Mercurial > repos > mingchen0919 > elastic_r_tidyverse
diff elastic_r_package_wrappers_macros.xml @ 9:06f38d3febdc draft default tip
planemo upload
| author | mingchen0919 |
|---|---|
| date | Wed, 28 Mar 2018 23:34:03 -0400 |
| parents | ea3271940757 |
| children |
line wrap: on
line diff
--- a/elastic_r_package_wrappers_macros.xml Tue Mar 27 23:42:53 2018 -0400 +++ b/elastic_r_package_wrappers_macros.xml Wed Mar 28 23:34:03 2018 -0400 @@ -14,43 +14,49 @@ </xml> <xml name="function_components"> - <repeat name="function_component_repeat" title="Call a function" min="1" default="1"> + <repeat name="function_components" title="Call a function" min="1" default="1"> <param type="select" name="function_name" multiple="false" label="==== Call function ===="> <option value="ggplot" selected="false">ggplot</option> + <option value="geom_point" selected="false">geom_point</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> <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="false">numeric</option> - <option value="boolean" selected="false">boolean</option> - <option value="variable" selected="false">variable</option> - </param> + <repeat name="function_arguments" title="argument name/value pairs" min="0" default="0"> + <conditional name="argument_type"> + <param name="argument_type_selector" type="select" label="Argument type"> + <option value="value" selected="false">user input value</option> + <option value="rdata" selected="false">value from RData output</option> + </param> + <when value="value"> + <param type="text" name="argument_name" label="argument name" /> + <param type="text" name="argument_value" label="argument value" /> + </when> + <when value="rdata"> + <param type="text" name="argument_name" label="argument name" /> + <param type="data" format="rdata" name="argument_value" optional="false" label="RData output" /> + </when> + </conditional> </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> + <param type="select" name="operator" label="connect to next function"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + <option value="%>%" selected="true">pipe (%>%)</option> + <option value="+" selected="false">plus (+)</option> + </param> </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="rdata" name="tool_rdata_output" label="${tool.name} RData output ${on_string}"/> <data format="txt" name="tool_log" label="${tool.name} log" /> </xml> @@ -70,18 +76,20 @@ ############ 3. save user inputs into arguments.txt ############ 3.1 table header - echo 'function|input_type|argument|argument_value|argument_value_type|operator' > $report.files_path/arguments.txt && + echo 'row_type|function_name|argument_name|argument_value|argument_value_type|operator' > $report.files_path/arguments.txt && ############ 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 && + #for fun_component in $function_components: + echo 'func|$fun_component.function_name||||' >> $report.files_path/arguments.txt && + + Rscript -e 'library(tidyverse); help($fun_component.function_name)' >> $report.files_path/$fun_component.function_name-help.txt && + + #for argument in $fun_component.function_arguments: + echo 'argument||$argument.argument_type.argument_name|$argument.argument_type.argument_value|$argument.argument_type.argument_type_selector|' >> $report.files_path/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' >> $report.files_path/arguments.txt && - #end for + echo 'operator|||||$fun_component.operator' >> $report.files_path/arguments.txt && + #end for ############ output_set ## '$report' @@ -91,12 +99,12 @@ ####################### export REPORT='$report' && export REPORT_FILES_PATH='$report.files_path' && - export TOOL_HELP_DOC='$tool_help_doc' && + export TOOL_RDATA_OUTPUT='$tool_rdata_output' && export TOOL_LOG='$tool_log' && ############ run render R script to render R markdowns - Rscript '${__tool_directory__}/elastic_tool_render.R' + Rscript '${__tool_directory__}/elastic_r_package_render.R' ]]></command> </xml>