_opts"> |
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236 <repeat name="linefilters"> |
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81ad914a0b08
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237 <conditional name="filter"> |
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238 <param name="filter_type" value="comment"/> |
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239 <param name="comment_char" value="35"/> |
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240 </conditional> |
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241 </repeat> |
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242 </section> |
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243 <section name="tbl_opts"> |
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244 <param name="col_names" value=",FirstName,LastName,,DOB,"/> |
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245 </section> |
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246 </repeat> |
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247 <repeat name="tables"> |
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81ad914a0b08
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248 <param name="table" ftype="tabular" value="sales.tsv"/> |
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249 <section name="input_opts"> |
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250 <repeat name="linefilters"> |
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251 <conditional name="filter"> |
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252 <param name="filter_type" value="skip"/> |
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253 <param name="skip_lines" value="1"/> |
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254 </conditional> |
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255 </repeat> |
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256 </section> |
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257 </repeat> |
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258 <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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259 <output name="output" file="sales_results.tsv"/> |
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260 </test> |
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261 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
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262 <!-- Test 3 --> |
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263 <test expect_num_outputs="1"> |
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264 <repeat name="tables"> |
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265 <param name="table" ftype="tabular" value="customers.tsv"/> |
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266 <section name="input_opts"> |
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267 <repeat name="linefilters"> |
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268 <conditional name="filter"> |
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269 <param name="filter_type" value="skip"/> |
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270 <param name="skip_lines" value="1"/> |
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271 </conditional> |
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272 </repeat> |
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273 </section> |
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274 <section name="tbl_opts"> |
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275 <param name="col_names" value=",FirstName,LastName,,BirthDate,"/> |
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276 </section> |
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277 </repeat> |
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278 <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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279 <output name="output" file="regex_results.tsv"/> |
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280 </test> |
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281 |
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13
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
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282 <!-- Test 4 --> |
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283 <test expect_num_outputs="1"> |
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284 <repeat name="tables"> |
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285 <param name="table" ftype="tabular" value="IEDB.tsv"/> |
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286 <section name="input_opts"> |
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287 <repeat name="linefilters"> |
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288 <conditional name="filter"> |
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289 <param name="filter_type" value="comment"/> |
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290 <param name="comment_char" value="35"/> |
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291 </conditional> |
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292 </repeat> |
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293 </section> |
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294 <section name="tbl_opts"> |
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295 <param name="table_name" value="iedb"/> |
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296 <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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297 </section> |
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298 </repeat> |
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299 <repeat name="tables"> |
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300 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/> |
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301 <section name="input_opts"> |
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302 <repeat name="linefilters"> |
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303 <conditional name="filter"> |
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304 <param name="filter_type" value="skip"/> |
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305 <param name="skip_lines" value="1"/> |
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306 </conditional> |
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307 </repeat> |
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308 </section> |
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309 <section name="tbl_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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310 <param name="table_name" value="mhc_summary"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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311 <param name="col_names" value="pos,peptide,logscore,affinity,Bind_Level,Protein,Allele"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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312 </section> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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313 </repeat> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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314 <param name="sqlquery" value="select iedb.ID,iedb.peptide,iedb.start,iedb.end,iedb.percentile_rank,mhc_summary.logscore,mhc_summary.affinity,mhc_summary.Bind_Level from iedb left outer join mhc_summary on iedb.peptide = mhc_summary.peptide order by affinity,Bind_Level,percentile_rank"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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315 <output name="output" file="query_results.tsv"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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316 </test> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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317 |
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13
b972f6137887
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
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318 <!-- Test 5 --> |
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319 <test expect_num_outputs="1"> |
