changeset 0:6259ffa3d2d3 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/elastic_tool.Rmd	Sun Apr 01 23:41:44 2018 -0400
@@ -0,0 +1,147 @@
+---
+title: 'Tool Report'
+output: html_document
+---
+
+<style>
+pre code, pre, code {
+  white-space: pre !important;
+  overflow-x: scroll !important;
+  word-break: keep-all !important;
+  word-wrap: initial !important;
+}
+</style>
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(error = TRUE)
+```
+
+## User input
+
+```{r, 'display user input', echo=FALSE}
+# get user input and save it into a data frame.
+df = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), 
+                sep = '|', header = TRUE)
+
+# if the input type is 'path_relative_to_a_tool', prepend A_TOOL_OUTPUT_PATH to the value to make
+# the value a full path.
+if (nrow(df[df$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]
+    df[df$type == 'path_relative_to_a_tool', ][i, 'value'] = paste(root_path, 
+                                                                   df[df$type == 'path_relative_to_a_tool', ][i, 'value'], 
+                                                                   sep = '/')
+  }
+}
+
+## 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$type == 'tool_name', 'value']
+
+# if the number of option/argument pairs is larger than 0, build script file
+df2 = df[df$type != 'tool_name', ]
+if (nrow(df2) > 0) {
+  # write tool name as the first line of the script.sh
+  # before running the job, cd into the ${REPORT_FILES_PATH} directory
+  write(paste0(tool_name, ' \\'), 
+        paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
+  df2 = df[df$type != 'tool_name', ]
+  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
+  # has an extra newline character '\' which causes a problem. We can either remove that extra
+  # '\' or add a new line to the end. We choose to add a new line.
+  
+  # add an extra line to the end to redirect stdout to stdout.txt and stderr to stderr.txt
+  write('  > ${REPORT_FILES_PATH}/stdout.txt 2>${REPORT_FILES_PATH}/stderr.txt', 
+        paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'), append = TRUE)
+} else {
+  # if no option/argument input, simply display the help message
+  write(paste0(tool_name, ' -h'), 
+        file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
+}
+```
+
+
+```{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.
+
+# create paths before running the job script
+df_paths = df[df$type == 'path_relative_to_this_tool', ]
+
+if (nrow(df_paths) > 0) {
+  for (i in 1:nrow(df_paths)) {
+    path = paste0(Sys.getenv('REPORT_FILES_PATH'), '/', df_paths[i, 'value'])
+    path_type = df_paths[i, 'path_type']
+  
+    # create file paths
+    if ((path_type == 'file_path') & !file.exists(path)) {
+      dir_path = paste(head(strsplit(path, '/')[[1]], -1), collapse = '/' )
+      if (!dir.exists(dir_path)) {
+        dir.create(dir_path, recursive = TRUE)
+      }
+      file.create(path)
+    }
+    
+    # create dir paths
+    if ((path_type == 'dir_path') & !dir.exists(path)) {
+      dir.create(path, recursive = TRUE)
+    }
+  }
+}
+```
+
+
+```{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, 'display script', results='asis', echo=FALSE}
+echo '## Job script'
+echo ''
+echo ''
+echo '```bash'
+cat ${REPORT_FILES_PATH}/script.sh
+echo '```'
+```
+
+
+```{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.
