comparison query_tabular.xml @ 15:cf4397560712 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit dd35055c76d86fe98985b5825c1751efb8208242

14:3a6b78c39dca

<tool id="query_tabular" name="Query Tabular" version="3.3.1">
    <description>using sqlite sql</description>

    <macros>
         <import>macros.xml</import>
    </macros>

#import json
#set $jtbldef = dict()
#set $jtbls = []
#set $jtbldef['tables'] = $jtbls
#for $i,$tbl in enumerate($tables):
  #set $jtbl = dict()
  #set $jtbl['file_path'] = str($tbl.table)
  #if $tbl.tbl_opts.table_name:
  #set $tname = str($tbl.tbl_opts.table_name)
  #else

                <param name="col_names" type="text" value="" optional="true" label="Specify Column Names (comma-separated list)">
                    <help>By default, table columns will be named: c1,c2,c3,...,cn  (column names for a table must be unique)
                          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.
                    </help>
                    <sanitizer sanitize="False"/>
                    <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+[^,"]*[]])?)*$</validator>
                </param>
                <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load the columns you have named into database"/>
                <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name"
                       help="Only creates this additional column when a name is entered. (This can not be the same name as any of the other columns in this table.)">
                        <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator>
                </param>
                <repeat name="indexes" title="Table Index">
                    <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/>
                    <param name="index_columns" type="text" value="" label="Index on Columns">
                        <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>
                        <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>
                        <sanitizer sanitize="False"/>
                    </param>
                </repeat>
            </section>
        </repeat>

            <filter>len(addqueries['queries']) > 2</filter>
        </data>
    </outputs>
    <tests>
        <!-- Test 1 -->
        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="customers.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            <param name="sqlquery" value="SELECT FirstName,LastName,sum(SaleAmount) as &quot;TotalSales&quot; FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC"/>
            <output name="output" file="sales_results.tsv"/>
        </test>

        <!-- Test 2 -->
        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="customers.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            <param name="sqlquery" value="SELECT FirstName,LastName,sum(t2.c3) as &quot;TotalSales&quot; FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;"/>
            <output name="output" file="sales_results.tsv"/>
        </test>

        <!-- Test 3 -->
        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="customers.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            <param name="sqlquery" value="select FirstName,LastName,re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as &quot;DOB&quot; from t1 WHERE re_search('[hp]er',c4)"/>
            <output name="output" file="regex_results.tsv"/>
        </test>

        <!-- Test 4 -->
        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="IEDB.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            <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"/>
            <output name="output" file="query_results.tsv"/>
        </test>

        <!-- Test 5 -->
        <test>
            <section name="add_to_database">
                <param name="withdb" ftype="sqlite" value="testdb.sqlite"/>
            </section>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="pets.tsv"/>

            <param name="sqlquery" value="SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name"/>
            <output name="output" file="add_to_db_results.tsv"/>
        </test>

        <!-- Test 6 -->
        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="pets.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            <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'"/>
            <output name="output" file="pet_normalized_query_results.tsv"/>
        </test>

        <!-- Test 7 -->
        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="psm_report.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            </conditional>
            <output name="output" file="psm_report_out1.tsv" compare="re_match"/>
        </test>

        <!-- Test 8 column_names_from_first_line -->
        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="psm_report.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            </conditional>
            <output name="output" file="psm_report_out2.tsv" compare="re_match"/>
        </test>

        <!-- Test 9  modify database -->
        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="psm_report.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            <output name="output" file="psm_dbmod_output.tsv" compare="re_match"/>
            <output name="output1" file="psm_dbmod_output1.tsv" compare="re_match"/>
        </test>

        <!-- Test 10 column_names_from_first_line -->
        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            </conditional>
            <output name="output" file="netMHC_summary_out1.tsv" ftype="tabular"/>
        </test>

        <!-- Test 11 -->
        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            </conditional>
            <output name="output" file="netMHC_summary_out2.tsv" ftype="tabular"/>
        </test>

        <!-- Test 12 math functions -->
        <test>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="math_input.tsv"/>
            </repeat>
            <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"/>
            <output name="output">

15:cf4397560712

<tool id="query_tabular" name="Query Tabular" version="3.3.2">
    <description>using sqlite sql</description>

    <macros>
         <import>macros.xml</import>
    </macros>

#import json
#set $jtbldef = dict()
#set $jtbls = []
#set $jtbldef['tables'] = $jtbls
#for $i,$tbl in enumerate($tables):
  #set $table = $tbl.table
  #set $jtbl = dict()
  #set $jtbl['file_path'] = str($tbl.table)
  #if $tbl.tbl_opts.table_name:
  #set $tname = str($tbl.tbl_opts.table_name)
  #else