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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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320 <section name="add_to_database"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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321 <param name="withdb" ftype="sqlite" value="testdb.sqlite"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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322 </section> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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323 <repeat name="tables"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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324 <param name="table" ftype="tabular" value="pets.tsv"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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325 <section name="input_opts"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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326 <repeat name="linefilters"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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327 <conditional name="filter"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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328 <param name="filter_type" value="regex"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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329 <param name="regex_pattern" value="^\d+"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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330 <param name="regex_action" value="include_find"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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331 </conditional> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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332 </repeat> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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333 <repeat name="linefilters"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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334 <conditional name="filter"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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335 <param name="filter_type" value="comment"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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336 <param name="comment_char" value="35"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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337 </conditional> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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338 </repeat> |
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81ad914a0b08
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339 <repeat name="linefilters"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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340 <conditional name="filter"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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341 <param name="filter_type" value="append_line_num"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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342 </conditional> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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343 </repeat> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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344 <repeat name="linefilters"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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345 <conditional name="filter"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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346 <param name="filter_type" value="select_columns"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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347 <param name="columns" value="7,2,3,4,1"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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348 </conditional> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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349 </repeat> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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350 <repeat name="linefilters"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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351 <conditional name="filter"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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352 <param name="filter_type" value="replace"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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353 <param name="column" value="c4"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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354 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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355 <param name="regex_replace" value="19\3-\2-\1"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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356 </conditional> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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357 </repeat> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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358 </section> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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359 <section name="tbl_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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360 <param name="table_name" value="people"/> |
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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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361 <param name="col_names" value="id,first,last,dob,pets"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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362 </section> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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363 </repeat> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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364 <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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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365 <output name="output" file="add_to_db_results.tsv"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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366 </test> |
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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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367 |
|
13
b972f6137887
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
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368 <!-- Test 6 --> |
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369 <test expect_num_outputs="1"> |
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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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370 <repeat name="tables"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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371 <param name="table" ftype="tabular" value="pets.tsv"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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372 <section name="input_opts"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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373 <repeat name="linefilters"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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374 <conditional name="filter"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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375 <param name="filter_type" value="regex"/> |
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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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376 <param name="regex_pattern" value="^\d+"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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377 <param name="regex_action" value="include_find"/> |
