comparison query_tabular.xml @ 3:3e3b3c883bec draft

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty

2:f5df461a6b90

<tool id="query_tabular" name="Query Tabular" version="0.1.0">
    <description>using sqlite sql</description>

    <requirements>
    </requirements>
    <stdio>

        -s $sqlitedb
        #else
        -s $workdb
        #end if
        -j $table_json
        #*
        ##          #for $i,$tbl in enumerate($tables):
        ##            #if $tbl.table_name
        ##            #set $tname = $tbl.table_name
        ##            #else
        ##            #set $tname = 't' + str($i + 1) 
        ##            #end if
        ##            #if $tbl.col_names:
        ##            #set $col_names = ':' + str($tbl.col_names)
        ##            #else 
        ##            #set $col_names = ''
        ##            #end if
        ##            -t ${tbl.table}=${tname}${$col_names}
        ##          #end for
        *#
        #if $sqlquery:
          -Q "$query_file" 
          $no_header
          -o $output
        #end if

  #set $tname = 't' + str($i + 1) 
  #end if
  #set $jtbl['table_name'] = $tname
  #if $tbl.col_names:
  #set $col_names = str($tbl.col_names)
  #else 
  #set $col_names = ''
  #end if
  #set $jtbl['column_names'] = $col_names
  #if str($tbl.skip_lines) != '':

            <param name="table" type="data" format="tabular" label="Dataset"/>
            <param name="table_name" type="text" value="" optional="true" label="Table name">
                <help>By default, tables will be named: t1,t2,...,tn</help>
                <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator>
            </param>
            <!--
            <param name="sel_cols" label="Include columns" type="data_column" multiple="true" data_ref="table" />
            -->
            <param name="col_names" type="text" value="" optional="true" label="Column names">
                <help>By default, table columns will be named: c1,c2,c3,...,cn</help>
                <validator type="regex" message="A List of separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores">^([A-Za-z]\w*)?(,([A-Za-z]\w*)?)*$</validator>
            </param>
            <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines" help="Leave blank to use the datatype comment lines metadata" />
        </repeat>
        <param name="sqlquery" type="text" area="true" size="10x80" value="" optional="true" label="SQL Query">
                <help>By default, tables will be named: t1,t2,...,tn</help>
                <sanitizer sanitize="False"/>

3:3e3b3c883bec

<tool id="query_tabular" name="Query Tabular" version="0.1.1">
    <description>using sqlite sql</description>

    <requirements>
    </requirements>
    <stdio>

        -s $sqlitedb
        #else
        -s $workdb
        #end if
        -j $table_json
        #if $sqlquery:
          -Q "$query_file" 
          $no_header
          -o $output
        #end if

  #set $tname = 't' + str($i + 1) 
  #end if
  #set $jtbl['table_name'] = $tname
  #if $tbl.col_names:
  #set $col_names = str($tbl.col_names)
    #if $tbl.load_named_columns:
      #set $jtbl['load_named_columns'] = True
    #end if
  #else 
  #set $col_names = ''
  #end if
  #set $jtbl['column_names'] = $col_names
  #if str($tbl.skip_lines) != '':

            <param name="table" type="data" format="tabular" label="Dataset"/>
            <param name="table_name" type="text" value="" optional="true" label="Table name">
                <help>By default, tables will be named: t1,t2,...,tn</help>
                <validator type="regex" message="Table name should start with a letter and may contain additional letters, digits, and underscores">^[A-Za-z]\w*$</validator>
            </param>
            <param name="col_names" type="text" value="" optional="true" label="Column names">
                <help>By default, table columns will be named: c1,c2,c3,...,cn</help>
                <sanitizer sanitize="False"/>
                <validator type="regex" message="A List of names separated by commas: Column names should start with a letter and may contain additional letters, digits, and underscores. Otherwise, the name must be eclosed in: double quotes, back quotes, or square brackets.">^([A-Za-z]\w*|"\S+[^,"]*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?(,([A-Za-z]\w*|"\S+.*"|`\S+[^,`]*`|[[]\S+[^,"]*[]])?)*$</validator>
            </param>
            <param name="load_named_columns" type="boolean" truevalue="load_named_columns" falsevalue="" checked="false" label="Only load named columns into database"/>
            <param name="skip_lines" type="integer" value="" min="0" optional="true" label="Skip lines" help="Leave blank to use the datatype comment lines metadata" />
        </repeat>
        <param name="sqlquery" type="text" area="true" size="10x80" value="" optional="true" label="SQL Query">
                <help>By default, tables will be named: t1,t2,...,tn</help>
                <sanitizer sanitize="False"/>