Mercurial > repos > mingchen0919 > aurora_skewer_site

changeset 0:ad0aa8d214c1 draft

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planemo upload
author mingchen0919
date Fri, 02 Mar 2018 10:20:53 -0500
parents
children 0483f55131d1
files skewer.Rmd skewer.sh skewer.xml skewer_index.Rmd skewer_render.R skewer_site.yml
diffstat 6 files changed, 272 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/skewer.Rmd	Fri Mar 02 10:20:53 2018 -0500
@@ -0,0 +1,56 @@
+---
+title: 'Skewer Trimming'
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = as.logical(opt$X_e), 
+  error = TRUE
+)
+```
+
+
+# Run Skewer
+
+```{bash}
+cd ${X_d}
+
+cat >temp.sh <<EOL
+skewer \\
+  -q ${X_A} \\
+  -Q ${X_B} \\
+  -x ${X_x} \\
+  -y ${X_y} \\
+  ${X_X} \\
+  ${X_Y} \\
+  -o ${X_d}/trim > /dev/null 2>&1
+EOL
+
+grep -v None temp.sh > skewer-job.sh
+
+# run skewer
+sh skewer-job.sh
+
+cp trim-trimmed-pair1.fastq ${X_f}
+cp trim-trimmed-pair2.fastq ${X_r}
+mv trim-trimmed.log trim-trimmed.txt
+```
+
+
+```{r}
+# display skewer job script
+skewer_sh = paste0(opt$X_d, '/skewer-job.sh')
+tags$code(tags$pre(readChar(skewer_sh, file.info(skewer_sh)$size )))
+```
+
+# Results
+
+```{r}
+tags$ul(
+  tags$li(tags$a(href = 'trim-trimmed.txt', 'trim-trimmed.log')),
+  tags$li(tags$a(href = 'trim-trimmed-pair1.fastq', 'trim-trimmed-pair1.fastq')),
+  tags$li(tags$a(href = 'trim-trimmed-pair2.fastq', 'trim-trimmed-pair2.fastq'))
+)
+```
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/skewer.sh	Fri Mar 02 10:20:53 2018 -0500
@@ -0,0 +1,17 @@
+Rscript '${__tool_directory__}/skewer_render.R'
+
+    -e $echo
+    -o $report
+    -d $report.files_path
+    -s $sink_message
+    -t '${__tool_directory__}'
+    
+    -X $first_reads
+    -Y $second_reads
+    -x $adapter_x
+    -y $adapter_y
+    -A $end_quality
+    -B $mean_quality
+    
+    -f $trimmed_r1
+    -r $trimmed_r2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/skewer.xml	Fri Mar 02 10:20:53 2018 -0500
@@ -0,0 +1,86 @@
+<tool id="aurora_skewer" name="Aurora Skewer" version="1.0.0">
+    <description>A fast and accurate adapter trimmer for next-generation sequencing paired-end reads&#xD;
+    </description>
+    <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.6">r-rmarkdown</requirement>
+        <requirement type="package" version="0.2.2">skewer</requirement>
+    </requirements>
+    <stdio>
+        <regex match="XXX" source="stderr" level="warning"
+               description="Check the warnings_and_errors.txt file for more details."/>
+    </stdio>
+    <command><![CDATA[Rscript '${__tool_directory__}/skewer_render.R'
+
+    -e $echo
+    -o $report
+    -d $report.files_path
+    -s $sink_message
+    -t '${__tool_directory__}'
+    
+    -X $first_reads
+    -Y $second_reads
+    -x $adapter_x
+    -y $adapter_y
+    -A $end_quality
+    -B $mean_quality
+    
+    -f $trimmed_r1
+    -r $trimmed_r2
+]]></command>
+    <inputs>
+        <param type="data" name="first_reads" label="First reads file" optional="False" format="fastq,fastqsanger"/>
+        <param type="data" name="second_reads" label="Second reads" optional="False" format="fastq,fastqsanger"/>
+        <param type="data" name="adapter_x" argument="-x" label="Adapter sequence file for the first reads"
+               optional="True" format="fasta,fa"/>
+        <param type="data" name="adapter_y" argument="-y" label="Adapter sequence file for the second reads"
+               optional="True" format="fasta,fa"/>
+        <param type="integer" name="end_quality" argument="-q" label="3&#x2019; end quality trimming"
+               help="Trim 3&#x2019; end until specified or higher quality reached. The default value is 0."
+               optional="False" value="0"/>
+        <param type="integer" name="mean_quality" argument="-Q" label="Reads filtering by average quality"
+               help="Specifies the lowest mean quality value allowed before trimming. The default value is 0."
