changeset 0:a246652032c1 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aurora_demo.Rmd	Sat Mar 10 01:44:02 2018 -0500
@@ -0,0 +1,43 @@
+---
+title: 'Aurora Galaxy Tool Demo'
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = TRUE, 
+  error = TRUE
+)
+```
+
+
+# Python script
+
+We first use Python code to generate a random data matrix and save the data into an output file.
+
+```{python}
+import numpy as np
+import os
+
+n_row = os.environ['X_r']
+n_col = os.environ['X_c']
+heatmap_data = np.power(10, np.random.randn(n_row, n_col))
+heatmap_file = os.environ['X_O']
+with open(heatmap_file, 'w') as f:
+  f.write(heatmap_data)
+```
+
+
+# Shell script
+
+Then we use shell script to display the file content.
+
+```{bash}
+cat ${X_O}
+```
+
+
+# R script
+
+Finally, we use R script to import the data and generate a heatmap.
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aurora_demo.sh	Sat Mar 10 01:44:02 2018 -0500
@@ -0,0 +1,11 @@
+Rscript '${__tool_directory__}/rmarkdown_report_render.R'
+      # user input
+      -r $row_number
+      -c $column_number
+
+      # output
+      -R $report
+      -O $heatmap_data
+      
+      # tool installation directory
+      -T '${__tool_directory__}'
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aurora_demo.xml	Sat Mar 10 01:44:02 2018 -0500
@@ -0,0 +1,41 @@
+<tool name="Tool report" id="tool_1" version="1.0.0">
+  <description> A demo tool for demonstrating how Aurora Galaxy tool works. This tool is developed under the R Markdown framework and use shell, python and R script together to generate a random heatmap.</description>
+  <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="2.2.1">r-ggplot2</requirement><requirement type="package" version="4.5.6">r-plotly</requirement></requirements>
+  <stdio>
+        <regex match="XXX" source="stderr" level="warning" description="Check the warnings_and_errors.txt file for more details."/></stdio>
+  <command><![CDATA[Rscript '${__tool_directory__}/rmarkdown_report_render.R'
+      # user input
+      -r $row_number
+      -c $column_number
+
+      # output
+      -R $report
+      -O $heatmap_data
+      
+      # tool installation directory
+      -T '${__tool_directory__}']]></command>
+  <inputs>
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?"/><param type="integer" name="row_number" label="Number of rows" optional="False" value="10"/><param type="integer" name="column_number" label="Number of columns" optional="False" value="5"/></inputs>
+  <outputs>
+        <data name="heatmap_data" format="txt" hidden="false"/></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{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        ]]></citation></citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aurora_demo_render.R	Sat Mar 10 01:44:02 2018 -0500
@@ -0,0 +1,26 @@
+
+#------------import libraries--------------------
+library(getopt)
+library(rmarkdown)
+#------------------------------------------------
+
+#------------1. collect input values in R--------
+#------------2. define environment variables-----
+spec_matrix = as.matrix(
+  data.frame(stringsAsFactors=FALSE,
+              long_flags = c("X_r", "X_c", "X_R", "X_O", "X_T"),
+             short_flags = c("r", "c", "R", "O", "T"),
+     argument_mask_flags = c(1L, 1L, 1L, 1L, 1L),
+         data_type_flags = c("integer", "integer", "character", "character", "character")
+  )
+)
+opt = getopt(spec_matrix)
+do.call(Sys.setenv, opt[-1])
+#------------------------------------------------
+
+
+#-----------------render Rmd--------------
+render(paste0(TOOL_DIR, '/aurora_demo.Rmd'), 
+       output_file = OUTPUT_REPORT)
+#------------------------------------------
+