# HG changeset patch
# User mingchen0919
# Date 1509978984 18000
# Node ID 7905d420f63eb1f9202137abda05cfd842588a59
# Parent  1b64a808c7636e07d3a8a74fff225c65b3cda126
Deleted selected files

diff -r 1b64a808c763 -r 7905d420f63e bdss_client.Rmd
--- a/bdss_client.Rmd	Tue Oct 17 00:08:00 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
----
-title: 'Download with BDSS client'
-output:
-    html_document:
-      number_sections: true
-      toc: true
-      theme: cosmo
-      highlight: tango
----
-
-```{r setup, include=FALSE, warning=FALSE, message=FALSE}
-knitr::opts_chunk$set(
-  echo = ECHO,
-  error=TRUE
-)
-```
-
-# Command line arguments
-
-```{r 'command line arguments'}
-str(opt)
-```
-
-# BDSS configuration file
-
-First, we create a bdss configuration file `bdss.cfg` in the current directory.
-
-```{r}
-system('echo "[metadata_repository]" > bdss.cfg')
-system('echo url=http://bdss.bioinfo.wsu.edu/ >> bdss.cfg')
-```
-
-# Download data
-
-```{r 'download and extract reads'}
-# create a directory to store read files
-dir.create('read_files_directory')
-# download and extract reads
-urls = strsplit(gsub(',', ' ', 'URLS'), ' ')[[1]]
-urls = urls[urls != '']
-# loop through SRA accessions to download and extract reads.
-for(url in urls) {
-    print(url)
-    bdss_command = paste0('/main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer --destination read_files_directory -u ', url)
-    print(bdss_command)
-    print(system(bdss_command, intern = TRUE))
-}
-# all files that need to be saved should be moved to REPORT_DIR directory
-# print(system('mv read_files_directory REPORT_DIR', intern = TRUE))
-```
-
-
diff -r 1b64a808c763 -r 7905d420f63e bdss_client.xml
--- a/bdss_client.xml	Tue Oct 17 00:08:00 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-<tool id="rmarkdown_bdss_client_main" name="BDSS client" version="1.0.0">
-    <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="1.2">r-rmarkdown</requirement>
-        <requirement type="package" version="0.3.5">r-htmltools</requirement>
-        <requirement type="package" version="0.5.0">r-dplyr</requirement>
-        <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement>
-        <requirement type="package" version="1.95_4.8">r-rcurl</requirement>
-    </requirements>
-    <description>
-        Download data with BDSS client.
-    </description>
-    <stdio>
-        <!--All stderr are redirected to a file. "XXX" is used to match with nothing-->
-        <regex match="XXX"
-               source="stderr"
-               level="warning"
-               description="Check the warnings_and_errors.txt file for more details."/>
-    </stdio>
-    <command>
-        <![CDATA[
-            Rscript '${__tool_directory__}/bdss_client_render.R'
-                -i '$urls'
-                -e $echo
-
-                -r $report
-                -d $report.files_path
-                -s $sink_message
-
-                -t '${__tool_directory__}/bdss_client.Rmd'
-        ]]>
-    </command>
-    <inputs>
-        <param type="text" name="urls" area="true" size="5x25" label="URLs to data files" />
-        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
-               label="Display analysis code in report?"/>
-    </inputs>
-    <outputs>
-        <data format="html" name="report" label="BDSS client report"/>
-        <data name="output" label="BDSS downloaded data">
-            <discover_datasets pattern="__name_and_ext__" directory="read_files_directory" visible="true"/>
-        </data>
-        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
-    </outputs>
-</tool>
\ No newline at end of file
diff -r 1b64a808c763 -r 7905d420f63e bdss_client_render.R
--- a/bdss_client_render.R	Tue Oct 17 00:08:00 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-library(getopt)
-library(rmarkdown)
-library(htmltools)
-library(dplyr)
-library(RCurl)
-
-
-##============ Sink warnings and errors to a file ==============
-## use the sink() function to wrap all code within it.
-##==============================================================
-zz = file('warnings_and_errors.txt')
-sink(zz)
-sink(zz, type = 'message')
-##---------below is the code for rendering .Rmd templates-----
-
-  ##=============STEP 1: handle command line arguments==========
-  ##
-  ##============================================================
-  # column 1: the long flag name
-  # column 2: the short flag alias. A SINGLE character string
-  # column 3: argument mask
-  #           0: no argument
-  #           1: argument required
-  #           2: argument is optional
-  # column 4: date type to which the flag's argument shall be cast.
