Repository 'rmarkdown_fastqc_site'
hg clone https://toolshed.g2.bx.psu.edu/repos/mingchen0919/rmarkdown_fastqc_site

Changeset 7:d820be692d74 (2017-08-08)
Previous changeset 6:2f4df2be0572 (2017-08-08) Next changeset 8:a12e19571cf5 (2017-08-08)
Commit message:
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
added:
01_evaluation_overview.Rmd
02_fastqc_original_reports.Rmd
1_per_base_quality_scores.Rmd
2_per_base_N_content.Rmd
3_per_sequence_quality_scores.Rmd
4_per_sequence_GC_content.Rmd
5_per_base_sequence_content.Rmd
_site.yml
fastqc_site.xml
fastqc_site_render.R
index.Rmd
removed:
wgcna_construct_network.Rmd
wgcna_construct_network.xml
wgcna_construct_network_render.R
wgcna_eigengene_visualization.Rmd
wgcna_eigengene_visualization.xml
wgcna_eigengene_visualization_render.R
wgcna_preprocessing.Rmd
wgcna_preprocessing.xml
wgcna_preprocessing_render.R
b
diff -r 2f4df2be0572 -r d820be692d74 01_evaluation_overview.Rmd
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/01_evaluation_overview.Rmd Tue Aug 08 12:36:13 2017 -0400
[
@@ -0,0 +1,123 @@
+---
+title: "Evaluation Overview"
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = ECHO)
+```
+
+```{bash 'copy data from datasets directory to working directory', echo=FALSE}
+# Copy uploaded data to the working directory
+for f in $(echo READS | sed "s/,/ /g")
+do
+    cp $f ./
+done
+```
+
+```{bash 'run fastqc', echo=FALSE}
+# run fastqc and place outputs into the report directory
+for r in $(ls *.dat)
+do
+    fastqc -o REPORT_OUTPUT_DIR $r > /dev/null 2>&1
+done
+```
+
+```{bash 'parse fastqc results', echo=FALSE}
+##==== copy fastqc generated zip files from report output directory to job work directory ==
+cp -r REPORT_OUTPUT_DIR/*zip ./
+
+# create a file to store data file paths
+echo "sample_id,file_path" > PWF_file_paths.txt # Pass, Warning, Fail
+echo "sample_id,file_path" > PBQS_file_paths.txt # Per Base Quality Score
+echo "sample_id,file_path" > PSQS_file_paths.txt # Per Sequence Quality Score
+echo "sample_id,file_path" > PSGC_file_paths.txt # Per Sequence GC Content
+echo "sample_id,file_path" > PBSC_file_paths.txt # Per Base Sequence Content
+echo "sample_id,file_path" > PBNC_file_paths.txt # Per Base N Content
+echo "sample_id,file_path" > SDL_file_paths.txt # Sequence Duplication Level
+echo "sample_id,file_path" > SLD_file_paths.txt # Sequence Length Distribution
+echo "sample_id,file_path" > KMC_file_paths.txt # Kmer Content
+
+for i in $(ls *.zip)
+do
+    BASE=$(echo $i | sed 's/\(.*\)\.zip/\1/g')
+    echo $BASE
+    unzip ${BASE}.zip > /dev/null 2>&1
+    
+    ##====== pass,warning,fail (WSF) =============
+    awk '/^>>/ {print}' "$BASE"/fastqc_data.txt | grep -v 'END_MODULE' | sed 's/>>//' > "$BASE"-PWF.txt
+    echo "${BASE},${BASE}-PWF.txt" >> PWF_file_paths.txt
+
+    ##====== per base quality scores (PBQS) ======
+    awk '/^>>Per base sequence quality/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PBQS.txt
+    echo "${BASE},${BASE}-PBQS.txt" >> PBQS_file_paths.txt
+
+    ##====== per sequence quality scores (PSQS)
+    awk '/^>>Per sequence quality scores/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PSQS.txt
+    echo "${BASE},${BASE}-PSQS.txt" >> PSQS_file_paths.txt
+
+    ##====== Per sequence GC content (PSGC)
+    awk '/^>>Per sequence GC content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PSGC.txt
+    echo "${BASE},${BASE}-PSGC.txt" >> PSGC_file_paths.txt
+    
+    ##====== Per Base Sequence Content (PBSC)
+    awk '/^>>Per base sequence content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PBSC.txt
+    echo "${BASE},${BASE}-PBSC.txt" >> PBSC_file_paths.txt
+    
+    ##====== Per Base N Content (PBNC)
+    awk '/^>>Per base N content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PBNC.txt
+    echo "${BASE},${BASE}-PBNC.txt" >> PBNC_file_paths.txt
+    
+    ##====== Sequence Duplication Level (SDL)
+    awk '/^>>Sequence Duplication Levels/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-SDL.txt
+    echo "${BASE},${BASE}-SDL.txt" >> SDL_file_paths.txt
+    
+    ##====== Sequence Length Distribution (SLD)
+    awk '/^>>Sequence Length Distribution/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-SLD.txt
+    echo "${BASE},${BASE}-SLD.txt" >> SLD_file_paths.txt
+    
+    ##====== Kmer Content ============
+    awk '/^>>Kmer Content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-KMC.txt
+    echo "${BASE},${BASE}-KMC.txt" >> KMC_file_paths.txt
+    
+done
+```
+
+
+## Evaluation Overview
+
+```{r 'overview'}
+PWF_file_paths = read.csv('PWF_file_paths.txt',
+                           header = TRUE, stringsAsFactors = FALSE)
+rm('PWF_df')
+for(i in 1:nrow(PWF_file_paths)) {
+  file_path = PWF_file_paths[i,2]
+  pwf_df = read.csv(file_path,
+                     sep='\t', header=FALSE, stringsAsFactors = FALSE)
+  colnames(pwf_df) = c('item', PWF_file_paths[i,1])
+  if (!exists('PWF_df')) {
+    PWF_df = pwf_df
+  } else {
+    PWF_df = cbind(PWF_df, pwf_df[,2,drop=FALSE])
+  }
+}
+```
+
+
+```{r}
+my_icon = c('ok', 'remove', 'star')
+names(my_icon) = c('pass', 'fail', 'warn')
+evaluate_list = list()
+for (i in colnames(PWF_df)[-1]) {
+  evaluate_list[[i]] = formatter(
+      "span", 
+      style = x ~ style("background-color" = ifelse(x =='pass', '#9CD027', ifelse(x == 'fail', '#CC0000', '#FF4E00')), 
+                        "color" = "white",
+                        "width" = "50px",
+                        "float" = "left",
+                        "padding-right" = "5px")
+    )
+}
+
+formattable(PWF_df, evaluate_list)
+```
\ No newline at end of file
b
diff -r 2f4df2be0572 -r d820be692d74 02_fastqc_original_reports.Rmd
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/02_fastqc_original_reports.Rmd Tue Aug 08 12:36:13 2017 -0400
[
@@ -0,0 +1,20 @@
+---
+title: "FastQC original reports"
+output: html_document
+---
+
+```{r 'FastQC original reports', include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = ECHO)
+```
+
+
+Below are links to ***Fastqc*** original html reports.
