Mercurial > repos > mingchen0919 > elastic_fastq_dump

changeset 1:1aeef205e648 draft

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planemo upload
author mingchen0919
date Sun, 01 Apr 2018 16:48:53 -0400
parents 28ce9fcb06c7
children 3e6452f224b2
files LICENSE README.md elastic_tool.Rmd elastic_tool.xml elastic_tool_macros.xml elastic_tool_wrappers_macros.xml
diffstat 6 files changed, 305 insertions(+), 229 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Sun Apr 01 16:48:53 2018 -0400
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Staton Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Sun Apr 01 16:48:53 2018 -0400
@@ -0,0 +1,63 @@
+# Elastic Galaxy Tools
+
+* [What are Elastic Galaxy Tools](#what-are-elastic-galaxy-tools?)
+* [How to use Elastic Galaxy Tools](#how-to-use-elastic-galaxy-tools?)
+* [How to develop an Elastic Galaxy Tool](#how-to-develop-an-elastic-galaxy-tool?)
+    + [Publish a Galaxy Tool](#publish-a-galaxy-tool)
+
+
+
+
+## What are Elastic Galaxy Tools?
+
+**Elastic Galaxy tools** is a type of Galaxy tools that have elastic user interfaces. Users can adjust the
+number of input fields a tool can have, just like using a command line tool. When using a command line tool,
+users can choose which (non-required) options to use. I hope Galaxy users can do the same thing, but without
+actually writing any command line scripts.
+ 
+
+## How to use Elastic Galaxy Tools?
+
+Although any (Elastic) Galaxy tool is a wrapper of a command line tool which enables performing data analysis
+through web interfaces without actually writing any command line script, understanding how to read command line
+manuals will help you use Elastic Galaxy tools. 
+
+Running a command line tool is very simple. You start with the tool name, then you specify options (also called flags) 
+that the tool can recognize. The tool manual should tell you which options the tool can recognize. An option may or may 
+not have a value followed. Some options are required and some are optional. You have to use all required options to 
+successfully run a command line tool. However, you can use as many optional options as you want in a call of a command 
+line tool.
+
+## How to develop an Elastic Galaxy Tool?
+
+### Publish a Galaxy tool
+
+We can use the tool **planemo** to easily publish our Galaxy tools to Tool Shed or test Tool Shed. 
+More details can be found **[here](http://planemo.readthedocs.io/en/latest/publishing.html)**.
+
+* Publish to test Tool Shed
+
+```bash
+planemo shed_create --shed_target testtoolshed
+``` 
+
+* Update tool repository in test Tool Shed
+
+```bash
+planemo shed_update --check_diff --shed_target testtoolshed
+```
+
+* Publish to Tool Shed
+
+```bash
+planemo shed_create --shed_target toolshed
+```
+
+* Update tool repository in Tool Shed
+
+```bash
+planemo shed_update --check_diff --shed_target toolshed
+```
+
+
+
--- a/elastic_tool.Rmd	Mon Mar 26 00:09:35 2018 -0400
+++ b/elastic_tool.Rmd	Sun Apr 01 16:48:53 2018 -0400
@@ -1,5 +1,5 @@
 ---
-title: 'Dynamic tool'
+title: 'Tool Report'
 output: html_document
 ---
 
@@ -18,14 +18,13 @@
 
 ## User input
 
-```{r, echo=FALSE}
-##-------- build script files -----------
-
-# build script file: script.sh
+```{r, 'display user input'}
+# get user input and save it into a data frame.
 df = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), 
                 sep = '|', header = TRUE)
 
-# prepend A_TOOL_OUTPUT_PATH
+# if the input type is 'path_relative_to_a_tool', prepend A_TOOL_OUTPUT_PATH to the value to make
+# the value a full path.
 if (nrow(df[df$type == 'path_relative_to_a_tool', ]) > 0) {
   for (i in 1:nrow(df[df$type == 'path_relative_to_a_tool', ])) {
     root_path = readLines(df[df$type == 'path_relative_to_a_tool', ][i, 'path_type'])[1]
@@ -35,13 +34,16 @@
   }
 }
 
-# get tool name
+## display user input as a table
+knitr::kable(df)
+```
+
+
+```{r, 'build script', echo=FALSE}
+##-------- build script files -----------
+
+# get tool name, the first line of the script is always the tool name.
 tool_name = df[df$type == 'tool_name', 'value']
-# build script for displaying help messages (this probably should be tool specific)
-write(paste0(tool_name, ' -h'), 
-        file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/help.sh'))
-
-knitr::kable(df)
 
