diff elastic_tool_wrappers_macros.xml @ 1:16e0f4b7a286 draft

planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d

--- a/elastic_tool_wrappers_macros.xml	Mon Mar 26 13:25:53 2018 -0400
+++ b/elastic_tool_wrappers_macros.xml	Mon Mar 26 18:40:39 2018 -0400
@@ -9,80 +9,23 @@
       <regex match="XXX" source="stderr" level="warning" description="Check the tool log output file for more details."/>
     </stdio>
   </xml>
-  <!--Tool name-->
-  <xml name="tool_name">
-    <param type="select" name="tool_name" multiple="false" label="Tool name">
-        <option value="cp" selected="false">cp</option></param>
-  </xml>
   <!--OPTION/ARGUMENT PAIRS and INPUT types-->
-  <!--input files-->
-  <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>
+
   <!--input path-->
   <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>
+      <param type="text" name="value" optional="true" label="relative path"/>
     </repeat>
   </xml>
-  <!--input values: string, float and integer-->
-  <xml name="option_argument_string_float_integer">
-    <repeat name="option_argument_string_float_integer_repeat" title="INPUT VALUE: string/float/integer" min="0" default="0">
-      <param type="text" name="flag" label="flag"/>
-      <param type="text" name="value" label="value"/>
-    </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"/>
-    <data name="asis">
-      <discover_datasets pattern="__name_and_ext__" directory="${report.files_path}/asis_dir"/>
-    </data>
-    <collection type="list" name="expose_to_list">
-      <discover_datasets pattern="__name_and_ext__" directory="${report.files_path}/list_dir" />
-    </collection>
-    <collection type="paired" name="expose_to_pair">
-      <discover_datasets pattern="__name_and_ext__" directory="${report.files_path}/pair_dir" />
-    </collection>
-    <collection type="list:paired" name="expose_to_list_pairs">
-      <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?"
-                         directory="${report.files_path}/list_pairs_dir"/>
-    </collection>
-  </xml>
+
   <!--shell command fragment-->
   <xml name="shell_command">
     <command><![CDATA[
+        echo $tool_name &&
 
         ############ first, create a directory to store all files
-        mkdir -p $report.files_path && cd $report.files_path &&
+        mkdir -p $report.files_path &&
 
 
         ############ save the tool installation directory to an environment variable
@@ -96,59 +39,29 @@
         #########################
 
         ## first line will be the header
-        echo 'type|flag|value|path_type' > options_and_arguments.txt &&
+        echo 'tool_output_dir|relative_path' > '$report.files_path/options_and_arguments.txt' &&
 
-        ############ tool_name
-        ##-t '$tool_name'
-        echo "tool_name|not available|${tool_name}|not available" >> options_and_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' >> 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' >> options_and_arguments.txt &&
-        #end for
-
 
         ############ 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' >> options_and_arguments.txt &&
+             #set $item = str($i.a_tool_output_dir) + "|" + str($i.value)
+             echo '$item' >> '$report.files_path/options_and_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' >> 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' >> options_and_arguments.txt &&
-        #end for
 
         ############ output_set
         ## '$report'
         ## '$report.files_path'
-        ## '$tool_help_doc'
-        ## '$tool_output_dir'
-        ## '$tool_log'
         #######################
         export REPORT='$report' &&
+        export TOOL_LOG='$tool_log' &&
         export REPORT_FILES_PATH='$report.files_path' &&
-        export TOOL_HELP_DOC='$tool_help_doc' &&
-        export TOOL_OUTPUT_DIR='$tool_output_dir' &&
-        export TOOL_LOG='$tool_log' &&
 
 
         ############ run render R script to render R markdowns
@@ -156,6 +69,22 @@
 
         ]]></command>
   </xml>
+
+  <!--<xml name="output_set">-->
+    <!--<data format="html" name="report" label="${tool.name} report"/>-->
+    <!--<data format="txt" name="tool_log" label="${tool.name} log"/>-->
+    <!--<collection type="list" name="list_collection">-->
+      <!--<discover_datasets pattern="__name_and_ext__" directory="list" />-->
+    <!--</collection>-->
+    <!--<collection type="paired" name="list_collection">-->
+      <!--<discover_datasets pattern="__name_and_ext__" directory="paired_dir" />-->
+    <!--</collection>-->
+    <!--<collection type="list:paired" name="list_collection">-->
+      <!--<discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?"-->
+                         <!--directory="list_paired"/>-->
+    <!--</collection>-->
+  <!--</xml>-->
+
   <!--tool citations-->
   <xml name="citations">
     <citation type="bibtex"><![CDATA[