                <param name="col_names" type="text" value="" optional="true" label="Specify Column Names (comma-separated list)">
                    <help>By default, table columns will be named: c1,c2,c3,...,cn  (column names for a table must be unique)
                          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.
                    </help>
                    <sanitizer sanitize="False"/>
                    <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+[^,`]*`|\[\S+[^,"]*\])?)*$</validator>
                </param>
                <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load the columns you have named into database"/>
                <param name="pkey_autoincr" type="text" value="" optional="true" label="Add an auto increment primary key column with this name"
                       help="Only creates this additional column when a name is entered. (This can not be the same name as any of the other columns in this table.)">
                        <validator type="regex" message="Column name">^([A-Za-z]\w*)?$</validator>
                </param>
                <repeat name="indexes" title="Table Index">
                    <param name="unique" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="This is a unique index"/>
                    <param name="index_columns" type="text" value="" label="Index on Columns">
                        <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>
                        <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>
                        <sanitizer sanitize="False"/>
                    </param>
                </repeat>
            </section>
        </repeat>

            <filter>len(addqueries['queries']) > 2</filter>
        </data>
    </outputs>
    <tests>
        <!-- Test 1 -->
        <test expect_num_outputs="1">
            <repeat name="tables">
                <param name="table" ftype="tabular" value="customers.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            <param name="sqlquery" value="SELECT FirstName,LastName,sum(SaleAmount) as &quot;TotalSales&quot; FROM customers join sales on customers.CustomerID = sales.CustomerID GROUP BY customers.CustomerID ORDER BY TotalSales DESC"/>
            <output name="output" file="sales_results.tsv"/>
        </test>

        <!-- Test 2 -->
        <test expect_num_outputs="1">
            <repeat name="tables">
                <param name="table" ftype="tabular" value="customers.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            <param name="sqlquery" value="SELECT FirstName,LastName,sum(t2.c3) as &quot;TotalSales&quot; FROM t1 join t2 on t1.c1 = t2.c1 GROUP BY t1.c1 ORDER BY TotalSales DESC;"/>
            <output name="output" file="sales_results.tsv"/>
        </test>

        <!-- Test 3 -->
        <test expect_num_outputs="1">
            <repeat name="tables">
                <param name="table" ftype="tabular" value="customers.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            <param name="sqlquery" value="select FirstName,LastName,re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as &quot;DOB&quot; from t1 WHERE re_search('[hp]er',c4)"/>
            <output name="output" file="regex_results.tsv"/>
        </test>

        <!-- Test 4 -->
        <test expect_num_outputs="1">
            <repeat name="tables">
                <param name="table" ftype="tabular" value="IEDB.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            <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"/>
            <output name="output" file="query_results.tsv"/>
        </test>

        <!-- Test 5 -->
        <test expect_num_outputs="1">
            <section name="add_to_database">
                <param name="withdb" ftype="sqlite" value="testdb.sqlite"/>
            </section>
            <repeat name="tables">
                <param name="table" ftype="tabular" value="pets.tsv"/>

            <param name="sqlquery" value="SELECT people.id,first,last,pets,quote FROM people JOIN contacts ON people.first = contacts.first_name"/>
            <output name="output" file="add_to_db_results.tsv"/>
        </test>

        <!-- Test 6 -->
        <test expect_num_outputs="1">
            <repeat name="tables">
                <param name="table" ftype="tabular" value="pets.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            <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'"/>
            <output name="output" file="pet_normalized_query_results.tsv"/>
        </test>

        <!-- Test 7 -->
        <test expect_num_outputs="1">
            <repeat name="tables">
                <param name="table" ftype="tabular" value="psm_report.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            </conditional>
            <output name="output" file="psm_report_out1.tsv" compare="re_match"/>
        </test>

        <!-- Test 8 column_names_from_first_line -->
        <test expect_num_outputs="1">
            <repeat name="tables">
                <param name="table" ftype="tabular" value="psm_report.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            </conditional>
            <output name="output" file="psm_report_out2.tsv" compare="re_match"/>
        </test>

        <!-- Test 9  modify database -->
        <test expect_num_outputs="2">
            <repeat name="tables">
                <param name="table" ftype="tabular" value="psm_report.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            <output name="output" file="psm_dbmod_output.tsv" compare="re_match"/>
            <output name="output1" file="psm_dbmod_output1.tsv" compare="re_match"/>
        </test>

        <!-- Test 10 column_names_from_first_line -->
        <test expect_num_outputs="1">
            <repeat name="tables">
                <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            </conditional>
            <output name="output" file="netMHC_summary_out1.tsv" ftype="tabular"/>
        </test>

        <!-- Test 11 -->
        <test expect_num_outputs="1">
            <repeat name="tables">
                <param name="table" ftype="tabular" value="netMHC_summary.tsv"/>
                <section name="input_opts">
                    <repeat name="linefilters">
                        <conditional name="filter">

            </conditional>
            <output name="output" file="netMHC_summary_out2.tsv" ftype="tabular"/>
        </test>

        <!-- Test 12 math functions -->
        <test expect_num_outputs="1">
            <repeat name="tables">
                <param name="table" ftype="tabular" value="math_input.tsv"/>
            </repeat>
            <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"/>
            <output name="output">