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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit a7ad932a1725b4ef26d522040c5395ae0026fb35-dirty
author mingchen0919
date Tue, 26 Sep 2017 12:34:02 -0400
parents 8dacd341b8b7
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---
title: 'Build collection: a paired datasets'
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
)
```

# Command line arguments

```{r 'command line arguments'}
str(opt)
```

# Rename files

```{r}
file.copy("FORWARD_INPUT", './OUTPUT_DIR/forward.FORMAT')
file.copy("REVERSE_INPUT", './OUTPUT_DIR/reverse.FORMAT')
```