+
+```{r 'html report links'}
+html_report_list = list()
+html_files = list.files('REPORT_OUTPUT_DIR', pattern = '.*html')
+for (i in html_files) {
+  html_report_list[[i]] = tags$li(tags$a(href=i, i))
+}
+tags$ul(html_report_list)
+```
\ No newline at end of file
b
diff -r 2f4df2be0572 -r d820be692d74 1_per_base_quality_scores.Rmd
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/1_per_base_quality_scores.Rmd Tue Aug 08 12:36:13 2017 -0400
[
@@ -0,0 +1,62 @@
+---
+title: "Per Base Quality Scores"
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = ECHO)
+```
+
+
+## Per Base Quality Scores
+
+```{r}
+PBQS_df = data.frame()
+PBQS_file_paths = read.csv('PBQS_file_paths.txt',
+                           header = TRUE, stringsAsFactors = FALSE)
+for(i in 1:nrow(PBQS_file_paths)) {
+  # file_path = paste0('REPORT_OUTPUT_DIR/', PBQS_file_paths[i,2])
+  file_path = PBQS_file_paths[i,2]
+  pbqs_df = read.csv(file_path,
+                     sep='\t', header=TRUE, stringsAsFactors = FALSE) %>%
+    mutate(Base1=as.numeric(str_split_fixed(X.Base, '-', 2)[,1]),
+           Base2=as.numeric(str_split_fixed(X.Base, '-', 2)[,2])) %>%
+  (function (df) {
+    df1 = select(df, -Base2)
+    df2 = select(df, -Base1) %>% filter(Base2 != '')
+    colnames(df1) = c(colnames(df1)[1:7], 'Base')
+    colnames(df2) = c(colnames(df2)[1:7], 'Base')
+    res = rbind(df1, df2) %>% arrange(Base)
+    return(res)
+  })
+  pbqs_df$sample_id = rep(PBQS_file_paths[i,1], nrow(pbqs_df))
+  PBQS_df = rbind(PBQS_df, pbqs_df)
+}
+```
+
+
+```{r}
+# datatable(PBQS_df)
+max_phred = max(PBQS_df$Mean) + 10
+hchart(PBQS_df, "line", hcaes(x = Base, y = Mean, group = sample_id)) %>%
+  hc_title(
+    text = "Per Base Quality Score"
+  ) %>%
+  hc_yAxis(
+    title = list(text = "Mean Base Quality Score"),
+    min = 0,
+    max = max_phred,
+    plotLines = list(
+      list(label = list(text = "Phred Score = 27"),
+           width = 2,
+           dashStyle = "dash",
+           color = "green",
+           value = 27),
+      list(label = list(text = "Phred Score = 20"),
+           width = 2,
+           color = "red",
+           value = 20)
+    )
+  ) %>% 
+  hc_exporting(enabled = TRUE)
+```
b
diff -r 2f4df2be0572 -r d820be692d74 2_per_base_N_content.Rmd
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/2_per_base_N_content.Rmd Tue Aug 08 12:36:13 2017 -0400
[
@@ -0,0 +1,58 @@
+---
+title: "Per Base N Content"
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = ECHO)
+```
+
+## Per Base N Content
+
+```{r}
+PBNC_df = data.frame()
+PBNC_file_paths = read.csv('PBNC_file_paths.txt',
+                           header = TRUE, stringsAsFactors = FALSE)
+for(i in 1:nrow(PBNC_file_paths)) {
+  # file_path = paste0('REPORT_OUTPUT_DIR/', PBNC_file_paths[i,2])
+  file_path = PBNC_file_paths[i,2]
+  pbnc_df = read.csv(file_path,
+                     sep='\t', header=TRUE, stringsAsFactors = FALSE) %>%
+    mutate(Base1=as.numeric(str_split_fixed(X.Base, '-', 2)[,1]),
+           Base2=as.numeric(str_split_fixed(X.Base, '-', 2)[,2])) %>%
+  (function (df) {
+    df1 = select(df, -Base2)
+    df2 = select(df, -Base1) %>% filter(Base2 != '')
+    colnames(df1) = c(colnames(df1)[1:2], 'Base')
+    colnames(df2) = c(colnames(df2)[1:2], 'Base')
+    res = rbind(df1, df2) %>% arrange(Base)
+    return(res)
+  })
+  pbnc_df$sample_id = rep(PBNC_file_paths[i,1], nrow(pbnc_df))
+  PBNC_df = rbind(PBNC_df, pbnc_df)
+}
+```
+
+
+```{r}
+PBNC_df$N.Count = PBNC_df$N.Count * 100
+max_phred = max(PBNC_df$N.Count) + 5
+hchart(PBNC_df, "line", hcaes(x = as.character(Base), y = N.Count, group = sample_id)) %>%
+  hc_title(
+    text = "Per Base N Content"
+  ) %>%
+  hc_xAxis(
+    title = list(text = "Base Position")
+  ) %>%
+  hc_yAxis(
+    title = list(text = "N %"),
+    plotLines = list(
+      list(label = list(text = "N = 5%"),
+           width = 2,
+           dashStyle = "dash",
+           color = "red",
+           value = 5)
+    )
+  ) %>% 
+  hc_exporting(enabled = TRUE)
+```
b
diff -r 2f4df2be0572 -r d820be692d74 3_per_sequence_quality_scores.Rmd
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/3_per_sequence_quality_scores.Rmd Tue Aug 08 12:36:13 2017 -0400
[
@@ -0,0 +1,50 @@
+---
+title: "Per Sequence Quality Scores"
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = ECHO)
+```
+
+## Per Sequence Quality Scores
+
+```{r}
+PSQS_df = data.frame()
+PSQS_file_paths = read.csv('PSQS_file_paths.txt', 
+                           header = TRUE, stringsAsFactors = FALSE)
+for(i in 1:nrow(PSQS_file_paths)) {
+  # file_path = paste0('REPORT_OUTPUT_DIR/', PSQS_file_paths[i,2])
+  file_path = PSQS_file_paths[i,2]
+  psqs_df = read.csv(file_path,
+                     sep='\t', header=TRUE, stringsAsFactors = FALSE) 
+  psqs_df$sample_id = rep(PSQS_file_paths[i,1], nrow(psqs_df))
+  PSQS_df = rbind(PSQS_df, psqs_df)
+}
+```
+
+
+```{r}
+max_phred = max(PSQS_df$X.Quality) + 5
+hchart(PSQS_df, "line", hcaes(x = X.Quality, y = Count, group = sample_id)) %>%
+  hc_title(
+    text = "Per Sequence Quality Score"
+  ) %>%
+  hc_xAxis(
+    title = list(text = "Mean Sequence Quality Score"),
+    min = 0,
+    max = max_phred,
+    plotLines = list(
+      list(label = list(text = "Phred Score = 27"),
+           width = 2,
+           dashStyle = "dash",
+           color = "green",
+           value = 27),
+      list(label = list(text = "Phred Score = 20"),
+           width = 2,
+           color = "red",
+           value = 20)
+    )
+  ) %>% 
+  hc_exporting(enabled = TRUE)
+```
b
diff -r 2f4df2be0572 -r d820be692d74 4_per_sequence_GC_content.Rmd
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/4_per_sequence_GC_content.Rmd Tue Aug 08 12:36:13 2017 -0400
[
@@ -0,0 +1,38 @@
+---
+title: "Per Sequence GC Content"
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = ECHO)
+```
+
+## Per Sequence GC Content
+
+
+```{r}
+PSGC_df = data.frame()
+PSGC_file_paths = read.csv('PSGC_file_paths.txt', 
+                           header = TRUE, stringsAsFactors = FALSE)
+for(i in 1:nrow(PSGC_file_paths)) {
+  # file_path = paste0('REPORT_OUTPUT_DIR/', PSGC_file_paths[i,2])
+  file_path = PSGC_file_paths[i,2]
+  psgc_df = read.csv(file_path,
+                     sep='\t', header=TRUE, stringsAsFactors = FALSE) 
+  psgc_df$sample_id = rep(PSGC_file_paths[i,1], nrow(psgc_df))
+  PSGC_df = rbind(PSGC_df, psgc_df)
+}
+```
+
+
+```{r}
+max_phred = max(PSGC_df$Count) + 5
+hchart(PSGC_df, "line", hcaes(x = X.GC.Content, y = Count, group = sample_id)) %>%
+  hc_title(
+    text = "Per Sequence GC Content"
+  ) %>%
+  hc_xAxis(
+    title = list(text = "% GC")
+  ) %>%
+  hc_exporting(enabled = TRUE)
+```
b
diff -r 2f4df2be0572 -r d820be692d74 5_per_base_sequence_content.Rmd
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/5_per_base_sequence_content.Rmd Tue Aug 08 12:36:13 2017 -0400
[
@@ -0,0 +1,45 @@
+---
+title: "Per Base Sequence Content"
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = ECHO)
+```
+
+## Per Base Sequence Content
+
+```{r}
+PBSC_df = data.frame()
+PBSC_file_paths = read.csv('PBSC_file_paths.txt',
+                           header = TRUE, stringsAsFactors = FALSE)
+for(i in 1:nrow(PBSC_file_paths)) {
+  # file_path = paste0('REPORT_OUTPUT_DIR/', PBSC_file_paths[i,2])
+  file_path = PBSC_file_paths[i,2]
+  pbsc_df = read.csv(file_path,
+                     sep='\t', header=TRUE, stringsAsFactors = FALSE) %>%
+    mutate(Base1=as.numeric(str_split_fixed(X.Base, '-', 2)[,1]),
