changeset 5:cf3fde5d0834 draft

planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/01_htseq_count_analysis.Rmd	Tue May 01 11:27:32 2018 -0400
@@ -0,0 +1,36 @@
+---
+title: 'HTSeq-count Analysis'
+output:
+    html_document:
+      highlight: pygments
+---
+
+## Job script
+
+```{bash, echo=FALSE}
+sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh
+```
+
+```{r echo=FALSE, comment='', results='asis'}
+cat('```bash\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/htseq-count.sh')), sep = '\n')
+cat('\n```')
+```
+
+## Counts
+
+Only the first few rows are displayed. 
+
+```{r, echo=FALSE}
+count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1)
+sample_names = trimws(strsplit(opt$X_B, ',')[[1]])
+colnames(count_data) = rep(sample_names, length = ncol(count_data))
+kable(head(count_data))
+
+# modify column names
+count_data = data.frame(feature_id = rownames(count_data), count_data)
+write.csv(count_data, 
+          file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/count_data.csv'),
+          quote = FALSE, row.names = FALSE)
+```
+

--- a/_site.yml	Tue May 01 11:20:13 2018 -0400
+++ b/_site.yml	Tue May 01 11:27:32 2018 -0400
@@ -1,17 +1,11 @@
-name: "Aurora Tool Website"
+name: "Aurora HTSeq-count"
 output_dir: "."
 navbar:
-    title: "Aurora Tool"
+    title: "Aurora HTSeq-count"
     type: inverse
     left:
-        - text: "Job 1"
-          href: 01_rmarkdown.html
-        - text: "Job 2"
-          menu:
-            - text: "Sub-job 1"
-              href: 02_rmarkdown.html
-            - text: "Sub-job 2"
-              href: 03_rmarkdown.html
+        - text: "HTSeq-count analysis"
+          href: 01_htseq_count_analysis.html
 
 output:
   html_document:

--- a/rmarkdown_report.Rmd	Tue May 01 11:20:13 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
----
-title: 'HTSeq-count Report'
-output:
-    html_document:
-      highlight: pygments
----
-
-```{r setup, include=FALSE, warning=FALSE, message=FALSE}
-knitr::opts_chunk$set(error = TRUE, echo = FALSE)
-```
-
-```{css echo=FALSE}
-# code chunks scrollable
-pre code, pre, code {
-  white-space: pre !important;
-  overflow-x: scroll !important;
-  word-break: keep-all !important;
-  word-wrap: initial !important;
-}
-```
-
-
-```{r, echo=FALSE}
-# to make the css theme to work, <link></link> tags cannot be added directly 
-# as <script></script> tags as below.
-# it has to be added using a code chunk with the htmltool functions!!!
-css_link = tags$link()
-css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css")
-css_link
-```
-
-```{r, eval=FALSE, echo=FALSE}
-# this code chunk is purely for adding comments
-# below is to add jQuery and jstree javascripts
-```
-<script src="https://code.jquery.com/jquery-3.3.1.min.js"></script>
-<script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
-
----
-# javascript code below is to build the file tree interface
-# see this for how to implement opening hyperlink: https://stackoverflow.com/questions/18611317/how-to-get-i-get-leaf-nodes-in-jstree-to-open-their-hyperlink-when-clicked-when
----
-<script>
-  $(function () {
-    // create an instance when the DOM is ready
-    $('#jstree').jstree().bind("select_node.jstree", function (e, data) {
-     window.open( data.node.a_attr.href, data.node.a_attr.target )
-    });
-  });
-</script>
-
----
-# ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE
----
-
-## Job script
-
-```{bash, echo=FALSE}
-sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh
-```
-
-```{r echo=FALSE, comment='', results='asis'}
-cat('```bash\n')
-cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/htseq-count.sh')), sep = '\n')
-cat('\n```')
-```
-
-## Counts
-
-Only the first few rows are displayed. 
-
-```{r, echo=FALSE}
-count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1)
-sample_names = trimws(strsplit(opt$X_B, ',')[[1]])
-colnames(count_data) = rep(sample_names, length = ncol(count_data))
-kable(head(count_data))
-
-# modify column names
-count_data = data.frame(feature_id = rownames(count_data), count_data)
-write.csv(count_data, 
-          file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/count_data.csv'),
-          quote = FALSE, row.names = FALSE)
-```
-

--- a/rmarkdown_report.xml	Tue May 01 11:20:13 2018 -0400
+++ b/rmarkdown_report.xml	Tue May 01 11:27:32 2018 -0400
@@ -1,6 +1,6 @@
-<tool name="aurora_htseq" id='aurora_htseq_report' version="2.0.1">
+<tool name="aurora_htseq_site" id='aurora_htseq_site_report' version="2.0.1">
     <description>
-        some description
+        counting reads in features
     </description>
     <requirements>
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>