-  #           possible values: logical, integer, double, complex, character.
-  #-------------------------------------------------------------
-  #++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
-  # 1. short flag alias should match the flag in the command section in the XML file.
-  # 2. long flag name can be any legal R variable names
-  # 3. two names in args_list can have common string but one name should not be a part of another name.
-  #    for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
-  #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-  ##------- 1. input data ---------------------
-  args_list=list()
-  args_list$URLS = c('urls', 'i', '1', 'character')
-  args_list$ECHO = c('echo', 'e', '1', 'character')
-  ##--------2. output report and outputs --------------
-  args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
-  args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
-  args_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character')
-  ##--------3. Rmd templates in the tool directory ----------
-  args_list$BDSS_CLIENT_RMD = c('bdss_client_rmd', 't', '1', 'character')
-  
-  opt = getopt(t(as.data.frame(args_list)))
-  
-  
-  ##=======STEP 2: create report directory (optional)==========
-  ##
-  ##===========================================================
-  dir.create(opt$report_dir)
-  
-  ##=STEP 3: replace placeholders in .Rmd with argument values=
-  ##
-  ##===========================================================
-  #++ need to replace placeholders with args values one by one+
-  #----- 01 bdss_client.Rmd -----------------------
-  readLines(opt$bdss_client_rmd) %>%
-    (function(x) {
-      gsub('URLS', opt$urls, x)
-    }) %>%
-    (function(x) {
-      gsub('ECHO', opt$echo, x)
-    }) %>%
-    (function(x) {
-      gsub('REPORT_DIR', opt$report_dir, x)
-    }) %>%
-    (function(x) {
-      fileConn = file('bdss_client.Rmd')
-      writeLines(x, con=fileConn)
-      close(fileConn)
-    })
-  
-  ##=============STEP 4: render .Rmd templates=================
-  ##
-  ##===========================================================
-  render('bdss_client.Rmd', output_file = opt$report_html)
-
-
-##--------end of code rendering .Rmd templates----------------
-sink()
-##=========== End of sinking output=============================
\ No newline at end of file
diff -r 1b64a808c763 -r 7905d420f63e bdss_client_sra.Rmd
--- a/bdss_client_sra.Rmd	Tue Oct 17 00:08:00 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,105 +0,0 @@
----
-title: 'Download and extract single end fastq/fasta data with BDSS client from SRA accessions'
-output:
-    html_document:
-      number_sections: true
-      toc: true
-      theme: cosmo
-      highlight: tango
----
-
-```{r setup, include=FALSE, warning=FALSE, message=FALSE}
-knitr::opts_chunk$set(
-  echo = ECHO,
-  error=TRUE
-)
-```
-
-# Command line arguments
-
-```{r 'command line arguments'}
-str(opt)
-```
-
-# BDSS configuration file
-
-First, we create a bdss configuration file `bdss.cfg` in the current directory.
-
-```{r}
-system('echo "[metadata_repository]" > bdss.cfg')
-system('echo url=http://bdss.bioinfo.wsu.edu/ >> bdss.cfg')
-```
-
-# Download and extract reads
-
-```{r 'download and extract reads'}
-# create two directories, one for single end and the other for paired end SRA reads.
-dir.create('se_read_files_directory')
-dir.create('pe_read_files_directory')
-# download and extract reads (single end)
-sra_ids_se = strsplit(gsub(',', ' ', 'SRA_IDS_SE'), ' ')[[1]]
-sra_ids_se = sra_ids_se[sra_ids_se != '']
-# loop through SRA accessions to download and extract reads.
