view 01_htseq_count_analysis.Rmd @ 5:cf3fde5d0834 draft

planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty

---
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)
```