diff elastic_expose_to_list_collection.xml @ 2:391394c022b8 draft

planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty

--- a/elastic_expose_to_list_collection.xml	Mon Mar 26 18:40:39 2018 -0400
+++ b/elastic_expose_to_list_collection.xml	Sat Mar 31 21:32:17 2018 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="elastic_expose_to_list_collection" name="expose to a list" version="1.0.0">
+<tool id="elastic_expose_to_list_collection" name="expose data (list)" version="1.0.0">
   <macros>
     <import>elastic_tool_wrappers_macros.xml</import>
   </macros>
@@ -8,9 +8,57 @@
     <expand macro="rmarkdown_requirements"/>
   </requirements>
   <expand macro="stdio"/>
-  <expand macro="shell_command"/>
+  <command><![CDATA[
+
+        ############ first, create a directory to store all files
+        mkdir -p $report.files_path &&
+
+
+        ############ save the tool installation directory to an environment variable
+        export TOOL_INSTALL_DIR='${__tool_directory__}' &&
+
+
+        #########################
+        ##
+        ## save user input option/argument pairs into a file
+        ##
+        #########################
+
+        ## first line will be the header
+        echo 'tool_output_dir|relative_path' > '$report.files_path/options_and_arguments.txt' &&
+
+
+
+        ####################################################
+        ## loop through repeats to get option/argument pairs
+        ####################################################
+
+
+        ############ option_argument_path_relative_to_a_tool
+        #for i in $option_argument_path_relative_to_a_tool_repeat:
+             #set $item = str($i.a_tool_output_dir) + "|" + str($i.value)
+             echo '$item' >> '$report.files_path/options_and_arguments.txt' &&
+        #end for
+
+
+        ############ output_set
+        ## '$report'
+        ## '$report.files_path'
+        #######################
+        export REPORT='$report' &&
+        export TOOL_LOG='$tool_log' &&
+        export REPORT_FILES_PATH='$report.files_path' &&
+
+
+        ############ run render R script to render R markdowns
+        Rscript '${__tool_directory__}/list_render.R'
+
+        ]]></command>
   <inputs>
-    <expand macro="option_argument_path_relative_to_a_tool"/>
+    <repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT DATA PATH: relative to a tool output directory" min="0" default="0">
+      <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/>
+      <param type="text" name="value" optional="true" label="relative path"/>
+    </repeat>
   </inputs>
   <outputs>
     <data format="html" name="report" label="${tool.name} report"/>