# HG changeset patch
# User mingchen0919
# Date 1522208573 14400
# Node ID ea3271940757c9103dbbad24602d6d92591dfde5
# Parent  01eaa66fcc2ebf1a26fa0e30c5eb8002179c636a
planemo upload

diff -r 01eaa66fcc2e -r ea3271940757 elastic_r_package_wrappers_macros.xml
--- a/elastic_r_package_wrappers_macros.xml	Tue Mar 27 14:15:12 2018 -0400
+++ b/elastic_r_package_wrappers_macros.xml	Tue Mar 27 23:42:53 2018 -0400
@@ -3,7 +3,7 @@
     <xml name="rmarkdown_requirements">
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
         <requirement type="package" version="1.6">r-rmarkdown</requirement>
-        <requirement type="package" version="1.2.1">r-tidyverse</requirement>
+        <requirement type="package" version="1.1.1">r-tidyverse</requirement>
     </xml>
 
     <xml name="stdio">
@@ -15,109 +15,42 @@
 
     <xml name="function_components">
         <repeat name="function_component_repeat" title="Call a function" min="1" default="1">
-            <expand macro="function_name" />
+            <param type="select" name="function_name" multiple="false" label="==== Call function ====">
+                <option value="ggplot" selected="false">ggplot</option>
+                <option value="aes" selected="false">ggplot</option>
+                <option value="read.table" selected="false">read.table</option>
+                <option value="write.csv" selected="false">write.csv</option>
+            </param>
             <expand macro="function_arguments" />
+            <param type="select" name="operator" label="connect to next function">
+                <option value="%>%" selected="false">pipe (%>%)</option>
+                <option value="+" selected="false">plus (+)</option>
+            </param>
         </repeat>
     </xml>
 
-    <!--Tool name-->
-    <xml name="function_name">
-        <param type="select" name="function_name" multiple="false" label="==== Call function ====">
-            <option value="ggplot" selected="false">ggplot</option>
-            <option value="aes" selected="false">ggplot</option>
-            <option value="read.table" selected="false">read.table</option>
-            <option value="write.csv" selected="false">write.csv</option>
-        </param>
-    </xml>
-
-    <!--input values: string, float and integer-->
     <xml name="function_arguments">
-        <repeat name="regular_argument_value" title="--------Argument value: from user input" min="0" default="0">
-            <param type="text" name="argument" label="argument"  />
-            <param type="text" name="argument_value"  label="argument value"  />
-            <param type="select" name="argument_type"  label="argument type">
-                <option value="string" selected="true">string</option>
-                <option value="numeric" selected="true">numeric</option>
-                <option value="boolean" selected="true">boolean</option>
-            </param>
-        </repeat>
-        <repeat name="rdata_argument_value" title="--------Argument value: from RData" min="0" default="0">
-            <param type="text" name="argument" label="argument"  />
-            <param type="data" format="rdata" name="argument_value" optional="false" label="RData output"  />
-        </repeat>
-        <repeat name="function_argument_value" title="--------Argument value: from function return" min="0" default="0">
-            <param type="text" name="argument" optional="false" label="argument"  />
-            <expand macro="function_name" />
-            <expand macro="nested_function_arguments" />
-        </repeat>
-        <param type="select" name="connect_to_next_function" label="connect to next function">
-            <option value="%>%" selected="false">pipe (%>%)</option>
-            <option value="+" selected="false">plus (+)</option>
-        </param>
-    </xml>
-
-    <xml name="nested_function_arguments">
-        <repeat name="regular_argument_value" title="--------Argument value: from user input" min="0" default="0">
+        <repeat name="regular_argument_value" title="Argument value: from user input" min="0" default="0">
             <param type="text" name="argument" label="argument"  />
             <param type="text" name="argument_value"  label="argument value"  />
             <param type="select" name="argument_type"  label="argument type">
                 <option value="string" selected="true">string</option>
-                <option value="numeric" selected="true">numeric</option>
-                <option value="boolean" selected="true">boolean</option>
+                <option value="numeric" selected="false">numeric</option>
+                <option value="boolean" selected="false">boolean</option>
+                <option value="variable" selected="false">variable</option>
             </param>
         </repeat>
-        <repeat name="rdata_argument_value" title="--------Argument value: from RData" min="0" default="0">
+        <repeat name="rdata_argument_value" title="Argument value: from RData" min="0" default="0">
             <param type="text" name="argument" label="argument"  />
-            <param type="text" name="argument_value"  label="RData output"  />
+            <param type="data" format="rdata" name="argument_value" optional="false" label="RData output"  />
         </repeat>
     </xml>
 