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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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378 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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379 </repeat> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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380 <repeat name="linefilters"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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381 <conditional name="filter"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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382 <param name="filter_type" value="comment"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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383 <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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384 </conditional> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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385 </repeat> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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386 <repeat name="linefilters"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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387 <conditional name="filter"> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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388 <param name="filter_type" value="append_line_num"/> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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389 </conditional> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
390 </repeat> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
391 <repeat name="linefilters"> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
392 <conditional name="filter"> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
393 <param name="filter_type" value="select_columns"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
394 <param name="columns" value="7,2,3,4,1"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
395 </conditional> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
396 </repeat> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
397 <repeat name="linefilters"> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
398 <conditional name="filter"> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
399 <param name="filter_type" value="replace"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
400 <param name="column" value="c4"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
401 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
402 <param name="regex_replace" value="19\3-\2-\1"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
403 </conditional> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
404 </repeat> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
405 </section> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
406 <section name="tbl_opts"> |
|
81ad914a0b08
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_name" value="people"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
408 <param name="col_names" value="id,first,last,dob,pets"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
409 </section> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
410 </repeat> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
411 <repeat name="tables"> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
412 <param name="table" ftype="tabular" value="pets.tsv"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
413 <section name="input_opts"> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
414 <repeat name="linefilters"> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
415 <conditional name="filter"> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
416 <param name="filter_type" value="regex"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
417 <param name="regex_pattern" value="^\d+"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
418 <param name="regex_action" value="include_find"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
419 </conditional> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
420 </repeat> |
|
81ad914a0b08
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"> |
|
81ad914a0b08
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"> |
|
81ad914a0b08
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="append_line_num"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
424 </conditional> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
425 </repeat> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
426 <repeat name="linefilters"> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
427 <conditional name="filter"> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
428 <param name="filter_type" value="select_columns"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
429 <param name="columns" value="c7,c5,c6"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
430 </conditional> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
431 </repeat> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
432 <repeat name="linefilters"> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
433 <conditional name="filter"> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
434 <param name="filter_type" value="normalize"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
435 <param name="columns" value="c2,c3"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
436 <param name="separator" value=","/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
437 </conditional> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
438 </repeat> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
439 </section> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
440 <section name="tbl_opts"> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
441 <param name="table_name" value="pet"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
442 <param name="col_names" value="id,name,animal"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
443 </section> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
444 </repeat> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
445 <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'"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
446 <output name="output" file="pet_normalized_query_results.tsv"/> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
447 </test> |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
448 |
|
13
b972f6137887
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
iuc
parents:
12
diff
changeset
|
449 <!-- Test 7 --> |
|
15
09dcef57a945
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit dd35055c76d86fe98985b5825c1751efb8208242
iuc
parents:
14
diff
changeset
|
450 <test expect_num_outputs="1"> |
|
1
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
451 <repeat name="tables"> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
452 <param name="table" ftype="tabular" value="psm_report.tsv"/> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
453 <section name="input_opts"> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
454 <repeat name="linefilters"> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
455 <conditional name="filter"> |
|
53c9f76c0788
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="filter_type" value="select_columns"/> |
|
53c9f76c0788
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="columns" value="1,3,2,6,14,19"/> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
458 </conditional> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
459 </repeat> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
460 </section> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
461 <section name="tbl_opts"> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
462 <param name="table_name" value="PSMs"/> |
|
53c9f76c0788
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="column_names_from_first_line" value="True"/> |
|
53c9f76c0788
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="col_names" value="Scan"/> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
465 </section> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
466 </repeat> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
467 <param name="sqlquery" value="SELECT * from PSMs"/> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
468 <conditional name="query_result"> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