-for(id in sra_ids_se) {
-    # build URL from SRA id
-    url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
-                 substr(id, 1, 3), '/',
-                 substr(id, 1, 6), '/', id, '/', id, '.sra')
-    # download sra file with bdss
-    bdss_command = paste0('/main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url)
-    system(bdss_command, intern = TRUE)
-    # convert .sra to .fastq/.fasta
-    if('FORMAT' == 'fasta') {
-      command = paste0('fastq-dump --fasta -O se_read_files_directory ', id, '.sra')
-    } else {
-      command = paste0('fastq-dump -O se_read_files_directory ', id, '.sra')
-    }
-    cat('----convert SRA to fastq/fasta------\n')
-    print(system(command, intern = TRUE))
-}
-
-# download and extract reads (paired end)
-sra_ids_pe = strsplit(gsub(',', ' ', 'SRA_IDS_PE'), ' ')[[1]]
-sra_ids_pe = sra_ids_pe[sra_ids_pe != '']
-# loop through SRA accessions to download and extract reads.
-for(id in sra_ids_pe) {
-    # build URL from SRA id
-    url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
-                 substr(id, 1, 3), '/',
-                 substr(id, 1, 6), '/', id, '/', id, '.sra')
-    # download sra file with bdss
-    bdss_command = paste0('/main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url)
-    system(bdss_command, intern = TRUE)
-    # convert .sra to .fastq/.fasta
-    if('FORMAT' == 'fasta') {
-      command = paste0('fastq-dump --fasta --split-files -O pe_read_files_directory ', id, '.sra')
-    } else {
-      command = paste0('fastq-dump --split-files -O pe_read_files_directory ', id, '.sra')
-    }
-    cat('----convert SRA to fastq/fasta------\n')
-    command_stdout = system(command, intern = TRUE)
-    print(command_stdout)
-    if(!(paste0(id, '_2.FORMAT') %in% list.files('pe_read_files_directory'))) {
-      # this is not a paired end SRA file. The corresponding file will be deleted.
-      cat(paste0(id, ' is not paired end SRA, the corresponding fastq/fasta file will deleted.'))
-      system(paste0('rm pe_read_files_directory/', id, '_1.*'), intern = TRUE)
-    }
-    
-}
-
-cat('-----single end files----\n')
-list.files('./se_read_files_directory')
-cat('-----paired end files----\n')
-list.files('./pe_read_files_directory')
-
-cat('-----Renaming files------\n')
-# rename files for paired end reads
-old_files = paste0('./pe_read_files_directory/', list.files('./pe_read_files_directory'))
-print(old_files)
-new_files = gsub('_1', '_forward', old_files)
-new_files = gsub('_2', '_reverse', new_files)
-print(new_files)
-file.rename(old_files, new_files)
-```
-
-
diff -r 1b64a808c763 -r 7905d420f63e bdss_client_sra.xml
--- a/bdss_client_sra.xml	Tue Oct 17 00:08:00 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-<tool id="rmarkdown_bdss_client_sra_main" name="BDSS client SRA" version="1.0.0">
-    <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="1.2">r-rmarkdown</requirement>
-        <requirement type="package" version="0.3.5">r-htmltools</requirement>
-        <requirement type="package" version="0.5.0">r-dplyr</requirement>
-        <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement>
-        <requirement type="package" version="1.95_4.8">r-rcurl</requirement>
-    </requirements>
-    <description>
-        Download data with BDSS client and generate list (single end SRA data) and list:paired dataset collection
-        (paired end SRA data).
-    </description>
-    <stdio>
-        <!--All stderr are redirected to a file. "XXX" is used to match with nothing-->
-        <regex match="XXX"
-               source="stderr"
-               level="warning"
-               description="Check the warnings_and_errors.txt file for more details."/>
-    </stdio>
-    <command>
-        <![CDATA[
-            Rscript '${__tool_directory__}/bdss_client_sra_render.R'
-                -i '$sra_ids_se'
-                -p '$sra_ids_pe'
-                -f $format
-                -e $echo
-
-                -r $report
-                -d $report.files_path
-                -s $sink_message
-
-                -t '${__tool_directory__}/bdss_client_sra.Rmd'
-        ]]>
-    </command>
-    <inputs>
-        <param type="text" name="sra_ids_se" area="true" size="5x25" label="SRR/DRR/ERR accessions of single end SRA"
-               help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR039885"/>
-        <param type="text" name="sra_ids_pe" area="true" size="5x25" label="SRR/DRR/ERR accessions of paired end SRA"
-               help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. ERR1748507"/>
-        <param type="select" name="format" label="Output format">
-            <option value="fastq" selected="true">fastq</option>
-            <option value="fasta">fasta</option>
-        </param>
-        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
-               label="Display analysis code in report?"/>
-    </inputs>
-    <outputs>
-        <data format="html" name="report" label="BDSS client report"/>
-        <!--list dataset collection for single end SRA data-->
-        <collection type="list" name="list_collection" label="BDSS download data (single end reads)">
-            <discover_datasets pattern="__name_and_ext__" directory="se_read_files_directory"/>
-        </collection>
-        <!--list:paired dataset collection for paired end SRA data-->
-        <collection type="list:paired" name="list:paired_collection" label="BDSS download data (paired end reads)">
-            <discover_datasets
-                    pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?"