+           Base2=as.numeric(str_split_fixed(X.Base, '-', 2)[,2])) %>%
+  (function (df) {
+    df1 = select(df, -Base2)
+    df2 = select(df, -Base1) %>% filter(Base2 != '')
+    colnames(df1) = c(colnames(df1)[1:5], 'Base')
+    colnames(df2) = c(colnames(df2)[1:5], 'Base')
+    res = rbind(df1, df2) %>% arrange(Base)
+    return(res)
+  })
+  pbsc_df$sample_id = rep(PBSC_file_paths[i,1], nrow(pbsc_df))
+  PBSC_df = rbind(PBSC_df, pbsc_df)
+}
+```
+
+
+```{r out.width="100%"}
+PBSC_df_2 = select(PBSC_df, -X.Base) %>%
+  melt(id = c('Base', 'sample_id'), value.name = 'base_percentage')
+p = ggplot(data = PBSC_df_2, aes(x = Base, y = base_percentage, group = variable, color = variable)) +
+  geom_line() +
+  facet_wrap(~ sample_id)
+ggplotly(p)
+```
+
b
diff -r 2f4df2be0572 -r d820be692d74 _site.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/_site.yml Tue Aug 08 12:36:13 2017 -0400
b
@@ -0,0 +1,29 @@
+name: "FastQC Website"
+output_dir: "my_site"
+navbar:
+    title: "FastQC"
+    type: inverse
+    left:
+        - text: "Home"
+          icon: fa-home
+          href: index.html
+        - text: "Evaluation Overview"
+          href: 01_evaluation_overview.html
+        - text: "Evaluation Items"
+          menu:
+            - text: "Per Base Quality Scores"
+              href: 1_per_base_quality_scores.html
+            - text: "Per Base N Content"
+              href: 2_per_base_N_content.html
+            - text: "Per Sequence Quality Scores"
+              href: 3_per_sequence_quality_scores.html
+            - text: "Per Sequence GC Content"
+              href: 4_per_sequence_GC_content.html
+            - text: "Per Base Sequence Content"
+              href: 5_per_base_sequence_content.html
+        - text: "Original FastQC Reports"
+          href: 02_fastqc_original_reports.html
+output:
+  html_document:
+    theme: cosmo
+    highlight: textmate
\ No newline at end of file
b
diff -r 2f4df2be0572 -r d820be692d74 fastqc_site.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqc_site.xml Tue Aug 08 12:36:13 2017 -0400
[
@@ -0,0 +1,124 @@
+<tool id="fastqc_site" name="Fastqc Site" version="1.0.0">
+    <requirements>
+        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.2">r-rmarkdown</requirement>
+        <requirement type="package" version="1.8.4">r-plyr</requirement>
+        <requirement type="package" version="1.1.0">r-stringr</requirement>
+        <requirement type="package" version="0.5.0">r-highcharter</requirement>
+        <requirement type="package" version="0.2">r-dt</requirement>
+        <requirement type="package" version="1.4.2">r-reshape2</requirement>
+        <requirement type="package" version="4.5.6">r-plotly</requirement>
+        <requirement type="package" version="0.2.0.1">r-formattable</requirement>
+        <requirement type="package" version="0.3.5">r-htmltools</requirement>
+        <requirement type="package" version="0.11.5">fastqc</requirement>
+    </requirements>
+    <description>
+        Implements FastQC analysis and display results in R Markdown website.
+    </description>
+    <stdio>
+        <regex match="Execution halted"
+               source="both"
+               level="fatal"
+               description="Execution halted." />
+        <regex match="Error in"
+               source="both"
+               level="fatal"
+               description="An undefined error occured, please check your intput carefully and contact your administrator." />
+        <regex match="Fatal error"
+               source="both"
+               level="fatal"
+               description="An undefined error occured, please check your intput carefully and contact your administrator." />
+    </stdio>
+    <command>
+        <![CDATA[
+
+        Rscript '${__tool_directory__}/fastqc_site_render.R'
+
+            ## 1. input data
+            -r $reads
+            -e $echo
+
+            ## 2. output report and report site directory
+     -o $fastqc_site
+     -d $fastqc_site.files_path
+
+     ## 3. Rmd templates sitting in the tool directory
+
+         ## _site.yml and index.Rmd template files
+                -s '${__tool_directory__}/_site.yml'
+                -i '${__tool_directory__}/index.Rmd'
+
+                ## other Rmd body template files
+         -p  '${__tool_directory__}/01_evaluation_overview.Rmd'
+         -a  '${__tool_directory__}/02_fastqc_original_reports.Rmd'
+         -b  '${__tool_directory__}/1_per_base_quality_scores.Rmd'
+         -c  '${__tool_directory__}/2_per_base_N_content.Rmd'
+         -f  '${__tool_directory__}/3_per_sequence_quality_scores.Rmd'
+         -g  '${__tool_directory__}/4_per_sequence_GC_content.Rmd'
+         -h  '${__tool_directory__}/5_per_base_sequence_content.Rmd'
+
+        ]]>
+    </command>
+    <inputs>
+        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" multiple="true" name="reads" type="data" label="Short reads data from history" />
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
+    </inputs>
+    <outputs>
+        <data format="html" name="fastqc_site" label="fastqc site" />
+    </outputs>
+    <citations>
+        <citation type="bibtex">
+            @misc{bioinformatics2014fastqc,
+            title={FastQC},
+            author={Bioinformatics, Babraham},
+            year={2014}
+            }
+        </citation>
+        <citation type="bibtex">
+            @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">
+            @book{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        </citation>
+        <citation type="bibtex">
+            @misc{plotly2017,
+            title = {plotly: Create Interactive Web Graphics via 'plotly.js'},
+            author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy},
+            year = {2017},
+            note = {R package version 4.6.0},
+            url = {https://CRAN.R-project.org/package=plotly},
+            }
+        </citation>
+        <citation type="bibtex">
+            @misc{highcharter2017,
+            title = {highcharter: A Wrapper for the 'Highcharts' Library},
+            author = {Joshua Kunst},
+            year = {2017},
+            note = {R package version 0.5.0},
+            url = {https://CRAN.R-project.org/package=highcharter},
+            }
+        </citation>
+        <citation type="bibtex">
+            @misc{formattable2016,
+            title = {formattable: Create 'Formattable' Data Structures},
+            author = {Kun Ren and Kenton Russell},
+            year = {2016},
+            note = {R package version 0.2.0.1},
+            url = {https://CRAN.R-project.org/package=formattable},
+            }
+        </citation>
+    </citations>
+</tool>
\ No newline at end of file
b
diff -r 2f4df2be0572 -r d820be692d74 fastqc_site_render.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqc_site_render.R Tue Aug 08 12:36:13 2017 -0400
b
@@ -0,0 +1,195 @@
+##======= Handle arguments from command line ========
+# setup R error handline to go to stderr
+options(show.error.messages=FALSE,
+        error=function(){
+          cat(geterrmessage(), file=stderr())
+          quit("no", 1, F)
+        })
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+# suppress warning
+options(warn = -1)
+
+options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
+args = commandArgs(trailingOnly=TRUE)
+
+suppressPackageStartupMessages({
+  library(getopt)
+  library(tools)
+})
+
+# 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.