469 <param name="header" value="yes"/> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
470 <param name="header_prefix" value=""/> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
471 </conditional> |
|
8
5c3d86bc259c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 1647065a8e6e8d8c98cd0d2194b695fb9425f541"
iuc
parents:
6
diff
changeset
|
472 <output name="output" file="psm_report_out1.tsv" compare="re_match"/> |
|
1
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
473 </test> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
474 |
|
13
b972f6137887
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
iuc
parents:
12
diff
changeset
|
475 <!-- Test 8 column_names_from_first_line --> |
|
15
09dcef57a945
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit dd35055c76d86fe98985b5825c1751efb8208242
iuc
parents:
14
diff
changeset
|
476 <test expect_num_outputs="1"> |
|
1
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
477 <repeat name="tables"> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
478 <param name="table" ftype="tabular" value="psm_report.tsv"/> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
479 <section name="input_opts"> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
480 <repeat name="linefilters"> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
481 <conditional name="filter"> |
|
53c9f76c0788
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="filter_type" value="select_columns"/> |
|
53c9f76c0788
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="columns" value="1,3,2,6,14,19"/> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
484 </conditional> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
485 </repeat> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
486 </section> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
487 <section name="tbl_opts"> |
|
53c9f76c0788
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="table_name" value="PSMs"/> |
|
53c9f76c0788
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="column_names_from_first_line" value="True"/> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
490 <param name="col_names" value="Scan"/> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
491 </section> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
492 </repeat> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
493 <param name="sqlquery" value="SELECT Scan,"m/z", "Precursor m/z Error [ppm]", Sequence, "Protein(s)" FROM PSMs WHERE NOT re_search(', ',"Protein(s)")"/> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
494 <conditional name="query_result"> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
495 <param name="header" value="yes"/> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
496 <param name="header_prefix" value=""/> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
497 </conditional> |
|
8
5c3d86bc259c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 1647065a8e6e8d8c98cd0d2194b695fb9425f541"
iuc
parents:
6
diff
changeset
|
498 <output name="output" file="psm_report_out2.tsv" compare="re_match"/> |
|
1
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
499 </test> |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
500 |
|
13
b972f6137887
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
iuc
parents:
12
diff
changeset
|
501 <!-- Test 9 modify database --> |
|
15
09dcef57a945
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit dd35055c76d86fe98985b5825c1751efb8208242
iuc
parents:
14
diff
changeset
|
502 <test expect_num_outputs="2"> |
|
4
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
503 <repeat name="tables"> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
504 <param name="table" ftype="tabular" value="psm_report.tsv"/> |
|
7be49fd649f7
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="input_opts"> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
506 <repeat name="linefilters"> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
507 <conditional name="filter"> |
|
7be49fd649f7
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="filter_type" value="select_columns"/> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
509 <param name="columns" value="1,3,2,6,14,19,23"/> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
510 </conditional> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
511 </repeat> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
512 </section> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
513 <section name="tbl_opts"> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
514 <param name="table_name" value="PSMs"/> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
515 <param name="column_names_from_first_line" value="True"/> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
516 <param name="col_names" value="scan,,,,,,confidence"/> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
517 </section> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
518 </repeat> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
519 <section name="modify_database"> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
520 <repeat name="sql_stmts"> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
521 <param name="sqlstmt" value="UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0"/> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
522 </repeat> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
523 </section> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
524 <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)")"/> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
525 <conditional name="query_result"> |
|
7be49fd649f7
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" value="yes"/> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
527 <param name="header_prefix" value="#"/> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
528 </conditional> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
529 <section name="addqueries"> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
530 <repeat name="queries"> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
531 <param name="sqlquery" value="SELECT * FROM psms WHERE confidence > 97.0"/> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
532 <conditional name="query_result"> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
533 <param name="header" value="yes"/> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
534 <param name="header_prefix" value=""/> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
535 </conditional> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
536 </repeat> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
537 </section> |
|
8
5c3d86bc259c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 1647065a8e6e8d8c98cd0d2194b695fb9425f541"
iuc
parents:
6
diff
changeset
|
538 <output name="output" file="psm_dbmod_output.tsv" compare="re_match"/> |
|
5c3d86bc259c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 1647065a8e6e8d8c98cd0d2194b695fb9425f541"
iuc
parents:
6
diff
changeset
|
539 <output name="output1" file="psm_dbmod_output1.tsv" compare="re_match"/> |
|
4
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
540 </test> |
|
7be49fd649f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
iuc
parents:
1
diff
changeset
|
541 |
|
13
b972f6137887
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
iuc
parents:
12
diff
changeset
|
542 <!-- Test 10 column_names_from_first_line --> |
|
15
09dcef57a945
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit dd35055c76d86fe98985b5825c1751efb8208242
iuc
parents:
14
diff
changeset
|
543 <test expect_num_outputs="1"> |
|
10
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
544 <repeat name="tables"> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
545 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
546 <section name="input_opts"> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
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|
547 <repeat name="linefilters"> |
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f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
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changeset
|
548 <conditional name="filter"> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
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changeset
|
549 <param name="filter_type" value="regex"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
