Mercurial > repos > mingchen0919 > dynamic_tool_test

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+++ b/LICENSE	Wed Mar 21 17:26:27 2018 -0400
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+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.
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+++ b/README.md	Wed Mar 21 17:26:27 2018 -0400
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+# Dynamic Galaxy Tool wrappers
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+++ b/dynamic_tool.Rmd	Wed Mar 21 17:26:27 2018 -0400
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+---
+title: 'Dynamic tool'
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(error = TRUE)
+```
+
+# Dynamic tools
+
+```{r}
+opt
+```
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dynamic_tool.csv	Wed Mar 21 17:26:27 2018 -0400
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+short flag,argument mask,data type,variable name,galaxy input type,description
+t,1,character,tool_name,
+o,1,character,one_dataset_itmes,
+m,1,character,multiple_dataset_items,
+u,1,character,path_relative_to_upstream_tool_items,
+s,1,character,string_items,
+f,1,character,float_items,
+i,1,character,integer_items,
+R,1,character,report,
+D,1,character,report.files_path,
+H,1,character,tool_help_doc,
+O,1,character,tool_output_dir,
+L,1,character,tool_log,
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dynamic_tool.xml	Wed Mar 21 17:26:27 2018 -0400
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+<tool id="dynamic_tool" name="dynamic tool" version="1.0.0">
+    <macros>
+        <import>dynamic_tool_wrappers_macros.xml</import>
+    </macros>
+    <description></description>
+    <requirements>
+        <expand macro="rmarkdown_requirements" />
+        <requirement type="package" version="0.11.7">fastqc</requirement>
+    </requirements>
+    <expand macro="stdio" />
+    <expand macro="shell_command" />
+    <inputs>
+        <expand macro="tool_name" />
+        <expand macro="option_argument_one_dataset" />
+        <expand macro="option_argument_multiple_datasets" />
+        <expand macro="option_argument_path_relative_to_upstream_tool" />
+        <expand macro="option_argument_string" />
+        <expand macro="option_argument_float" />
+        <expand macro="option_argument_integer" />
+    </inputs>
+    <outputs>
+        <expand macro="output_set" />
+    </outputs>
+    <citations>
+        <expand macro="citations" />
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dynamic_tool_render.R	Wed Mar 21 17:26:27 2018 -0400
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+##============ Sink warnings and errors to a file ==============
+## use the sink() function to wrap all code within it.
+##==============================================================
+zz = file('tool_log.txt')
+sink(zz)
+sink(zz, type = 'message')
+
+#------------import libraries--------------------
+options(stringsAsFactors = FALSE)
+
+library(getopt)
+library(rmarkdown)
+#------------------------------------------------
+
+
+#------------get arguments into R--------------------
+# load helper function
+source(paste0(Sys.getenv('TOOL_DIR'), '/helper.R'))
+# import getopt specification matrix from a csv file
+opt = getopt(getopt_specification_matrix('/dynamic_tool.csv'))
+opt$X_T = Sys.getenv('TOOL_DIR')
+#----------------------------------------------------
+
+
+#-----------using passed arguments in R
+#           to define system environment variables---
+do.call(Sys.setenv, opt[-1])
+#----------------------------------------------------
+
+#---------- often used variables ----------------
+# OUTPUT_DIR: path to the output associated directory, which stores all outputs
+# TOOL_DIR: path to the tool installation directory
+OUTPUT_REPORT = opt$X_R
+OUTPUT_DIR = opt$X_D
+TOOL_DIR =   opt$X_T
+RMD_NAME = 'dynamic_tool.Rmd'
+
+# create the output associated directory to store all outputs
+dir.create(OUTPUT_DIR, recursive = TRUE)
+
+#-----------------render Rmd--------------
+render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT)
+#------------------------------------------
+
+#==============the end==============
+
+
+##--------end of code rendering .Rmd templates----------------
+sink()
+##=========== End of sinking output=============================
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dynamic_tool_wrappers_macros.xml	Wed Mar 21 17:26:27 2018 -0400
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+<macros>
+
+    <xml name="rmarkdown_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>
+    </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="fastqc" selected="false">fastqc</option>
+        </param>
+    </xml>
+
+    <!--OPTION/ARGUMENT PAIRS and INPUT types-->
+    <!--input files-->
+    <xml name="option_argument_one_dataset">
+        <repeat name="option_argument_one_dataset_repeat" title="OPTION and ARGUMENT: input one dataset" min="0" default="0">
+            <param type="text" name="flag" optional="true" label="flag" />
+            <param name="one_dataset" type="data" optional="true" multiple="false" label="value"/>
+        </repeat>
+    </xml>
+    <xml name="option_argument_multiple_datasets">
+        <repeat name="option_argument_multiple_datasets_repeat" title="OPTION and ARGUMENT: input multiple datasets" min="0" default="0">
+            <param type="text" name="flag" optional="true" label="flag" />
+            <param name="multiple_datasets" type="data" optional="true" multiple="true" label="value" />
+        </repeat>
+    </xml>
+    <xml name="option_argument_path_relative_to_upstream_tool">
+        <repeat name="option_argument_path_relative_to_upstream_tool_repeat" title="OPTION and ARGUMENT: path relative to upstream tool" min="0" default="0">
+            <param type="text" name="flag" optional="true" label="flag" />
+            <param name="upstream_tool_output_dir" type="data" optional="true" multiple="false" label="upstream tool output directory"/>