-                    directory="pe_read_files_directory"/>
-        </collection>
-        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
-    </outputs>
-</tool>
\ No newline at end of file
diff -r 1b64a808c763 -r 7905d420f63e bdss_client_sra_render.R
--- a/bdss_client_sra_render.R	Tue Oct 17 00:08:00 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,90 +0,0 @@
-library(getopt)
-library(rmarkdown)
-library(htmltools)
-library(dplyr)
-library(RCurl)
-
-
-##============ Sink warnings and errors to a file ==============
-## use the sink() function to wrap all code within it.
-##==============================================================
-zz = file('warnings_and_errors.txt')
-sink(zz)
-sink(zz, type = 'message')
-##---------below is the code for rendering .Rmd templates-----
-
-##=============STEP 1: handle command line arguments==========
-##
-##============================================================
-# column 1: the long flag name
-# column 2: the short flag alias. A SINGLE character string
-# column 3: argument mask
-#           0: no argument
-#           1: argument required
-#           2: argument is optional
-# column 4: date type to which the flag's argument shall be cast.
-#           possible values: logical, integer, double, complex, character.
-#-------------------------------------------------------------
-#++++++++++++++++++++ Best practice ++++++++++++++++++++++++++
-# 1. short flag alias should match the flag in the command section in the XML file.
-# 2. long flag name can be any legal R variable names
-# 3. two names in args_list can have common string but one name should not be a part of another name.
-#    for example, one name is "ECHO", if another name is "ECHO_XXX", it will cause problems.
-#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-##------- 1. input data ---------------------
-args_list=list()
-args_list$SRA_IDS_SE = c('sra_ids_se', 'i', '1', 'character')
-args_list$SRA_IDS_PE = c('sra_ids_pe', 'p', '1', 'character')
-args_list$FORMAT = c('format', 'f', '1', 'character')
-args_list$ECHO = c('echo', 'e', '1', 'character')
-##--------2. output report and outputs --------------
-args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
-args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
-args_list$SINK_OUTPUT = c('sink_message', 's', '1', 'character')
-##--------3. Rmd templates in the tool directory ----------
-args_list$BDSS_CLIENT_RMD = c('bdss_client_rmd', 't', '1', 'character')
-
-opt = getopt(t(as.data.frame(args_list)))
-
-
-##=======STEP 2: create report directory (optional)==========
-##
-##===========================================================
-dir.create(opt$report_dir)
-
-##=STEP 3: replace placeholders in .Rmd with argument values=
-##
-##===========================================================
-#++ need to replace placeholders with args values one by one+
-#----- 01 bdss_client.Rmd -----------------------
-readLines(opt$bdss_client_rmd) %>%
-  (function(x) {
-    gsub('SRA_IDS_SE', opt$sra_ids_se, x)
-  }) %>%
-  (function(x) {
-    gsub('SRA_IDS_PE', opt$sra_ids_pe, x)
-  }) %>%
-  (function(x) {
-    gsub('FORMAT', opt$format, x)
-  }) %>%
-  (function(x) {
-    gsub('ECHO', opt$echo, x)
-  }) %>%
-  (function(x) {
-    gsub('REPORT_DIR', opt$report_dir, x)
-  }) %>%
-  (function(x) {
-    fileConn = file('bdss_client.Rmd')
-    writeLines(x, con=fileConn)
-    close(fileConn)
-  })
-
-##=============STEP 4: render .Rmd templates=================
-##
-##===========================================================
-render('bdss_client.Rmd', output_file = opt$report_html)
-
-
-##--------end of code rendering .Rmd templates----------------
-sink()
-##=========== End of sinking output=============================
\ No newline at end of file