diff elastic_tool_wrappers_macros.xml @ 0:b503fbd571a6 draft default tip

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/elastic_tool_wrappers_macros.xml	Tue Mar 27 10:05:29 2018 -0400
@@ -0,0 +1,169 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<macros>
+  <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="2.3.4.1">bowtie2</requirement>
+  </xml>
+  <xml name="stdio">
+    <stdio>
+      <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="bowtie2" selected="false">bowtie2</option><option value="bowtie2-build" selected="false">bowtie2-build</option><option value="bowtie2-inspect" selected="false">bowtie2-inspect</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>
+    </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"/>
+  </xml>
+  <!--shell command fragment-->
+  <xml name="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 'type|flag|value|path_type' > $report.files_path/options_and_arguments.txt &&
+
+        ############ tool_name
+        ##-t '$tool_name'
+        echo "tool_name|not available|${tool_name}|not available" >> $report.files_path/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' >> $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
+
+
+        ############ 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
+
+        ############ 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' >> $report.files_path/options_and_arguments.txt &&
+        #end for
+
+        ############ output_set
+        ## '$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='$tool_log' &&
+
+
+        ############ run render R script to render R markdowns
+        Rscript '${__tool_directory__}/elastic_tool_render.R'
+
+        ]]></command>
+  </xml>
+  <!--tool citations-->
+  <xml name="citations">
+    <citation type="bibtex"><![CDATA[
+            @article{allaire2016rmarkdown,
+            title={rmarkdown: Dynamic Documents for R, 2016},
+            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
+            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+            journal={R package version 0.9},
+            volume={6},
+            year={2016}
+            }
+        ]]></citation>
+    <citation type="bibtex"><![CDATA[
+            @book{xie2015elastic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        ]]></citation>
+  </xml>
+</macros>