+
+cat('##All output files')
+cat('\n\n')
+all_files = list.files(path = Sys.getenv('REPORT_FILES_PATH'), 
+                       full.names = TRUE, 
+                       recursive = TRUE)
+
+for (f in sub(Sys.getenv('REPORT_FILES_PATH'), '.', all_files) ) {
+  cat('* [', f, '](', f, ')\n')
+}
+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'))
+```

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/elastic_tool.xml	Sun Apr 01 23:41:44 2018 -0400
@@ -0,0 +1,136 @@
+<tool id="elastic_fastq_dump" name="elastic fastq-dump" version="1.0.0">
+    <macros>
+        <import>elastic_tool_macros.xml</import>
+    </macros>
+    <expand macro="tool_description"/>
+    <requirements>
+        <expand macro="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_other_tool
+        #for i in $option_argument_path_relative_to_other_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) + "|" + $report.files_path + '/' + str($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="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="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_other_tool_repeat"
+                title="PATH: relative to other 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_path_relative_to_this_tool_repeat"
+                title="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>
+        <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>
+    </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>
+    <expand macro="tool_help" />
+    <citations>
+        <expand macro="citations"/>
+    </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/elastic_tool_macros.xml	Sun Apr 01 23:41:44 2018 -0400
@@ -0,0 +1,82 @@
+<macros>
+
+    <!--change tool_id and elastic tool in the first line of elastic_tool.xml with appropriate tool_id and tool_name.-->
+
+    <!--add 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="2.8.2">sra-tools</requirement>
+    </xml>
+
+    <!--add tool description-->
+    <xml name="tool_description">
+        <description>a collection of tools and libraries for using data in the INSDC Sequence Read Archives.</description>
+    </xml>
+
+    <!--add tool options-->
+    <xml name="tool_options">
+        <option value="fastq-dump" selected="true">fastq-dump</option>
+        <option value="prefetch" selected="false">prefetch</option>
+        <option value="sam-dump" selected="false">sam-dump</option>
+        <option value="sra-pileup" selected="false">sra-pileup</option>
+        <option value="vdb-config" selected="false">vdb-config</option>
+        <option value="vdb-decrypt" selected="false">vdb-decrypt</option>
+        <option value="abi-dump" selected="false">abi-dump</option>
+        <option value="illumina-dump" selected="false">illumina-dump</option>
+        <option value="sff-dump" selected="false">sff-dump</option>
+        <option value="sra-stat" selected="false">sra-stat</option>
+        <option value="vdb-dump" selected="false">vdb-dump</option>
+        <option value="vdb-encrypt" selected="false">vdb-encrypt</option>
+        <option value="vdb-validate" selected="false">vdb-validate</option>
+    </xml>
+
+    <!--add tool help-->
+    <xml name="tool_help">
+        <help><![CDATA[
+            [SRA Toolkit Documentation](http://ncbi.github.io/sra-tools/)
+            
+            Example 1: download paired end reads and split them into forward and reverse reads.
+              Tool name: fastq-dump
+              + 1: PATH: relative to this tool output directory
+                  * option: -O
+                  * value: SRA
+                  * path type: directory path
+              + 1: INPUT VALUE: string/float/integer
+                  * option: --split-files
+                  * value: SRR6077558 ERR343809
+                  
+            Example 2: download single end reads
+              Tool name: fastq-dump
+              + 1: PATH: relative to this tool output directory
+                  * option: -O
+                  * value: SRA
+                  * path type: directory path
+              + 1: INPUT VALUE: string/float/integer
+                  * value: SRR6077558 ERR343809
+        ]]></help>
+    </xml>
+
+    <!--add 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>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/elastic_tool_render.R	Sun Apr 01 23:41:44 2018 -0400
@@ -0,0 +1,33 @@
+##============ Sink warnings and errors to a file ==============
+## use the sink() function to wrap all code within it.
+##==============================================================
+zz = file(Sys.getenv('TOOL_LOG'))
+sink(zz)
+sink(zz, type = 'message')
+
+#------------import libraries--------------------
+options(stringsAsFactors = FALSE)
+
+library(rmarkdown)
+#------------------------------------------------
+
+#------------------------------------------------
+options_and_arguments = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), 
+                                   sep = '|', header = TRUE)
+
+
+#-----------------render Rmd--------------
+render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/elastic_tool.Rmd'),
+       output_file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/report.html'))
+
+# for some unknow reason, directly using REPORT as the input value for output_file parameter
+# in the render function can cause empty report file when the tool runs in batch mode.
+# the solution is to render the rmarkdown to a explicitly specified file and then copy the
+# file to ${REPORT}
+system(command = 'cp ${REPORT_FILES_PATH}/report.html ${REPORT}')
+#------------------------------------------
+
+
+##--------end of code rendering .Rmd templates----------------
+sink()
+##=========== End of sinking output=============================
\ No newline at end of file