Mercurial > repos > iuc > query_tabular

comparison query_tabular.xml @ 4:973f03d82c86 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
author iuc
date Thu, 03 May 2018 10:16:38 -0400
parents 8a33b442ecd9
children ad79e7bb1a9e
comparison
equal deleted inserted replaced
3:1ea4e668bf73 4:973f03d82c86
1 <tool id="query_tabular" name="Query Tabular" version="2.0.0"> 1 <tool id="query_tabular" name="Query Tabular" version="3.0.0">
2 <description>using sqlite sql</description> 2 <description>using sqlite sql</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
15 cp '$add_to_database.withdb' '$sqlitedb' && 15 cp '$add_to_database.withdb' '$sqlitedb' &&
16 #else: 16 #else:
17 cp '$add_to_database.withdb' '$workdb' && 17 cp '$add_to_database.withdb' '$workdb' &&
18 #end if 18 #end if
19 #end if 19 #end if
20 python '$__tool_directory__/query_tabular.py' 20 python '$__tool_directory__/query_tabular.py' -d
21 #if $save_db 21 #if $save_db
22 -s '$sqlitedb' 22 -s '$sqlitedb'
23 #else 23 #else
24 -s '$workdb' 24 -s '$workdb'
25 #end if 25 #end if
86 #if $input_filters: 86 #if $input_filters:
87 #set $jtbl['filters'] = $input_filters 87 #set $jtbl['filters'] = $input_filters
88 #end if 88 #end if
89 #set $jtbls += [$jtbl] 89 #set $jtbls += [$jtbl]
90 #end for 90 #end for
91 #set $jstmts = []
92 #for $i,$stmt in enumerate($modify_database.sql_stmts):
93 #set $jstmts += [str($stmt.sqlstmt)]
94 #end for
95 #if len($jstmts) > 0:
96 #set $jtbldef['sql_stmts'] = $jstmts
97 #end if
98 #set $jqueries = []
99 #for $i,$query in enumerate($addqueries.queries):
100 #set $jquery = dict()
101 #set $jquery['query'] = str($query.sqlquery)
102 #set $jquery['result_file'] = 'results' + str($i) + '.tsv'
103 #if $query.query_result.header == 'yes':
104 #set $header_prefix = ''
105 #if $query.query_result.header_prefix:
106 #set $header_prefix = chr(int(str($query.query_result.header_prefix)))
107 #end if
108 #set $jquery['header'] = $header_prefix
109 #end if
110 #set $jqueries += [$jquery]
111 #end for
112 #if len($jqueries) > 0:
113 #set $jtbldef['queries'] = $jqueries
114 #end if
91 #echo $json.dumps($jtbldef) 115 #echo $json.dumps($jtbldef)
92 </configfile> 116 </configfile>
93 </configfiles> 117 </configfiles>
94 <inputs> 118 <inputs>
95 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/> 119 <param name="workdb" type="hidden" value="workdb.sqlite" label=""/>
130 <sanitizer sanitize="False"/> 154 <sanitizer sanitize="False"/>
131 </param> 155 </param>
132 </repeat> 156 </repeat>
133 </section> 157 </section>
134 </repeat> 158 </repeat>
159 <section name="modify_database" expanded="false" title="Modify the database">
160 <repeat name="sql_stmts" title="Database Manipulation SQL Statements" min="0">
161 <param name="sqlstmt" type="text" area="true" size="20x80" value="" optional="true" label="SQL Query to modify the database">
162 <help>These modify the SQLite database</help>
163 <sanitizer sanitize="False"/>
164 </param>
165 </repeat>
166 </section>
135 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history" 167 <param name="save_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save the sqlite database in your history"
136 help="SQLite to tabular tool can run additional queries on this database"/> 168 help="SQLite to tabular tool can run additional queries on this database"/>
137 <param name="sqlquery" type="text" area="true" size="20x80" value="" optional="true" label="SQL Query to generate tabular output"> 169 <expand macro="sql_query_input"/>
138 <help>By default: tables are named: t1,t2,...,tn and columns in each table: c1,c2,...,cn</help>
139 <sanitizer sanitize="False"/>
140 <validator type="regex" message="">^(?ims)\s*select\s+.*\s+from\s+.*$</validator>
141 </param>
142 <expand macro="result_results_header_line" /> 170 <expand macro="result_results_header_line" />