+spec_list=list()
+
+##------- 1. input data ---------------------
+spec_list$READS = c('reads', 'r', '1', 'character')
+spec_list$ECHO = c('echo', 'e', '1', 'character')
+
+##--------2. output report and report site directory --------------
+spec_list$FASTQC_SITE = c('fastqc_site', 'o', '1', 'character')
+spec_list$FASTQC_SITE_DIR = c('fastqc_site_dir', 'd', '1', 'character')
+
+##--------3. Rmd templates sitting in the tool directory ----------
+
+    ## _site.yml and index.Rmd files
+    spec_list$SITE_YML = c('site_yml', 's', 1, 'character')
+    spec_list$INDEX_Rmd = c('index_rmd', 'i', 1, 'character')
+    
+    ## other Rmd body template files
+    spec_list$x01 = c('x01_evaluation_overview', 'p', '1', 'character')
+    spec_list$x02 = c('x02_fastqc_original_reports', 'a', '1', 'character')
+    spec_list$x1 = c('x1_per_base_quality_scores', 'b', '1', 'character')
+    spec_list$x2 = c('x2_per_base_N_content', 'c', '1', 'character')
+    spec_list$x3 = c('x3_per_sequence_quality_scores', 'f', '1', 'character')
+    spec_list$x4 = c('x4_per_sequence_GC_content', 'g', '1', 'character')
+    spec_list$x5 = c('x5_per_base_sequence_content', 'h', '1', 'character')
+
+##------------------------------------------------------------------
+
+spec = t(as.data.frame(spec_list))
+opt = getopt(spec)
+# arguments are accessed by long flag name (the first column in the spec matrix)
+#                        NOT by element name in the spec_list
+# example: opt$help, opt$expression_file
+##====== End of arguments handling ==========
+
+#------ Load libraries ---------
+library(rmarkdown)
+library(plyr)
+library(stringr)
+library(dplyr)
+library(highcharter)
+library(DT)
+library(reshape2)
+library(plotly)
+library(formattable)
+library(htmltools)
+
+
+#----- 1. create the report directory ------------------------
+paste0('mkdir -p ', opt$fastqc_site_dir) %>%
+  system()
+
+#----- 2. generate Rmd files with Rmd templates --------------
+#   a. templates without placeholder variables:
+#         copy templates from tool directory to the working directory.
+#   b. templates with placeholder variables:
+#         substitute variables with user input values and place them in the working directory.
+
+
+    #----- Copy index.Rmd and _site.yml files to job working direcotry -----
+    file.copy(opt$index_rmd, 'index.Rmd', recursive=TRUE)
+    file.copy(opt$site_yml, '_site.yml', recursive=TRUE)
+    #---------------------------------------------------------
+    
+    #----- 01_evaluation_overview.Rmd -----------------------
+    readLines(opt$x01_evaluation_overview) %>%
+      (function(x) {
+        gsub('ECHO', opt$echo, x)
+      }) %>%
+      (function(x) {
+        gsub('READS', opt$reads, x)
+      }) %>%
+      (function(x) {
+        gsub('REPORT_OUTPUT_DIR', opt$fastqc_site_dir, x)
+      }) %>%
+      (function(x) {
+        fileConn = file('01_evaluation_overview.Rmd')
+        writeLines(x, con=fileConn)
+        close(fileConn)
+      })
+    
+    #----- 1_per_base_quality_scores.Rmd --------------------
+    readLines(opt$x1_per_base_quality_scores) %>%
+      (function(x) {
+        gsub('ECHO', opt$echo, x)
+      }) %>%
+      (function(x) {
+        fileConn = file('1_per_base_quality_scores.Rmd')
+        writeLines(x, con=fileConn)
+        close(fileConn)
+      })
+    
+    #----- 2_per_base_N_content.Rmd -------------------------
+    readLines(opt$x2_per_base_N_content) %>%
+      (function(x) {
+        gsub('ECHO', opt$echo, x)
+      }) %>%
+      (function(x) {
+        fileConn = file('2_per_base_N_content.Rmd')
+        writeLines(x, con=fileConn)
+        close(fileConn)
+      })
+    
+    #----- 3_per_sequence_quality_scores.Rmd ----------------
+    readLines(opt$x3_per_sequence_quality_scores) %>%
+      (function(x) {
+        gsub('ECHO', opt$echo, x)
+      }) %>%
+      (function(x) {
+        fileConn = file('3_per_sequence_quality_scores.Rmd')
+        writeLines(x, con=fileConn)
+        close(fileConn)
+      })
+    
+    
+    #----- 4_per_sequence_GC_content.Rmd --------------------
+    readLines(opt$x4_per_sequence_GC_content) %>%
+      (function(x) {
+        gsub('ECHO', opt$echo, x)
+      }) %>%
+      (function(x) {
+        fileConn = file('4_per_sequence_GC_content.Rmd')
+        writeLines(x, con=fileConn)
+        close(fileConn)
+      })
+    
+    
+    #----- 5_per_base_sequence_content.Rmd ------------------
+    readLines(opt$x5_per_base_sequence_content) %>%
+      (function(x) {
+        gsub('ECHO', opt$echo, x)
+      }) %>%
+      (function(x) {
+        fileConn = file('5_per_base_sequence_content.Rmd')
+        writeLines(x, con=fileConn)
+        close(fileConn)
+      })
+
+    #----- 02_fastqc_original_reports.Rmd -------------------
+    readLines(opt$x02_fastqc_original_reports) %>%
+      (function(x) {
+        gsub('ECHO', opt$echo, x)
+      }) %>%
+      (function(x) {
+        gsub('REPORT_OUTPUT_DIR', opt$fastqc_site_dir, x)
+      }) %>%
+      (function(x) {
+        fileConn = file('02_fastqc_original_reports.Rmd')
+        writeLines(x, con=fileConn)
+        close(fileConn)
+      })
+
+
+
+#------ 3. render all Rmd files with render_site() --------
+render_site()    
+
+
+#-------4. manipulate outputs -----------------------------
+#   a. copy index.html to the report output path
+#   b. copy all files in 'my_site' to the report output directory
+file.copy('my_site/index.html', opt$fastqc_site, recursive=TRUE)
+paste0('cp -r my_site/* ', opt$fastqc_site_dir) %>%
+  system()
+
+
b
diff -r 2f4df2be0572 -r d820be692d74 index.Rmd
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/index.Rmd Tue Aug 08 12:36:13 2017 -0400
b
@@ -0,0 +1,20 @@
+---
+title: "FastQC Report"
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+
+
+## References
+
+* Andrews, Simon. "FastQC: a quality control tool for high throughput sequence data." (2010): 175-176.
+* Goecks, Jeremy, Anton Nekrutenko, and James Taylor. "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences." Genome biology 11.8 (2010): R86.
+* Afgan, Enis, et al. "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update." Nucleic acids research (2016): gkw343.
+* Highcharts. https://www.highcharts.com/. (access by May 26, 2017).
+* R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
+* Joshua Kunst (2017). highcharter: A Wrapper for the 'Highcharts' Library. R package version 0.5.0. https://CRAN.R-project.org/package=highcharter
+* Carson Sievert, Chris Parmer, Toby Hocking, Scott Chamberlain, Karthik Ram, Marianne Corvellec and Pedro Despouy (2017). plotly: Create Interactive Web Graphics via 'plotly.js'. R package version 4.6.0. https://CRAN.R-project.org/package=plotly
b
diff -r 2f4df2be0572 -r d820be692d74 wgcna_construct_network.Rmd
--- a/wgcna_construct_network.Rmd Tue Aug 08 12:35:11 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
@@ -1,178 +0,0 @@
----
-title: 'WGCNA: construct network'
-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
-)
-```
-
-# Import workspace 
-
-This step imports workspace from the **WGCNA: preprocessing** step.
-
-```{r}
-fcp = file.copy("PREPROCESSING_WORKSPACE", "deseq.RData")
-load("deseq.RData")
-```
-
-
-# Processing outliers {.tabset}
-
-## Before removing outliers
-
-```{r}
-plot(sampleTree, main = "Sample clustering to detect outliers", sub="", xlab="", cex.lab = 1.5,
-     cex.axis = 1, cex.main = 1, cex = 0.5)
-if(!is.na(HEIGHT_CUT)) {
-  # plot a line to show the cut
-  abline(h = HEIGHT_CUT, col = "red")
-  # determine cluster under the line
-  clust = cutreeStatic(sampleTree, cutHeight = HEIGHT_CUT, minSize = 10)
-  keepSamples = (clust==1)
-  expression_data = expression_data[keepSamples, ]
-}
-```
-
-## After removing outliers
-
-```{r}
-sampleTree = hclust(dist(expression_data), method = "average");
-plot(sampleTree, main = "Sample clustering to detect outliers", sub="", xlab="",
-     cex.axis = 1, cex.main = 1, cex = 0.5)
-```
-
-
-# Trait data {.tabeset}
-
-If trait data is provided, the first 100 rows from the data will be displayed here. A plot consisting of sample cluster dendrogram and trait heatmap will also be gerenated.
-
-## Trait data table
-
-```{r}
-trait_data = data.frame()
-if ("TRAIT_DATA" != 'None') {
-  trait_data = read.csv("TRAIT_DATA", header = TRUE, row.names = 1)
-  # form a data frame analogous to expression data that will hold the traits.