-    <!--&lt;!&ndash;OPTION/ARGUMENT PAIRS and INPUT types&ndash;&gt;-->
-    <!--&lt;!&ndash;input files&ndash;&gt;-->
-    <!--<xml name="option_argument_single_dataset">-->
-        <!--<repeat name="option_argument_single_dataset_repeat" title="INPUT DATA FROM HISTORY: single data set" min="0" default="0">-->
-            <!--<param type="text" name="flag" optional="true" label="flag" />-->
-            <!--<param name="value" type="data" optional="false" multiple="false" label="value"/>-->
-        <!--</repeat>-->
-    <!--</xml>-->
-
-    <!--<xml name="option_argument_multiple_datasets">-->
-        <!--<repeat name="option_argument_multiple_datasets_repeat" title="INPUT DATA FROM HISTORY: multiple data sets" min="0" default="0">-->
-            <!--<param type="text" name="flag" optional="true" label="flag" />-->
-            <!--<param name="value" type="data" optional="false" multiple="true" label="value"/>-->
-            <!--<param type="select" name="delimiter" multiple="false" label="file delimiter">-->
-                <!--<option value=" " selected="false">space</option>-->
-                <!--<option value="," selected="false">comma</option>-->
-            <!--</param>-->
-        <!--</repeat>-->
-    <!--</xml>-->
-
-    <!--&lt;!&ndash;input path&ndash;&gt;-->
-    <!--<xml name="option_argument_path_relative_to_a_tool">-->
-        <!--<repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT DATA PATH: relative to a tool output directory" min="0" default="0">-->
-            <!--<param type="text" name="flag" optional="true" label="flag"  />-->
-            <!--<param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/>-->
-            <!--<param type="text" name="value" optional="true" label="value"  />-->
-        <!--</repeat>-->
-    <!--</xml>-->
-    <!--<xml name="option_argument_path_relative_to_this_tool">-->
-        <!--<repeat name="option_argument_path_relative_to_this_tool_repeat" title="OUTPUT PATH: relative to this tool output directory" min="0" default="0">-->
-            <!--<param type="text" name="flag" optional="true" label="flag"  />-->
-            <!--<param type="text" name="value" optional="false" label="value"  />-->
-            <!--<param type="select" name="path_type" multiple="false" label="path type">-->
-                <!--<option value="file_path" selected="false">file path</option>-->
-                <!--<option value="dir_path" selected="false">directory path</option>-->
-            <!--</param>-->
-        <!--</repeat>-->
-    <!--</xml>-->
-
-
 
     <!--output set-->
     <xml name="output_set">
         <data format="html" name="report" label="${tool.name} report"/>
         <data format="txt" name="tool_help_doc" label="${tool.name} help doc"/>
-        <data format="txt" name="tool_output_dir" label="${tool.name} output directory"/>
         <data format="txt" name="tool_log" label="${tool.name} log" />
     </xml>
 
@@ -126,73 +59,39 @@
     <xml name="shell_command">
         <command><![CDATA[
 
-        ############ first, create a directory to store all files
+        ############ 1. create a directory to store all files
         mkdir -p $report.files_path &&
 
 
-        ############ save the tool installation directory to an environment variable
+        ############ 2. save the tool installation directory to an environment variable
         export TOOL_INSTALL_DIR='${__tool_directory__}' &&
 
 
-        #########################
-        ##
-        ## save user input option/argument pairs into a file
-        ##
-        #########################
-
-        ## first line will be the header
-        echo 'type|flag|value|path_type' > $report.files_path/options_and_arguments.txt &&
-
-        ############ function_name
-        ##-t '$function_name'
-        echo "function_name|not available|${function_name}|not available" >> $report.files_path/options_and_arguments.txt &&
+        ############ 3. save user inputs into arguments.txt
 
-        ####################################################
-        ## loop through repeats to get option/argument pairs
-        ####################################################
-
-        ############ option_argument_single_dataset
-        #for i in $option_argument_single_dataset_repeat:
-            #set $item = 'single_dataset|' + str($i.flag) + "|" + str($i.value) + "|"
-            echo '$item' >> $report.files_path/options_and_arguments.txt &&
-        #end for
-
-        ############ option_argument_multiple_datasets
-        #for i in $option_argument_multiple_datasets_repeat:
-            #set $item = 'multiple_datasets|' + str($i.flag) + "|" + str($i.value).replace(',', str($i.delimiter)) + "|"
-            echo '$item' >> $report.files_path/options_and_arguments.txt &&
-        #end for
+        ############    3.1 table header
+        echo 'function|input_type|argument|argument_value|argument_value_type|operator' > $report.files_path/arguments.txt &&
 
 
-        ############ option_argument_path_relative_to_a_tool
-        #for i in $option_argument_path_relative_to_a_tool_repeat:
-             #set $item = 'path_relative_to_a_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.a_tool_output_dir)
-             echo '$item' >> $report.files_path/options_and_arguments.txt &&
-        #end for
+        ############    3.2 loop through function component repeat
+        #for $fun_component in $function_components:
+            #for reg_arg in $fun_component.regular_argument_value
+                echo '$fun_component.function_name|regular|$reg_arg.argument|$arg_arg.argument_value|$arg_arg.argument_value_type|$fun_component.operator' >> $report.files_path/arguments.txt &&
+            #end for
 
-        ############ option_argument_path_relative_to_this_tool
-        #for i in $option_argument_path_relative_to_this_tool_repeat:
-             #set $item = 'path_relative_to_this_tool|' + str($i.flag) + "|" + str($i.value) + "|" + str($i.path_type)
-             echo '$item' >> $report.files_path/options_and_arguments.txt &&
-        #end for
-
-        ############ option_argument_string_float_integer
-        #for i in $option_argument_string_float_integer_repeat:
-             #set $item = 'value|' + str($i.flag) + "|" + str($i.value) + "|"
-             echo '$item' >> $report.files_path/options_and_arguments.txt &&
-        #end for
+            #for rdata_arg in $fun_component.rdata_argument_value
+                echo '$fun_component.function_name|rdata|$rdata_arg.argument|$arg_arg.argument_value|rdata|$fun_component.operator' >> $report.files_path/arguments.txt &&
+            #end for
 
         ############ output_set
         ## '$report'
         ## '$report.files_path'
         ## '$tool_help_doc'
-        ## '$tool_output_dir'
         ## '$tool_log'
         #######################
         export REPORT='$report' &&
         export REPORT_FILES_PATH='$report.files_path' &&
         export TOOL_HELP_DOC='$tool_help_doc' &&
-        export TOOL_OUTPUT_DIR='$tool_output_dir' &&
         export TOOL_LOG='$tool_log' &&