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changeset
|
550 <param name="regex_pattern" value="peptide"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
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diff
changeset
|
551 <param name="regex_action" value="include_find"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
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diff
changeset
|
552 </conditional> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
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changeset
|
553 </repeat> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
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changeset
|
554 </section> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
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changeset
|
555 <section name="tbl_opts"> |
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f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
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changeset
|
556 <param name="table_name" value="epitope"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
557 <param name="column_names_from_first_line" value="True"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
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|
558 </section> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
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diff
changeset
|
559 </repeat> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
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diff
changeset
|
560 <param name="sqlquery" value="SELECT * FROM epitope"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
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diff
changeset
|
561 <conditional name="query_result"> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
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diff
changeset
|
562 <param name="header" value="yes"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
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changeset
|
563 <param name="header_prefix" value=""/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
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diff
changeset
|
564 </conditional> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
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diff
changeset
|
565 <output name="output" file="netMHC_summary_out1.tsv" ftype="tabular"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
566 </test> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
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diff
changeset
|
567 |
|
13
b972f6137887
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
iuc
parents:
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diff
changeset
|
568 <!-- Test 11 --> |
|
15
09dcef57a945
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit dd35055c76d86fe98985b5825c1751efb8208242
iuc
parents:
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diff
changeset
|
569 <test expect_num_outputs="1"> |
|
10
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
570 <repeat name="tables"> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
571 <param name="table" ftype="tabular" value="netMHC_summary.tsv"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
572 <section name="input_opts"> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
573 <repeat name="linefilters"> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
574 <conditional name="filter"> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
575 <param name="filter_type" value="regex"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
576 <param name="regex_pattern" value="NOT TO BE FOUND"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
577 <param name="regex_action" value="include_find"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
578 </conditional> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
579 </repeat> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
580 </section> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
581 <section name="tbl_opts"> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
582 <param name="table_name" value="epitope"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
583 <param name="column_names_from_first_line" value="False"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
584 <param name="col_names" value="pos,peptide,logscore,,,,Allele"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
585 </section> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
586 </repeat> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
587 <param name="sqlquery" value="SELECT pos,peptide,logscore,Allele FROM epitope"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
588 <conditional name="query_result"> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
589 <param name="header" value="yes"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
590 <param name="header_prefix" value=""/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
591 </conditional> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
592 <output name="output" file="netMHC_summary_out2.tsv" ftype="tabular"/> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
593 </test> |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
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changeset
|
594 |
|
13
b972f6137887
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
iuc
parents:
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diff
changeset
|
595 <!-- Test 12 math functions --> |
|
15
09dcef57a945
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit dd35055c76d86fe98985b5825c1751efb8208242
iuc
parents:
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diff
changeset
|
596 <test expect_num_outputs="1"> |
|
12
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
597 <repeat name="tables"> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
598 <param name="table" ftype="tabular" value="math_input.tsv"/> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
599 </repeat> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
600 <param name="sqlquery" value="SELECT c1, c2, trunc(c2), floor(c2), ceil(c2), abs(c1), fabs(c2), mod(c1,2), fmod(c2, 1.5), sqrt(c1), sqrt(c2), degrees(c1), radians(c1), log(c1), log10(c1), pow(c1,2), exp(c2), exp(c1), cos(c1), sin(c1), tan(c1), cosh(c1), sinh(c1), tanh(c1), acos(c1), asin(c1),acosh(c1), asinh(c1) FROM t1"/> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
601 <output name="output"> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
602 <assert_contents> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
603 <has_text_matching expression="-2\t-2.222\t-2\t-3\t-2\t2\t2.222\t0\t-0.722\t\t\t-114.59155\d*\t-0.03490\d*\t\t\t4.0\t0.10839\d*\t0.13533\d*\t-0.41614\d*\t-0.90929\d*\t2.18503\d*\t3.76219\d*\t-3.62686\d*\t-0.96402\d*\t\t\t\t-1.44363\d*" /> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
604 <has_text_matching expression="-1\t-1.999\t-1\t-2\t-1\t1\t1.999\t1\t-0.49900\d*\t\t\t-57.29577\d*\t-0.01745\d*\t\t\t1.0\t0.13547\d*\t0.36787\d*\t0.54030\d*\t-0.84147\d*\t-1.55740\d*\t1.54308\d*\t-1.17520\d*\t-0.76159\d*\t3.14159\d*\t-1.57079\d*\t\t-0.88137\d*" /> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
605 <has_text_matching expression="0\t0.0\t0\t0\t0\t0\t0.0\t0\t0.0\t0.0\t0.0\t0.0\t0.0\t\t\t0.0\t1.0\t1.0\t1.0\t0.0\t0.0\t1.0\t0.0\t0.0\t1.57079\d*\t0.0\t\t0.0" /> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
606 <has_text_matching expression="1\t1.0\t1\t1\t1\t1\t1.0\t1\t1.0\t1.0\t1.0\t57.29577\d*\t0.01745\d*\t0.0\t0.0\t1.0\t2.71828\d*\t2.71828\d*\t0.54030\d*\t0.84147\d*\t1.55740\d*\t1.54308\d*\t1.17520\d*\t0.76159\d*\t0.0\t1.57079\d*\t0.0\t0.88137\d*" /> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
607 <has_text_matching expression="2\t2.22\t2\t2\t3\t2\t2.22\t0\t0.72000\d*\t1.41421\d*\t1.48996\d*\t114.59155\d*\t0.03490\d*\t0.69314\d*\t0.30102\d*\t4.0\t9.20733\d*\t7.38905\d*\t-0.41614\d*\t0.90929\d*\t-2.18503\d*\t3.76219\d*\t3.62686\d*\t0.96402\d*\t\t\t1.31695\d*\t1.44363\d*" /> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
608 <has_text_matching expression="3\t3.33333\d*\t3\t3\t4\t3\t3.33333\d*\t1\t0.33333\d*\t1.73205\d*\t1.82574\d*\t171.88733\d*\t0.05235\d*\t1.09861\d*\t0.47712\d*\t9.0\t28.03153\d*\t20.08553\d*\t-0.98999\d*\t0.14112\d*\t-0.14254\d*\t10.06766\d*\t10.01787\d*\t0.99505\d*\t\t\t1.76274\d*\t1.81844\d*" /> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