+               optional="False" value="0"/>
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
+               label="Display analysis code in report?"/>
+    </inputs>
+    <outputs>
+        <data name="report" format="html" label="Skewer trimmed" hidden="false"/>
+        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
+        <data name="trimmed_r1" format="fastq" label="${tool.name} trimmed first reads on ${on_string}" hidden="false"/>
+        <data name="trimmed_r2" format="fastq" label="${tool.name} trimmed second reads on ${on_string}"
+              hidden="false"/>
+    </outputs>
+    <citations>
+        <citation type="bibtex"><![CDATA[
+            @article{allaire2016rmarkdown,
+            title={rmarkdown: Dynamic Documents for R, 2016},
+            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
+            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+            journal={R package version 0.9},
+            volume={6},
+            year={2016}
+            }
+        ]]></citation>
+        <citation type="bibtex"><![CDATA[
+            @book{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        ]]></citation>
+        <citation type="bibtex"><![CDATA[@article{jiang2014skewer,
+  title={Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads},
+  author={Jiang, Hongshan and Lei, Rong and Ding, Shou-Wei and Zhu, Shuifang},
+  journal={BMC bioinformatics},
+  volume={15},
+  number={1},
+  pages={182},
+  year={2014},
+  publisher={BioMed Central}
+}]]></citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/skewer_index.Rmd	Fri Mar 02 10:20:53 2018 -0500
@@ -0,0 +1,16 @@
+---
+title: "Analysis Report"
+output: html_document
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = TRUE, error = TRUE)
+```
+
+# Skewer
+
+**A fast and accurate adapter trimmer for next-generation sequencing paired-end reads**.
+
+# References
+
+Jiang, Hongshan, et al. "Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads." BMC bioinformatics 15.1 (2014): 182.
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/skewer_render.R	Fri Mar 02 10:20:53 2018 -0500
@@ -0,0 +1,82 @@
+##============ 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')
+
+#------------import libraries--------------------
+options(stringsAsFactors = FALSE)
+
+library(getopt)
+library(rmarkdown)
+library(htmltools)
+#------------------------------------------------
+
+
+#------------get arguments into R--------------------
+# library(dplyr)
+# getopt_specification_matrix(extract_short_flags('skewer.xml')) %>%
+#   write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)
+
+
+spec_matrix = as.matrix(
+  data.frame(stringsAsFactors=FALSE,
+             long_flags = c("X_e", "X_o", "X_d", "X_s", "X_t", "X_X", "X_Y",
+                            "X_x", "X_y", "X_A", "X_B", "X_f", "X_r"),
+             short_flags = c("e", "o", "d", "s", "t", "X", "Y", "x", "y", "A",
+                             "B", "f", "r"),
+             argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
+             data_type_flags = c("character", "character", "character", "character",
+                                 "character", "character", "character",
+                                 "character", "character", "character", "character",
+                                 "character", "character")
+  )
+)
+opt = getopt(spec_matrix)
+#----------------------------------------------------
+
+
+#-----------using passed arguments in R 
+#           to define system environment variables---
+do.call(Sys.setenv, opt[-1])
+#----------------------------------------------------
+
+#---------- often used variables ----------------
+# OUTPUT_REPORT: path to galaxy output report
+# OUTPUT_DIR: path to the output associated directory, which stores all outputs
+# TOOL_DIR: path to the tool installation directory
+OUTPUT_DIR = opt$X_d
+TOOL_DIR =   opt$X_t
+OUTPUT_REPORT = opt$X_o
+
+
+# create the output associated directory to store all outputs
+dir.create(OUTPUT_DIR, recursive = TRUE)
+
+#-----------------render site--------------
+# copy site generating materials into OUTPUT_DIR
+dir.create(paste0(OUTPUT_DIR, '/site_generator'), recursive = TRUE)
+system(paste0('cp -r ', TOOL_DIR, '/skewer.Rmd ', OUTPUT_DIR, '/site_generator/skewer.Rmd'))
+system(paste0('cp -r ', TOOL_DIR, '/skewer_site.yml ', OUTPUT_DIR, '/site_generator/_site.yml'))
+system(paste0('cp -r ', TOOL_DIR, '/skewer_index.Rmd ', OUTPUT_DIR, '/site_generator/index.Rmd'))
+# render site to OUTPUT_DIR/_site, this is configured in the "_site.yml" file
+render_site(input = paste0(OUTPUT_DIR, '/site_generator'))
+# remove site generating materials from output associated directory
+unlink(paste0(OUTPUT_DIR, '//site_generator'), recursive = TRUE)
+# move _site/* into output associated directory
+move_cmd = paste0('mv ', OUTPUT_DIR, '/_site/* ', OUTPUT_DIR)
+system(move_cmd)
+#------------------------------------------
+
+#-----link index.html to output-----
+cp_index = paste0('cp ', OUTPUT_DIR, '/index.html ', OUTPUT_REPORT)
+system(cp_index)
+#-----------------------------------
+
+#==============the end==============
+
+
+##--------end of code rendering .Rmd templates----------------
+sink()
+##=========== End of sinking output=============================
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/skewer_site.yml	Fri Mar 02 10:20:53 2018 -0500
@@ -0,0 +1,15 @@
+name: "Analysis Report"
+output_dir: "../_site"
+navbar:
+    title: ""
+    type: inverse
+    left:
+        - text: "Home"
+          icon: fa-home
+          href: index.html
+        - text: "Skewer Trimming"
+          href: skewer.html
+output:
+  html_document:
+    theme: cosmo
+    highlight: textmate
\ No newline at end of file