 # if the number of option/argument pairs is larger than 0, build script file
 df2 = df[df$type != 'tool_name', ]
@@ -51,7 +53,7 @@
   write(paste0(tool_name, ' \\'), 
         paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
   df2 = df[df$type != 'tool_name', ]
-  write(paste(' ', df2$flag, df2$value, '\\', sep = ' '), 
+  write(paste(' ', df2$option, df2$value, '\\', sep = ' '),
         file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'), 
         append = TRUE )
   # remember that after writing option/argument lines to the script.sh, the last line
@@ -66,17 +68,13 @@
   write(paste0(tool_name, ' -h'), 
         file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
 }
-
 ```
 
 
-```{bash, echo=FALSE}
-## code to open help documentation
-sh ${REPORT_FILES_PATH}/help.sh > ${TOOL_HELP_DOC}
-```
+```{r, 'create paths if they do not exist', echo=FALSE}
+## if the input type is 'path_relative_to_this_tool', that means 
+## we need to create a directory or file path.
 
-
-```{r, echo=FALSE}
 # create paths before running the job script
 df_paths = df[df$type == 'path_relative_to_this_tool', ]
 
@@ -103,15 +101,14 @@
 ```
 
 
-```{bash, echo=FALSE}
-# run job script
-# it's important to run the job within the REPORT_FILES_PATH
-cd ${REPORT_FILES_PATH} && sh script.sh
+```{bash, 'run jobs', echo=FALSE}
+# run job script, always use absolute path. 
+# we want to run all jobs within the working path.
+sh ${REPORT_FILES_PATH}/script.sh
 ```
 
 
-
-```{bash, results='asis', echo=FALSE}
+```{bash, 'display script', results='asis', echo=FALSE}
 echo '## Job script'
 echo ''
 echo ''
@@ -121,16 +118,10 @@
 ```
 
 
-```{r, echo=FALSE}
-## obtain REPORT_FILES_PAHT and save it to a galaxy output.
-database_root = paste(head(strsplit(Sys.getenv('TOOL_LOG'), '/')[[1]], -1), collapse = '/')
-tool_output_dir_id = tail(strsplit(Sys.getenv('REPORT_FILES_PATH'), '/')[[1]], 1)
-tool_output_dir = paste0(database_root, '/', tool_output_dir_id)
-write(tool_output_dir, Sys.getenv('TOOL_OUTPUT_DIR'))
-```
+```{r, 'display output directory contents', results='asis', echo=FALSE}
+## after the job is done, we list all files from the output directory.
+## full relative path to the output directory needs to be displayed.
 