171 <section name="addqueries" expanded="false" title="Additional Queries">
172 <repeat name="queries" title="Database Manipulation SQL Statements" min="0" max="3">
173 <expand macro="sql_query_input"/>
174 <expand macro="result_results_header_line" />
175 </repeat>
176 </section>
143 </inputs> 177 </inputs>
144 <outputs> 178 <outputs>
145 <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}"> 179 <data format="sqlite" name="sqlitedb" label="sqlite db of ${on_string}">
146 <filter>save_db</filter> 180 <filter>save_db</filter>
147 </data> 181 </data>
148 <data format="tabular" name="output" label="query results on ${on_string}"> 182 <data format="tabular" name="output" label="query results on ${on_string}">
149 <filter>not save_db or (sqlquery and len(sqlquery.strip()) > 0)</filter> 183 <filter>not save_db or (sqlquery and len(sqlquery.strip()) > 0)</filter>
150 </data> 184 </data>
185 <data format="tabular" name="output1" label="query 1 results on ${on_string}" from_work_dir="results0.tsv">
186 <filter>len(addqueries['queries']) > 0</filter>
187 </data>
188 <data format="tabular" name="output2" label="query 2 results on ${on_string}" from_work_dir="results1.tsv">
189 <filter>len(addqueries['queries']) > 1</filter>
190 </data>
191 <data format="tabular" name="output3" label="query 3 results on ${on_string}" from_work_dir="results2.tsv">
192 <filter>len(addqueries['queries']) > 2</filter>
193 </data>
151 </outputs> 194 </outputs>
152 <tests> 195 <tests>
153 <test> 196 <test>
154 <repeat name="tables"> 197 <repeat name="tables">
155 <param name="table" ftype="tabular" value="customers.tsv"/> 198 <param name="table" ftype="tabular" value="customers.tsv"/>
444 <conditional name="query_result"> 487 <conditional name="query_result">
445 <param name="header" value="yes"/> 488 <param name="header" value="yes"/>
446 <param name="header_prefix" value=""/> 489 <param name="header_prefix" value=""/>
447 </conditional> 490 </conditional>
448 <output name="output" file="psm_report_out2.tsv"/> 491 <output name="output" file="psm_report_out2.tsv"/>
492 </test>
493
494 <test>
495 <repeat name="tables">
496 <param name="table" ftype="tabular" value="psm_report.tsv"/>
497 <section name="input_opts">
498 <repeat name="linefilters">
499 <conditional name="filter">
500 <param name="filter_type" value="select_columns"/>
501 <param name="columns" value="1,3,2,6,14,19,23"/>
502 </conditional>
503 </repeat>
504 </section>
505 <section name="tbl_opts">
506 <param name="table_name" value="PSMs"/>
507 <param name="column_names_from_first_line" value="True"/>
508 <param name="col_names" value="scan,,,,,,confidence"/>
509 </section>
510 </repeat>
511 <section name="modify_database">
512 <repeat name="sql_stmts">
513 <param name="sqlstmt" value="UPDATE psms SET confidence = 99.999 WHERE confidence = 100.0"/>
514 </repeat>
515 </section>
516 <param name="sqlquery" value="SELECT scan,&quot;m/z&quot;, &quot;Precursor m/z Error [ppm]&quot;, Sequence, &quot;Protein(s)&quot;, confidence FROM PSMs WHERE NOT re_search(', ',&quot;Protein(s)&quot;)"/>
517 <conditional name="query_result">
518 <param name="header" value="yes"/>
519 <param name="header_prefix" value="#"/>
520 </conditional>
521 <section name="addqueries">
522 <repeat name="queries">
523 <param name="sqlquery" value="SELECT * FROM psms WHERE confidence > 97.0"/>
524 <conditional name="query_result">
525 <param name="header" value="yes"/>
526 <param name="header_prefix" value=""/>
527 </conditional>
528 </repeat>
529 </section>
530 <output name="output" file="psm_dbmod_output.tsv"/>
531 <output name="output1" file="psm_dbmod_output1.tsv"/>
449 </test> 532 </test>
450 533
451 </tests> 534 </tests>
452 <help><![CDATA[ 535 <help><![CDATA[
453 ============= 536 =============