609 <has_text_matching expression="4\t4.00444\d*\t4\t4\t5\t4\t4.00444\d*\t0\t1.00443\d*\t2.0\t2.00110\d*\t229.18311\d*\t0.06981\d*\t1.38629\d*\t0.60205\d*\t16.0\t54.84110\d*\t54.59815\d*\t-0.65364\d*\t-0.75680\d*\t1.15782\d*\t27.30823\d*\t27.28991\d*\t0.99932\d*\t\t\t2.06343\d*\t2.09471\d*" /> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
610 <has_text_matching expression="5\t5.555\t5\t5\t6\t5\t5.555\t1\t1.05499\d*\t2.23606\d*\t2.35690\d*\t286.47889\d*\t0.08726\d*\t1.60943\d*\t0.69897\d*\t25.0\t258.52696\d*\t148.41315\d*\t0.28366\d*\t-0.95892\d*\t-3.38051\d*\t74.20994\d*\t74.20321\d*\t0.99990\d*\t\t\t2.29243\d*\t2.31243\d*" /> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
611 </assert_contents> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
612 </output> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
613 </test> |
|
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
614 |
|
0
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
615 </tests> |
|
12
504f24a8eb76
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"
iuc
parents:
11
diff
changeset
|
616 |
|
0
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
617 <help><![CDATA[ |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
618 ============= |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
619 Query Tabular |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
620 ============= |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
621 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
622 **Inputs** |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
623 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
624 Loads tabular datasets into a SQLite_ data base. |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
625 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
626 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. |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
627 |
|
10
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
628 **NOTE:** If there are no data rows in an input tabular dataset, query_tabular will fail unless: |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
629 |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
630 - There is a row header line in the dataset and **Use first line as column names** is selected |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
631 - **Specify Column Names** is used to provide column names |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
632 |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
633 in which case an empty table will be created with those columns |
|
f777a82b7a15
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 67db58361546009a77b2cbd140967fbc634d425b"
iuc
parents:
9
diff
changeset
|
634 |
|
0
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
635 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
636 @LINEFILTERS_HELP@ |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
637 |
|
1
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
638 **Table Options** |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
639 |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
640 Specify Name for Table: |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
641 |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
642 - By default tables will be named: t1, t2, t3, etc. |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
643 |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
644 - **Specify Name for Table** |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
645 You can provide your own name for a database table, the name should begin with a letter and only contain letters, digits, or underscores. |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
646 The name should not be a SQLite key word: https://sqlite.org/lang_keywords.html |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
647 |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
648 |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
649 There are several ways to name columns in a table: |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
650 |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
651 - By default table columns will be named: c1, c2, c3, etc. |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
652 |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
653 - 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. |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
654 Any missing column name will be assigned cn where *n* is the ordinal position of the column, |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
655 e.g. a blank header for the second column would be named: c2. |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
656 The column names will be quoted is they are not valid identifiers, |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
657 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. |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
658 The precedent for quoting is to enclose the identifier in double quotes, |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
659 else if it contains a double quote enclose in square brackets, |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
660 else if it contains a square bracket enclose in grave accents. |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
661 **NOTE:** that this is the first line after line filtering has been applied. |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
662 If a line filter *prepend a line number column* had been used, the name of the first column would be "1". |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
663 You could rename that column using **Specify Column Names** |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
664 |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
665 - **Specify Column Names** (comma-separated list) |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
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diff
changeset
|
666 This will override any previously assigned column names. |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
667 You can also choose to only load those columns for which you provided a name, |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
668 but that is better accomplished with the line filter: *select columns*. |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
669 |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
670 |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
671 **Table Index** |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
672 |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
673 Queries on larger tables can be much faster if indexes are specified. |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
674 In general, specifiy an index for table columns used in joins with other tables, |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
675 or on columns used in SQL query WHERE clauses or in GROUP BY clauses. |
|
53c9f76c0788
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents:
0
diff
changeset
|
676 |
|
0
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
677 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
678 **Outputs** |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
679 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
680 The results of a SQL query are output to the history as a tabular file. |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
681 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
682 The SQLite_ data base can also be saved and output as a dataset in the history. |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
683 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
684 *(The* **SQLite to tabular** *tool can run additional queries on this database.)* |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
685 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
686 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
687 @QUERY_HELP@ |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
688 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
689 @LINEFILTERS_HELP_EXAMPLE@ |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
690 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