-
-```{r, results='asis', echo=FALSE}
 cat('##All output files')
 cat('\n\n')
 all_files = list.files(path = Sys.getenv('REPORT_FILES_PATH'), 
@@ -143,3 +134,14 @@
 cat('\n')
 ```
 
+
+```{r, 'save output directory of this tool', echo=FALSE}
+## each elastic tool has a galaxy history output which contains the REPORT_FILES_PATH of this tool
+## so that other tools can reference the outputs from this tool.
+
+## obtain REPORT_FILES_PAHT and save it to a galaxy output.
+database_root = paste(head(strsplit(Sys.getenv('TOOL_LOG'), '/')[[1]], -1), collapse = '/')
+tool_output_dir_id = tail(strsplit(Sys.getenv('REPORT_FILES_PATH'), '/')[[1]], 1)
+tool_output_dir = paste0(database_root, '/', tool_output_dir_id)
+write(tool_output_dir, Sys.getenv('TOOL_OUTPUT_DIR'))
+```
--- a/elastic_tool.xml	Mon Mar 26 00:09:35 2018 -0400
+++ b/elastic_tool.xml	Sun Apr 01 16:48:53 2018 -0400
@@ -1,26 +1,154 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="elastic_fastq_dump" name="elastic fastq-dump" version="1.0.0">
-  <macros>
-    <import>elastic_tool_wrappers_macros.xml</import>
-  </macros>
-  <description/>
-  <requirements>
-    <expand macro="rmarkdown_requirements"/>
-  </requirements>
-  <expand macro="stdio"/>
-  <expand macro="shell_command"/>
-  <inputs>
-    <expand macro="tool_name"/>
-    <expand macro="option_argument_single_dataset"/>
-    <expand macro="option_argument_multiple_datasets"/>
-    <expand macro="option_argument_path_relative_to_a_tool"/>
-    <expand macro="option_argument_path_relative_to_this_tool"/>
-    <expand macro="option_argument_string_float_integer"/>
-  </inputs>
-  <outputs>
-    <expand macro="output_set"/>
-  </outputs>
-  <citations>
-    <expand macro="citations"/>
-  </citations>
+<tool id="elastic_fastq_dump" name="elastic fastq-dump" version="1.0.1">
+    <macros>
+        <import>elastic_tool_macros.xml</import>
+    </macros>
+    <expand macro="tool_description"/>
+    <requirements>
+        <expand macro="elastic_tool_requirements"/>
+    </requirements>
+    <stdio>
+        <regex match="XXX" source="stderr" level="warning"
+               description="Check the tool log output file for more details."/>
+    </stdio>
+    <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|option|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.option) + "|" + 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.option) + "|" + 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.option) + "|" + 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.option) + "|" + 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.option) + "|" + str($i.value) + "|"
+             echo '$item' >> $report.files_path/options_and_arguments.txt &&
+        #end for
+
+        ############ output_set
+        ## '$report'
+        ## '$report.files_path'
+        ## '$tool_output_dir'
+        ## '$tool_log'
+        #######################
+        export REPORT='$report' &&
+        export REPORT_FILES_PATH='$report.files_path' &&
+        export TOOL_OUTPUT_DIR='$tool_output_dir' &&
+        export TOOL_LOG='$tool_log' &&
+
+
+        ############ run render R script to render R markdowns
+        Rscript '${__tool_directory__}/elastic_tool_render.R'
+
+        ]]></command>
+    <inputs>
+        <param type="select" name="tool_name" multiple="false" label="Tool name">
+            <expand macro="tool_options"/>
+        </param>
+        <repeat name="option_argument_single_dataset_repeat" title="INPUT DATA FROM HISTORY: single data set" min="0"
+                default="0">
+            <param type="text" name="option" optional="true" label="option"/>
+            <param name="value" type="data" optional="false" multiple="false" label="value"/>
+        </repeat>
+        <repeat name="option_argument_multiple_datasets_repeat" title="INPUT DATA FROM HISTORY: multiple data sets"
+                min="0" default="0">
+            <param type="text" name="option" optional="true" label="option"/>
+            <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>
+        <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="option" optional="true" label="option"/>
+            <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>
+        <repeat name="option_argument_string_float_integer_repeat" title="INPUT VALUE: string/float/integer" min="0"
+                default="0">
+            <param type="text" name="option" label="option"/>
+            <param type="text" name="value" label="value"/>
+        </repeat>
+        <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="option" optional="true" label="option"/>
+            <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>
+    </inputs>
+    <outputs>
+        <data format="html" name="report" label="${tool.name} report ${on_string}"/>
+        <data format="txt" name="tool_output_dir" label="${tool.name} output directory ${on_string}"/>
+        <data format="txt" name="tool_log" label="${tool.name} log ${on_string}"/>
+    </outputs>
+    <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>
+        <expand macro="citations"/>
+    </citations>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/elastic_tool_macros.xml	Sun Apr 01 16:48:53 2018 -0400
@@ -0,0 +1,31 @@
+<macros>
+
+    <!--tool requirements-->
+    <xml name="tool_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="0.6.2">parallel-fastq-dump</requirement>
+    </xml>
+
+    <!--tool description-->
+    <xml name="tool_description">
+        <description>fastq-dump tool wrapper with elastic user interface.</description>
+    </xml>
+
+    <!--tool options-->
+    <xml name="tool_options">
+        <option value="tool_command" selected="false">tool command</option>
+    </xml>
+
+    <!--tool help-->
+    <xml name="tool_help">
+        <help><![CDATA[
+            Here is your tool help documentation.
+        ]]></help>
+    </xml>
+
+    <!--tool citations-->
+    <xml name="citations">
+        <citation type="doi"></citation>
+    </xml>
+</macros>
--- a/elastic_tool_wrappers_macros.xml	Mon Mar 26 00:09:35 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,169 +0,0 @@
-<?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="0.6.2">parallel-fastq-dump</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="fastq-dump" selected="false">fastq-dump</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 && cd $report.files_path &&
-
-
-        ############ save the tool installation directory to an environment variable
-        export TOOL_INSTALL_DIR='${__tool_directory__}' &&
-
-
-        #########################
-        ##
-        ## save user input option/argument pairs into a file
-        ##
-        #########################
-
-        ## first line will be the header
-        echo 'type|flag|value|path_type' > 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 &&
-        #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 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>