-  sample_names = rownames(expression_data)
-  trait_rows = match(sample_names, rownames(trait_data))
-  trait_data = trait_data[trait_rows, ]
-  datatable(head(trait_data, 100), style="bootstrap", filter = 'top',
-          class="table-condensed", options = list(dom = 'tp', scrollX = TRUE))
-}
-```
-
-## Dendrogram and heatmap
-
-```{r fig.align='center', fig.width=8, fig.height=9}
-if (nrow(trait_data) != 0) {
-  traitColors = numbers2colors(trait_data, signed = FALSE)
-  plotDendroAndColors(sampleTree, traitColors,
-                      groupLabels = names(trait_data),
-                      main = "Sample dendrogram and trait heatmap",
-                      cex.dendroLabels = 0.5)
-}
-```
-
-
-# The thresholding power
-
-```{r}
-powers = c(1:10, seq(12, 20, 2))
-soft_threshold = pickSoftThreshold(expression_data, powerVector = powers, verbose = 5)
-```
-
-```{r fig.align='center'}
-par(mfrow=c(1,2))
-plot(soft_threshold$fitIndices[,1], -sign(soft_threshold$fitIndices[,3])*soft_threshold$fitIndices[,2],
-     xlab="Soft Threshold (power)",
-     ylab="Scale Free Topology Model Fit,signed R^2",type="n",
-     main = paste("Scale independence"),
-     cex.lab = 0.5);
-text(soft_threshold$fitIndices[,1], -sign(soft_threshold$fitIndices[,3])*soft_threshold$fitIndices[,2],
-     labels=powers,cex=0.5,col="red");
-
-# calculate soft threshold power
-y = -sign(soft_threshold$fitIndices[,3])*soft_threshold$fitIndices[,2]
-r2_cutoff = 0.9
-for(i in 1:length(powers)) {
-  if(y[i] > r2_cutoff) {
-    soft_threshold_power = soft_threshold$fitIndices[,1][i]
-    r2_cutoff_new = y[i]
-    break
-  } 
-  soft_threshold_power = soft_threshold$fitIndices[,1][length(powers)]
-}
-abline(h=r2_cutoff, col="red")
-abline(v=soft_threshold_power, col="blue")
-text(soft_threshold_power+1, r2_cutoff-0.1, 
-     paste0('R^2 cutoff = ', round(r2_cutoff_new,2)),
-     cex = 0.5, col = "red")
-
-plot(soft_threshold$fitIndices[,1], soft_threshold$fitIndices[,5],
-     xlab="Soft Threshold (power)",ylab="Mean Connectivity", type="n",
-     main = paste("Mean connectivity"),
-     cex.lab = 0.5)
-text(soft_threshold$fitIndices[,1], soft_threshold$fitIndices[,5], labels=powers, cex=0.5,col="red")
-par(mfrow=c(1,1))
-```
-
-
-# Construct network 
-
-The gene network is constructed based on **soft threshold power = `r soft_threshold_power`**
-
-```{r}
-gene_network = blockwiseModules(expression_data, power = soft_threshold_power,
-                                TOMType = "unsigned", minModuleSize = 30,
-                                reassignThreshold = 0, mergeCutHeight = 0.25,
-                                numericLabels = TRUE, pamRespectsDendro = FALSE,
-                                verbose = 3)
-```
-
-
-# Gene modules {.tabset}
-
-## Idenfity gene modules 
-
-```{r}
-modules = table(gene_network$colors)
-n_modules = length(modules) - 1
-module_size_upper = modules[2]
-module_size_lower = modules[length(modules)]
-
-module_table = data.frame(model_label = c(0, 1:n_modules),
-                          gene_size = as.vector(modules))
-datatable(t(module_table))
-```
-
-The results above indicates that there are **`r n_modules` gene modules**, labeled 1 through `r length(n_modules)` in order of descending size. The largest module has **`r module_size_upper` genes**, and the smallest module has **`r module_size_lower` genes**. The label 0 is reserved for genes outside of all modules. 
-
-
-## Dendrogram and module plot
-
-```{r}
-# Convert labels to colors for plotting
-module_colors = labels2colors(gene_network$colors)
-# Plot the dendrogram and the module colors underneath
-plotDendroAndColors(gene_network$dendrograms[[1]], module_colors[gene_network$blockGenes[[1]]],
-                    "Module colors",
-                    dendroLabels = FALSE, hang = 0.03,
-                    addGuide = TRUE, guideHang = 0.05)
-```
-
-
-```{r echo=FALSE}
-# save workspace
-rm("opt")
-save(list=ls(all.names = TRUE), file='CONSTRUCT_NETWORK_WORKSPACE')
-```
-
-
b
diff -r 2f4df2be0572 -r d820be692d74 wgcna_construct_network.xml
--- a/wgcna_construct_network.xml Tue Aug 08 12:35:11 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
@@ -1,105 +0,0 @@
-<tool id="wgcna_construct_network" name="WGCNA: construct network" version="1.0.0">
-    <requirements>
-        <requirement type="package" version="1.20.0">r-getopt</requirement>
-        <requirement type="package" version="1.2">r-rmarkdown</requirement>
-        <requirement type="package" version="1.8.4">r-plyr</requirement>
-        <requirement type="package" version="0.4.0">r-highcharter</requirement>
-        <requirement type="package" version="0.2">r-dt</requirement>
-        <requirement type="package" version="0.3.5">r-htmltools</requirement>
-        <requirement type="package" version="1.51">r-wgcna</requirement>
-    </requirements>
-    <description>
-        Construct gene network.
-    </description>
-    <stdio>
-        <regex match="Execution halted"
-               source="both"
-               level="fatal"
-               description="Execution halted." />
-        <regex match="Error in"
-               source="both"
-               level="fatal"
-               description="An undefined error occured, please check your intput carefully and contact your administrator." />
-        <regex match="Fatal error"
-               source="both"
-               level="fatal"
-               description="An undefined error occured, please check your intput carefully and contact your administrator." />
-    </stdio>
-    <command>
-        <![CDATA[
-
-        Rscript '${__tool_directory__}/wgcna_construct_network_render.R'
-
-            ## 1. input data
-            -e $echo
-            -w $preprocessing_workspace
-            -h '$height_cut'
-            -t $trait_data
-
-
-
-            ## 2. output report and report site directory
-     -o $wgcna_construct_network
-     -d $wgcna_construct_network.files_path
-     -W $construct_network_workspace
-
-
-     ## 3. Rmd templates in the tool directory
-
-         ## _site.yml and index.Rmd template files
-                -M '${__tool_directory__}/wgcna_construct_network.Rmd'
-
-
-
-        ]]>
-    </command>
-    <inputs>
-        <param type="data" name="preprocessing_workspace" format="rdata" optional="false"
-               label="R workspace from WGCNA: preprocessing" />
-        <param type="float" name="height_cut" optional="true" label="Height"
-               help="Refer to the sample clustering plot from WGCNA: preprocessing and choose a height cut that will
-                    remove outliers. If there is not outlier, leave this field blank." />
-        <param type="data" name="trait_data" format="csv" optional="true"
-               label="Trait data"
-               help="If trait data is provided, a plot consisting of sample clustering and trait heatmap will
-                    be generated. This field is optional. "/>
-
-        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
-    </inputs>
-    <outputs>
-        <data name="wgcna_construct_network" format="html" label="WGCNA: construct_network" />
-        <data name="construct_network_workspace" format="rdata" label="R workspace: WGCNA construct_network" />
-    </outputs>
-    <citations>
-        <citation type="bibtex">
-            @article{langfelder2008wgcna,
-            title={WGCNA: an R package for weighted correlation network analysis},
-            author={Langfelder, Peter and Horvath, Steve},
-            journal={BMC bioinformatics},
-            volume={9},
-            number={1},
-            pages={559},
-            year={2008},
-            publisher={BioMed Central}
-            }
-        </citation>
-        <citation type="bibtex">
-            @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">
-            @book{xie2015dynamic,
-            title={Dynamic Documents with R and knitr},
-            author={Xie, Yihui},
-            volume={29},
-            year={2015},
-            publisher={CRC Press}
-            }
-        </citation>
-    </citations>
-</tool>
\ No newline at end of file
b
diff -r 2f4df2be0572 -r d820be692d74 wgcna_construct_network_render.R
--- a/wgcna_construct_network_render.R Tue Aug 08 12:35:11 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,112 +0,0 @@
-##======= Handle arguments from command line ========
-# setup R error handline to go to stderr
-options(show.error.messages=FALSE,
-        error=function(){
-          cat(geterrmessage(), file=stderr())
-          quit("no", 1, F)
-        })
-
-# we need that to not crash galaxy with an UTF8 error on German LC settings.
-loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
-
-# suppress warning
-options(warn = -1)
-
-options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
-args = commandArgs(trailingOnly=TRUE)
-
-suppressPackageStartupMessages({
-  library(getopt)
-  library(tools)
-})
-
-# 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.
-spec_list=list()
-
-##------- 1. input data ---------------------
-spec_list$ECHO = c('echo', 'e', '1', 'character')
-spec_list$PREPROCESSING_WORKSPACE = c('preprocessing_workspace', 'w', '1', 'character')
-spec_list$HEIGHT_CUT = c('height_cut', 'h', '2', 'double')
-spec_list$TRAIT_DATA = c('trait_data', 't', '2', 'character')
-
-
-##--------2. output report and report site directory --------------
-spec_list$OUTPUT_HTML = c('wgcna_construct_network_html', 'o', '1', 'character')
-spec_list$OUTPUT_DIR = c('wgcna_construct_network_dir', 'd', '1', 'character')
-spec_list$CONSTRUCT_NETWORK_WORKSPACE = c('construct_network_workspace', 'W', '1', 'character')
-
-
-##--------3. Rmd templates in the tool directory ----------
-
-spec_list$WGCNA_PREPROCESSING_RMD = c('wgcna_construct_network_rmd', 'M', '1', 'character')
-
-
-
-##------------------------------------------------------------------
-
-spec = t(as.data.frame(spec_list))
-opt = getopt(spec)
-# arguments are accessed by long flag name (the first column in the spec matrix)
-#                        NOT by element name in the spec_list
-# example: opt$help, opt$expression_file
-##====== End of arguments handling ==========
-
-#------ Load libraries ---------
-library(rmarkdown)
-library(WGCNA)
-library(DT)
-library(htmltools)
-library(ggplot2)
-
-
-#----- 1. create the report directory ------------------------
-system(paste0('mkdir -p ', opt$wgcna_construct_network_dir))
-
-
-#----- 2. generate Rmd files with Rmd templates --------------
-#   a. templates without placeholder variables:
-#         copy templates from tool directory to the working directory.
-#   b. templates with placeholder variables:
-#         substitute variables with user input values and place them in the working directory.
-
-
-#----- 01 wgcna_construct_network.Rmd -----------------------
-readLines(opt$wgcna_construct_network_rmd) %>%
-  (function(x) {
-    gsub('ECHO', opt$echo, x)
-  }) %>%
-  (function(x) {
-    gsub('PREPROCESSING_WORKSPACE', opt$preprocessing_workspace, x)
-  }) %>%
-  (function(x) {
-    gsub('HEIGHT_CUT', opt$height_cut, x)
-  }) %>%
-  (function(x) {
-    gsub('TRAIT_DATA', opt$trait_data, x)
-  }) %>%
-  (function(x) {
-    gsub('OUTPUT_DIR', opt$wgcna_construct_network_dir, x)
-  }) %>%
-  (function(x) {
-    gsub('CONSTRUCT_NETWORK_WORKSPACE', opt$construct_network_workspace, x)
-  }) %>%
-  (function(x) {
-    fileConn = file('wgcna_construct_network.Rmd')
-    writeLines(x, con=fileConn)
-    close(fileConn)
-  })
-
-
-#------ 3. render all Rmd files --------
-render('wgcna_construct_network.Rmd', output_file = opt$wgcna_construct_network_html)
-
-#-------4. manipulate outputs -----------------------------
-
-
b
diff -r 2f4df2be0572 -r d820be692d74 wgcna_eigengene_visualization.Rmd
--- a/wgcna_eigengene_visualization.Rmd Tue Aug 08 12:35:11 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
@@ -1,121 +0,0 @@
----
-title: 'WGCNA: eigengene visualization'
-output:
-    html_document:
-      number_sections: true
-      toc: true
-      theme: cosmo
-      highlight: tango
----
-
-```{r setup, include=FALSE, warning=FALSE, message=FALSE}
-knitr::opts_chunk$set(
-  echo = ECHO
-)
-```
-
-# Import workspace 
-
-This step imports workspace from the **WGCNA: construct network** step.
-
-```{r}
-fcp = file.copy("CONSTRUCT_NETWORK_WORKSPACE", "deseq.RData")
-load("deseq.RData")
-```
-
-
-# Gene modules {.tabset}
-
-```{r}
-if(!is.na(SOFT_THRESHOLD_POWER)) soft_threshold_power = SOFT_THRESHOLD_POWER
-```
-
-## Identify gene modules
-
-The gene network is constructed based on **soft threshold power = `r soft_threshold_power`**
-
-```{r}
-gene_network = blockwiseModules(expression_data, power = soft_threshold_power,
-                                TOMType = "unsigned", minModuleSize = 30,
-                                reassignThreshold = 0, mergeCutHeight = 0.25,
-                                numericLabels = TRUE, pamRespectsDendro = FALSE,
-                                verbose = 3)
-```
-
-
-```{r}
-modules = table(gene_network$colors)
-n_modules = length(modules) - 1
-module_size_upper = modules[2]
-module_size_lower = modules[length(modules)]
-
-module_table = data.frame(model_label = c(0, 1:n_modules),
-                          gene_size = as.vector(modules))
-datatable(t(module_table))
-```
-
-The results above indicates that there are **`r n_modules` gene modules**, labeled 1 through `r length(n_modules)` in order of descending size. The largest module has **`r module_size_upper` genes**, and the smallest module has **`r module_size_lower` genes**. The label 0 is reserved for genes outside of all modules. 
-
-
-## Dendrogram and module plot
-
-```{r}
-# Convert labels to colors for plotting
-module_colors = labels2colors(gene_network$colors)
-# Plot the dendrogram and the module colors underneath
-plotDendroAndColors(gene_network$dendrograms[[1]], module_colors[gene_network$blockGenes[[1]]],
-                    "Module colors",
-                    dendroLabels = FALSE, hang = 0.03,
-                    addGuide = TRUE, guideHang = 0.05)
-```
-
-
-# Gene module correlation
-
-We can calculate eigengenes and use them as representative profiles to quantify similarity of found gene modules.
-
-```{r}
-n_genes = ncol(expression_data)
-n_samples = nrow(expression_data)
-```
-
-```{r}
-diss_tom = 1-TOMsimilarityFromExpr(expression_data, power = soft_threshold_power)
-set.seed(123)
-select_genes = sample(n_genes, size = PLOT_GENES)
-select_diss_tom = diss_tom[select_genes, select_genes]
-
-# calculate gene tree on selected genes
-select_gene_tree = hclust(as.dist(select_diss_tom), method = 'average')
-select_module_colors = module_colors[select_genes]
-
-# transform diss_tom with a power to make moderately strong connections more visiable in the heatmap.
-plot_diss_tom = select_diss_tom^7
-# set diagonal to NA for a nicer plot
-diag(plot_diss_tom) = NA
-```
-
-
-```{r fig.align='center'}
-TOMplot(plot_diss_tom, select_gene_tree, select_module_colors, main = "Network heatmap")
-```
-
-
-# Eigengene visualization {.tabset}
-
-## Eigengene dendrogram
-
-```{r fig.align='center'}
-module_eigengenes = moduleEigengenes(expression_data, module_colors)$eigengenes
-plotEigengeneNetworks(module_eigengenes, "Eigengene dendrogram", 
-                      plotHeatmaps = FALSE)
-```
-
-## Eigengene adjacency heatmap
-
-```{r fig.align='center'}
-plotEigengeneNetworks(module_eigengenes, "Eigengene adjacency heatmap", 
-                      marHeatmap = c(2, 3, 2, 2),
-                      plotDendrograms = FALSE, xLabelsAngle = 90)
-```
-
b
diff -r 2f4df2be0572 -r d820be692d74 wgcna_eigengene_visualization.xml
--- a/wgcna_eigengene_visualization.xml Tue Aug 08 12:35:11 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
@@ -1,100 +0,0 @@
-<tool id="wgcna_eigengene_visualization" name="WGCNA: eigengene visualization" version="1.0.0">
-    <requirements>
-        <requirement type="package" version="1.20.0">r-getopt</requirement>
-        <requirement type="package" version="1.2">r-rmarkdown</requirement>
-        <requirement type="package" version="1.8.4">r-plyr</requirement>
-        <requirement type="package" version="0.4.0">r-highcharter</requirement>
-        <requirement type="package" version="0.2">r-dt</requirement>
-        <requirement type="package" version="0.3.5">r-htmltools</requirement>
-        <requirement type="package" version="1.51">r-wgcna</requirement>
-    </requirements>
-    <description>
-        Eigengene visualization.