+            <param type="text" name="option_argument_path" optional="true" label="value" />
+        </repeat>
+    </xml>
+
+    <!--input values: string, float and integer-->
+    <xml name="option_argument_string">
+        <repeat name="option_argument_string_repeat" title="OPTION and ARGUMENT: input string" min="0" default="0">
+            <param type="text" name="flag" label="flag" />
+            <param type="text" name="option_argument_string"  label="value" />
+        </repeat>
+    </xml>
+    <xml name="option_argument_float">
+        <repeat name="option_argument_float_repeat" title="OPTION and ARGUMENT: input float" min="0" default="0">
+            <param type="text" name="flag" label="flag" />
+            <param type="text" name="option_argument_float"  label="value" />
+        </repeat>
+    </xml>
+    <xml name="option_argument_integer">
+        <repeat name="option_argument_integer_repeat" title="OPTION and ARGUMENT: input integer" min="0" default="0">
+            <param type="text" name="flag" label="flag" />
+            <param type="text" name="option_argument_integer"  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="${tool.name} log" from_work_dir="tool_log.txt"/>
+    </xml>
+
+
+    <!--shell command fragment-->
+    <xml name="shell_command">
+        <command><![CDATA[
+        export TOOL_DIR='${__tool_directory__}' &&
+
+        Rscript '${__tool_directory__}/dynamic_tool_render.R'
+
+        ############ tool_name
+        -t '$tool_name'
+
+        ############ option_argument_one_dataset
+        #set sep = ''
+        #set one_dataset_items = ''
+        #for i in $option_argument_one_dataset_repeat:
+            #set one_dataset_items += $sep + $option_argument_one_dataset_repeat.flag + " " + $option_argument_one_dataset_repeat.value + "'"
+            #### separate values set by repeat
+            $set sep = '|'
+        #end for
+
+        -o '$one_dataset_items'
+
+
+
+        ############ option_argument_multiple_datasets
+        #set sep = ''
+        #set multiple_datasets_items = ''
+        #for i in $option_argument_multiple_datasets_repeat:
+            #set multiple_datasets_items += $sep + $option_argument_multiple_datasets_repeat.flag + " " + $option_argument_multiple_datasets_repeat.value + "'"
+            #### separate values set by repeat
+            $set sep = '|'
+        #end for
+
+        -m '$multiple_datasets_items'
+
+
+        ############ option_argument_path_relative_to_upstream_tool
+        #set sep = ''
+        #set path_relative_to_upstream_tool_items = ''
+        #for i in $option_argument_path_relative_to_upstream_tool_repeat:
+            #set path_relative_to_upstream_tool_items += $sep + $option_argument_path_relative_to_upstream_tool_repeat.flag + " " + $option_argument_path_relative_to_upstream_tool_repeat.value + "'"
+            #### separate values set by repeat
+            $set sep = '|'
+        #end for
+
+        -u '$path_relative_to_upstream_tool_items'
+
+
+
+        ############ option_argument_string
+        #set sep = ''
+        #set string_items = ''
+        #for i in $option_argument_string_repeat:
+            #set string_items += $sep + $option_argument_string_repeat.flag + " " + $option_argument_string_repeat.value + "'"
+            #### separate values set by repeat
+            $set sep = '|'
+        #end for
+
+        -s '$string_items'
+
+
+        ############ option_argument_float
+        #set sep = ''
+        #set float_items = ''
+        #for i in $option_argument_float_repeat:
+            #set float_items += $sep + $option_argument_float_repeat.flag + " " + $option_argument_float_repeat.value + "'"
+            #### separate values set by repeat
+            $set sep = '|'
+        #end for
+
+        -f '$float_items'
+
+        ############ option_argument_integer
+        #set sep = ''
+        #set integer_items = ''
+        #for i in $option_argument_integer_repeat:
+            #set integer_items += $sep + $option_argument_integer_repeat.flag + " " + $option_argument_integer_repeat.value + "'"
+            #### separate values set by repeat
+            $set sep = '|'
+        #end for
+
+        -i '$integer_items'
+
+
+        ############ output_set
+        -R '$report'
+        -D '$report.files_path'
+        -H '$tool_help_doc'
+        -O '$tool_output_dir'
+        -L '$tool_log'
+
+        ]]></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{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        ]]></citation>
+    </xml>
+</macros>
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/helper.R	Wed Mar 21 17:26:27 2018 -0400
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+#' \code{getopt_specification_matrix} returns a getopt specification matrix.
+#'
+#' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data.
+#' The first column are short flags, the second column are argument masks, the third column
+#' is data types. The fourth column are variable names used in the tool XML. These three columns are required.
+#' @param gtg_name the name of a running GTG.
+getopt_specification_matrix = function(specification_file, gtg_name = 'gtg', tool_dir = Sys.getenv('TOOL_DIR')) {
+  df = read.csv(paste0(tool_dir, specification_file),
+                header = TRUE, stringsAsFactors = FALSE)
+  # check if there are duplicated short flags
+  short_flags = df[, 1]
+  if (length(unique(short_flags)) < length(short_flags)) {
+    cat('----Duplicated short flags found ----\n')
+    cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n')
+    stop('Duplicated short flags are not allowed.')
+  }
+
+  # use short flags to generate long flags
+  long_flags = paste0('X_', df[, 1])
+
+  # specification matrix
+  df2 = data.frame(long_flags = long_flags,
+                   short_flags = df[, 1],
+                   argument_mask = df[, 2],
+                   data_type = df[, 3])
+
+  as.matrix(df2)
+}
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