691 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
692 Table name: pets |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
693 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
694 Table columns: Pets,FirstName,LastName,Birthdate,PetNames,PetType,line_num,entry_num,row_num |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
695 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
696 Query: SELECT * FROM pets |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
697 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
698 Result: |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
699 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
700 ====== ========== ======== ========== ========= ======== ========= ========== ======== |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
701 #Pets FirstName LastName BirthDate PetNames PetType line_num entry_num row_num |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
702 ====== ========== ======== ========== ========= ======== ========= ========== ======== |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
703 2 Paula Brown 1978-05-24 Rex dog 3 1 1 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
704 2 Paula Brown 1978-05-24 Fluff cat 3 1 2 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
705 1 Steven Jones 1974-04-04 Allie cat 4 2 3 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
706 0 Jane Doe 1978-05-24 5 3 4 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
707 1 James Smith 1980-10-20 Spot 6 4 5 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
708 ====== ========== ======== ========== ========= ======== ========= ========== ======== |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
709 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
710 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
711 **Normalizing by Line Filtering into 2 Tables** |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
712 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
713 *Relational database opertions work with single-valued column entries. |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
714 To apply relational operations to tabular files that contain fields with lists of values, |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
715 we need to "normalize" those fields, duplicating lines for each item in the list. |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
716 In this example we create 2 tables, one for single-valued fields and a second with list-valued fields normalized. |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
717 Becauce we add a line number first for each table, we can join the 2 tables on the line number column.* |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
718 https://en.wikipedia.org/wiki/First_normal_form |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
719 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
720 *People Table* |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
721 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
722 :: |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
723 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
724 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number) |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
725 Filter 2 - append a line number column: |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
726 Filter 3 - regex replace value in column[4]: '(\d+)/(\d+)/(\d+)' '19\3-\2-\1' (convert dates to sqlite format) |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
727 Filter 4 - select columns 7,2,3,4,1 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
728 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
729 Table: People |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
730 Columns: id,FirstName,LastName,DOB,Pets |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
731 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
732 == ========= ======== ========== ==== |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
733 id FirstName LastName DOB Pets |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
734 == ========= ======== ========== ==== |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
735 1 Paula Brown 1978-05-24 2 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
736 2 Steven Jones 1974-04-04 1 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
737 3 Jane Doe 1978-05-24 0 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
738 4 James Smith 1980-10-20 1 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
739 == ========= ======== ========== ==== |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
740 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
741 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
742 *Pet Table* |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
743 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
744 :: |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
745 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
746 Filter 1 - by regex expression matching [include]: '^\d+' (include lines that start with a number) |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
747 Filter 2 - append a line number column: |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
748 Filter 3 - by regex expression matching [exclude]: '^0\t' (exclude lines with no pets) |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
749 Filter 4 - normalize list columns[5,6]: |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
750 Filter 5 - select columns 7,5,6 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
751 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
752 Table: Pet |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
753 Columns: id,PetName,PetType |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
754 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
755 == ======== ======== |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
756 id PetName PetType |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
757 == ======== ======== |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
758 1 Rex dog |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
759 1 Fluff cat |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
760 2 Allie cat |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
761 4 Spot |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
762 == ======== ======== |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
763 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
764 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
765 Query: SELECT FirstName,LastName,PetName FROM People JOIN Pet ON People.id = Pet.id WHERE PetType = 'cat'; |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
766 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
767 Result: |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
768 |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
769 ========= ======== ======== |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
770 FirstName LastName PetName |
|
81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff
changeset
|
771 ========= ======== ======== |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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772 Paula Brown Fluff |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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773 Steven Jones Allie |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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774 ========= ======== ======== |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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775 |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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776 |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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777 ]]></help> |
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5b557716b4b3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 43d0f694b024cf9b1f0e26d803d3f19f38c95ee9
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778 <expand macro="citations" /> |
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81ad914a0b08
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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779 </tool> |