-    </description>
-    <stdio>
-        <regex match="Execution halted"
-               source="both"
-               level="fatal"
-               description="Execution halted." />
-        <regex match="Error in"
-               source="both"
-               level="fatal"
-               description="An undefined error occured, please check your intput carefully and contact your administrator." />
-        <regex match="Fatal error"
-               source="both"
-               level="fatal"
-               description="An undefined error occured, please check your intput carefully and contact your administrator." />
-    </stdio>
-    <command>
-        <![CDATA[
-        ## Add tools to PATH
-        export PATH=/opt/R-3.2.5/bin:\$PATH &&
-
-        Rscript '${__tool_directory__}/wgcna_eigengene_visualization_render.R'
-
-            ## 1. input data
-            -e $echo
-            -w $construct_network_workspace
-            -p '$soft_threshold_power'
-            -n $plot_genes
-
-
-            ## 2. output report and report site directory
-     -o $wgcna_eigengene_visualization
-     -d $wgcna_eigengene_visualization.files_path
-
-     ## 3. Rmd templates in the tool directory
-
-                -M '${__tool_directory__}/wgcna_eigengene_visualization.Rmd'
-
-
-
-        ]]>
-    </command>
-    <inputs>
-        <param type="data" name="construct_network_workspace" format="rdata" optional="false"
-               label="R workspace from WGCNA: construct network" />
-        <param type="integer" name="soft_threshold_power" optional="true" label="Soft threshold power"
-               help="Refer to the scale independence plot from 'WGCNA: construct network' and choose an optimal soft threshold power.
-               An optimal power will be calculated automatically if no value is provided." />
-        <param type="integer" name="plot_genes" value="400" min="1" label="Number of genes" optional="false"
-               help="The number of genes that will be used. It is possible to speed up the plotting by providing a subset of
-                    genes. However, the gene dendrogram may ofter look different from dendrogram of all genes." />
-        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
-    </inputs>
-    <outputs>
-        <data name="wgcna_eigengene_visualization" format="html" label="WGCNA: eigengene visualization" />
-    </outputs>
-    <citations>
-        <citation type="bibtex">
-            @article{langfelder2008wgcna,
-            title={WGCNA: an R package for weighted correlation network analysis},
-            author={Langfelder, Peter and Horvath, Steve},
-            journal={BMC bioinformatics},
-            volume={9},
-            number={1},
-            pages={559},
-            year={2008},
-            publisher={BioMed Central}
-            }
-        </citation>
-        <citation type="bibtex">
-            @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">
-            @book{xie2015dynamic,
-            title={Dynamic Documents with R and knitr},
-            author={Xie, Yihui},
-            volume={29},
-            year={2015},
-            publisher={CRC Press}
-            }
-        </citation>
-    </citations>
-</tool>
\ No newline at end of file
b
diff -r 2f4df2be0572 -r d820be692d74 wgcna_eigengene_visualization_render.R
--- a/wgcna_eigengene_visualization_render.R Tue Aug 08 12:35:11 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,109 +0,0 @@
-##======= Handle arguments from command line ========
-# setup R error handline to go to stderr
-options(show.error.messages=FALSE,
-        error=function(){
-          cat(geterrmessage(), file=stderr())
-          quit("no", 1, F)
-        })
-
-# we need that to not crash galaxy with an UTF8 error on German LC settings.
-loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
-
-# suppress warning
-options(warn = -1)
-
-options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
-args = commandArgs(trailingOnly=TRUE)
-
-suppressPackageStartupMessages({
-  library(getopt)
-  library(tools)
-})
-
-# 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.
-spec_list=list()
-
-##------- 1. input data ---------------------
-spec_list$ECHO = c('echo', 'e', '1', 'character')
-spec_list$CONSTRUCT_NETWORK_WORKSPACE = c('construct_network_workspace', 'w', '1', 'character')
-spec_list$SOFT_THRESHOLD_POWER = c('soft_threshold_power', 'p', '2', 'double')
-spec_list$PLOT_GENES = c('plot_genes', 'n', '1', 'integer')
-
-
-##--------2. output report and report site directory --------------
-spec_list$OUTPUT_HTML = c('wgcna_eigengene_visualization_html', 'o', '1', 'character')
-spec_list$OUTPUT_DIR = c('wgcna_eigengene_visualization_dir', 'd', '1', 'character')
-
-
-
-##--------3. Rmd templates in the tool directory ----------
-
-spec_list$WGCNA_EIGENGENE_VISUALIZATION_RMD = c('wgcna_eigengene_visualization_rmd', 'M', '1', 'character')
-
-
-
-##------------------------------------------------------------------
-
-spec = t(as.data.frame(spec_list))
-opt = getopt(spec)
-# arguments are accessed by long flag name (the first column in the spec matrix)
-#                        NOT by element name in the spec_list
-# example: opt$help, opt$expression_file
-##====== End of arguments handling ==========
-
-#------ Load libraries ---------
-library(rmarkdown)
-library(WGCNA)
-library(DT)
-library(htmltools)
-library(ggplot2)
-
-
-#----- 1. create the report directory ------------------------
-system(paste0('mkdir -p ', opt$wgcna_eigengene_visualization_dir))
-
-
-#----- 2. generate Rmd files with Rmd templates --------------
-#   a. templates without placeholder variables:
-#         copy templates from tool directory to the working directory.
-#   b. templates with placeholder variables:
-#         substitute variables with user input values and place them in the working directory.
-
-
-#----- 01 wgcna_eigengene_visualization.Rmd -----------------------
-readLines(opt$wgcna_eigengene_visualization_rmd) %>%
-  (function(x) {
-    gsub('ECHO', opt$echo, x)
-  }) %>%
-  (function(x) {
-    gsub('CONSTRUCT_NETWORK_WORKSPACE', opt$construct_network_workspace, x)
-  }) %>%
-  (function(x) {
-    gsub('SOFT_THRESHOLD_POWER', opt$soft_threshold_power, x)
-  }) %>%
-  (function(x) {
-    gsub('PLOT_GENES', opt$plot_genes, x)
-  }) %>%
-  (function(x) {
-    gsub('OUTPUT_DIR', opt$wgcna_eigengene_visualization_dir, x)
-  }) %>%
-  (function(x) {
-    fileConn = file('wgcna_eigengene_visualization.Rmd')
-    writeLines(x, con=fileConn)
-    close(fileConn)
-  })
-
-
-#------ 3. render all Rmd files --------
-render('wgcna_eigengene_visualization.Rmd', output_file = opt$wgcna_eigengene_visualization_html)
-
-#-------4. manipulate outputs -----------------------------
-
-
b
diff -r 2f4df2be0572 -r d820be692d74 wgcna_preprocessing.Rmd
--- a/wgcna_preprocessing.Rmd Tue Aug 08 12:35:11 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
@@ -1,76 +0,0 @@
----
-title: 'WGCNA: data preprocessing'
-output:
-    html_document:
-      number_sections: true
-      toc: true
-      theme: cosmo
-      highlight: tango
----
-
-```{r setup, include=FALSE, warning=FALSE, message=FALSE}
-knitr::opts_chunk$set(
-  echo = ECHO
-)
-```
-
-```{r}
-str(opt)
-```
-
-# Import data
-
-Each row represents a gene and each column represents a sample.
-
-```{r}
-expression_data = read.csv('EXPRESSION_DATA', header = TRUE, row.names = 1)
-```
-
-Display the first 100 genes.
-
-```{r}
-datatable(head(expression_data, 100), style="bootstrap", filter = 'top',
-          class="table-condensed", options = list(dom = 'tp', scrollX = TRUE))
-```
-
-Transpose expression data matrix so that each row represents a sample and each column represents a gene.
-
-```{r}
-expression_data = as.data.frame(t(expression_data))
-```
-
-# Checking data
-
-Checking data for excessive missing values and identification of outlier microarray samples.
-
-```{r}
-gsg = goodSamplesGenes(expression_data, verbose = 3)
-if (!gsg$allOK) {
-  # Optionally, print the gene and sample names that were removed:
-  if (sum(!gsg$goodGenes)>0)
-    printFlush(paste("Removing genes:", paste(names(expression_data)[!gsg$goodGenes], collapse = ", ")));
-  if (sum(!gsg$goodSamples)>0)
-    printFlush(paste("Removing samples:", paste(rownames(expression_data)[!gsg$goodSamples], collapse = ", ")));
-  # Remove the offending genes and samples from the data:
-  expression_data = expression_data[gsg$goodSamples, gsg$goodGenes]
-} else {
-  print('all genes are OK!')
-}
-```
-
-# Clustering samples
-
-If there are any outliers, choose a height cut that will remove the offending sample. Remember this number since you will need this number in further analysis.
-
-```{r fig.align='center'}
-sampleTree = hclust(dist(expression_data), method = "average");
-plot(sampleTree, main = "Sample clustering to detect outliers", sub="", xlab="",
-     cex.axis = 1, cex.main = 1, cex = 0.5)
-```
-
-
-```{r echo=FALSE}
-rm("opt")
-save(list=ls(all.names = TRUE), file='PREPROCESSING_WORKSPACE')
-```
-
b
diff -r 2f4df2be0572 -r d820be692d74 wgcna_preprocessing.xml
--- a/wgcna_preprocessing.xml Tue Aug 08 12:35:11 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
@@ -1,96 +0,0 @@
-<tool id="wgcna_preprocessing" name="WGCNA: preprocessing" version="1.0.0">
-    <requirements>
-        <requirement type="package" version="1.20.0">r-getopt</requirement>
-        <requirement type="package" version="1.2">r-rmarkdown</requirement>
-        <requirement type="package" version="1.8.4">r-plyr</requirement>
-        <requirement type="package" version="0.4.0">r-highcharter</requirement>
-        <requirement type="package" version="0.2">r-dt</requirement>
-        <requirement type="package" version="0.3.5">r-htmltools</requirement>
-        <requirement type="package" version="1.51">r-wgcna</requirement>
-    </requirements>
-    <description>
-        Data clearning and preprocessing.
-    </description>
-    <stdio>
-        <regex match="Execution halted"
-               source="both"
-               level="fatal"
-               description="Execution halted." />
-        <regex match="Error in"
-               source="both"
-               level="fatal"
-               description="An undefined error occured, please check your intput carefully and contact your administrator." />
-        <regex match="Fatal error"
-               source="both"
-               level="fatal"
-               description="An undefined error occured, please check your intput carefully and contact your administrator." />
-    </stdio>
-    <command>
-        <![CDATA[
-        ## Add tools to PATH
-        export PATH=/opt/R-3.2.5/bin:\$PATH &&
-
-        Rscript '${__tool_directory__}/wgcna_preprocessing_render.R'
-
-            ## 1. input data
-            -e $echo
-            -E $expression_data
-
-
-            ## 2. output report and report site directory
-     -o $wgcna_preprocessing
-     -d $wgcna_preprocessing.files_path
-     -w $preprocessing_workspace
-
-     ## 3. Rmd templates sitting in the tool directory
-
-         ## _site.yml and index.Rmd template files
-                -D '${__tool_directory__}/wgcna_preprocessing.Rmd'
-
-
-
-        ]]>
-    </command>
-    <inputs>
-        <param type="data" name="expression_data" format="csv" optional="false" label="Gene expression data"
-               help="Each row represents a gene and each column represents a sample."/>
-
-        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
-    </inputs>
-    <outputs>
-        <data name="wgcna_preprocessing" format="html" label="WGCNA: preprocessing" />
-        <data name="preprocessing_workspace" format="rdata" label="R workspace: WGCNA preprocessing" />
-    </outputs>
-    <citations>
-        <citation type="bibtex">
-            @article{langfelder2008wgcna,
-            title={WGCNA: an R package for weighted correlation network analysis},
-            author={Langfelder, Peter and Horvath, Steve},
-            journal={BMC bioinformatics},
-            volume={9},
-            number={1},
-            pages={559},
-            year={2008},
-            publisher={BioMed Central}
-            }
-        </citation>
-        <citation type="bibtex">
-            @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">
-            @book{xie2015dynamic,
-            title={Dynamic Documents with R and knitr},
-            author={Xie, Yihui},
-            volume={29},
-            year={2015},
-            publisher={CRC Press}
-            }
-        </citation>
-    </citations>
-</tool>
\ No newline at end of file
b
diff -r 2f4df2be0572 -r d820be692d74 wgcna_preprocessing_render.R
--- a/wgcna_preprocessing_render.R Tue Aug 08 12:35:11 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,102 +0,0 @@
-##======= Handle arguments from command line ========
-# setup R error handline to go to stderr
-options(show.error.messages=FALSE,
-        error=function(){
-          cat(geterrmessage(), file=stderr())
-          quit("no", 1, F)
-        })
-
-# we need that to not crash galaxy with an UTF8 error on German LC settings.
-loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
-
-# suppress warning
-options(warn = -1)
-
-options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
-args = commandArgs(trailingOnly=TRUE)
-
-suppressPackageStartupMessages({
-  library(getopt)
-  library(tools)
-})
-
-# 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.
-spec_list=list()
-
-##------- 1. input data ---------------------
-spec_list$ECHO = c('echo', 'e', '1', 'character')
-spec_list$EXPRESSION_DATA = c('expression_data', 'E', '1', 'character')
-
-
-##--------2. output report and report site directory --------------
-spec_list$OUTPUT_HTML = c('wgcna_preprocessing_html', 'o', '1', 'character')
-spec_list$OUTPUT_DIR = c('wgcna_preprocessing_dir', 'd', '1', 'character')
-spec_list$PREPROCESSING_WORKSPACE = c('preprocessing_workspace', 'w', '1', 'character')
-
-##--------3. Rmd templates sitting in the tool directory ----------
-
-spec_list$WGCNA_PREPROCESSING_RMD = c('wgcna_preprocessing_rmd', 'D', '1', 'character')
-
-
-
-##------------------------------------------------------------------
-
-spec = t(as.data.frame(spec_list))
-opt = getopt(spec)
-# arguments are accessed by long flag name (the first column in the spec matrix)
-#                        NOT by element name in the spec_list
-# example: opt$help, opt$expression_file
-##====== End of arguments handling ==========
-
-#------ Load libraries ---------
-library(rmarkdown)
-library(WGCNA)
-library(DT)
-library(htmltools)
-
-
-#----- 1. create the report directory ------------------------
-system(paste0('mkdir -p ', opt$wgcna_preprocessing_dir))
-
-
-#----- 2. generate Rmd files with Rmd templates --------------
-#   a. templates without placeholder variables:
-#         copy templates from tool directory to the working directory.
-#   b. templates with placeholder variables:
-#         substitute variables with user input values and place them in the working directory.
-
-
-#----- 01 wgcna_preprocessing.Rmd -----------------------
-readLines(opt$wgcna_preprocessing_rmd) %>%
-  (function(x) {
-    gsub('ECHO', opt$echo, x)
-  }) %>%
-  (function(x) {
-    gsub('EXPRESSION_DATA', opt$expression_data, x)
-  }) %>%
-  (function(x) {
-    gsub('OUTPUT_DIR', opt$wgcna_preprocessing_dir, x)
-  }) %>%
-  (function(x) {
-    gsub('PREPROCESSING_WORKSPACE', opt$preprocessing_workspace, x)
-  }) %>%
-  (function(x) {
-    fileConn = file('wgcna_preprocessing.Rmd')
-    writeLines(x, con=fileConn)
-    close(fileConn)
-  })
-
-
-#------ 3. render all Rmd files --------
-render('wgcna_preprocessing.Rmd', output_file = opt$wgcna_preprocessing_html)
-
-#-------4. manipulate outputs -----------------------------
-
-