# HG changeset patch
# User youyuh48
# Date 1512789341 18000
# Node ID a049d0d5a05e240e6b815491f332538504c180a1
# Parent  527c214feb7d1805c57881fa5fe32fb36d114d05
Uploaded

diff -r 527c214feb7d -r a049d0d5a05e r-sleuth.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r-sleuth.R	Fri Dec 08 22:15:41 2017 -0500
@@ -0,0 +1,87 @@
+#!/usr/bin/env Rscript
+
+# A command-line interface to sleuth for use with Galaxy
+# This script modified from
+# https://github.com/pachterlab/bears_analyses/blob/master/sleuth.R
+
+# setup R error handling to go to stderr
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "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")
+
+library("getopt")
+library("tools")
+options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
+args <- commandArgs(trailingOnly = TRUE)
+
+# get options, using the spec as defined by the enclosed list.
+spec <- matrix(c(
+  "quiet",          "q", 0, "logical",
+  "help",           "h", 0, "logical",
+  "indir",          "i", 1, "character",
+  "metadata",       "m", 1, "character",
+  "full_model",     "f", 1, "character",
+  "reduced_model",  "r", 1, "character",
+  "gene_anno_name", "a", 2, "character"
+  ), byrow=TRUE, ncol=4)
+opt <- getopt(spec)
+
+# if help was asked for print a friendly message
+# and exit with a non-zero error code
+if (!is.null(opt$help)) {
+  cat(getopt(spec, usage=TRUE))
+  q(status=1)
+}
+
+# enforce the following required arguments
+if (is.null(opt$indir)) {
+  cat("'indir' is required\n")
+  q(status=1)
+}
+if (is.null(opt$metadata)) {
+  cat("'metadata' is required\n")
+  q(status=1)
+}
+if (is.null(opt$full_model)) {
+  cat("'full_model' is required\n")
+  q(status=1)
+}
+if (is.null(opt$reduced_model)) {
+  cat("'reduced_model' is required\n")
+  q(status=1)
+}
+
+verbose <- if (is.null(opt$quiet)) {
+  TRUE
+} else {
+  FALSE
+}
+
+suppressPackageStartupMessages({
+  library("sleuth")
+  library("biomaRt")
+})
+
+s2c <- read.table(file.path(opt$metadata), header = TRUE, stringsAsFactors=FALSE)
+run_dirs <- s2c$sample
+kal_dirs <- c()
+
+for (dir in run_dirs) {
+	kal_dirs <- c(kal_dirs, file.path(opt$indir, dir, "kallisto"))
+}
+
+s2c <- dplyr::mutate(s2c, path = kal_dirs)
+
+if (!is.null(opt$gene_anno_name)) {
+    mart <- biomaRt::useMart(biomart = "ensembl", dataset = opt$gene_anno_name)
+    t2g <- biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id", "external_gene_name"), mart = mart)
+    t2g <- dplyr::rename(t2g, target_id = ensembl_transcript_id, ens_gene = ensembl_gene_id, ext_gene = external_gene_name)
+    so <- sleuth_prep(s2c, as.formula(opt$full_model), target_mapping = t2g, read_bootstrap_tpm=TRUE, extra_bootstrap_summary=TRUE)
+} else {
+    so <- sleuth_prep(s2c, as.formula(opt$full_model), read_bootstrap_tpm=TRUE, extra_bootstrap_summary=TRUE)
+}
+so <- sleuth_fit(so, as.formula(opt$full_model), "full")
+so <- sleuth_fit(so, as.formula(opt$reduced_model), "reduced")
+so <- sleuth_lrt(so, "reduced", "full")
+sleuth_deploy(so, opt$indir)
diff -r 527c214feb7d -r a049d0d5a05e r-sleuth.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r-sleuth.xml	Fri Dec 08 22:15:41 2017 -0500
@@ -0,0 +1,79 @@
+<tool id="r-sleuth" name="r-sleuth" version="0.29.0">
+  <description>Sleuth is an R library for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto.</description>
+  <requirements>
+    <requirement type="package" version="1.20.0">r-getopt</requirement>
+    <requirement type="package" version="0.29.0">r-sleuth</requirement>
+    <requirement type="package" version="2.34.0">bioconductor-biomart</requirement>
+  </requirements>
+  <version_command>
+    <![CDATA[
+      echo $(R --version | grep version | grep -v GNU)", r-sleuth version" $(R --vanilla --slave -e "library(sleuth); cat(sessionInfo()\$otherPkgs\$sleuth\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+    ]]>
+  </version_command>
+  <command detect_errors="aggressive">
+    <![CDATA[
+      #import re
+      ## create symlinks to input datasets
+      #for $file in $input_files
+        #set $sname = re.sub('\.h5$', '', str($file.element_identifier))
+        mkdir -p 'data/${sname}/kallisto' &&
+        ln -s '$file' 'data/${sname}/kallisto/abundance.h5' &&
+      #end for
+
+      Rscript '${__tool_directory__}/r-sleuth.R'
+        --indir 'data'
+        --metadata '$metadata'
+        --full_model '~${full_model}'
+        --reduced_model '~${reduced_model}'
+        --gene_anno_name 'hsapiens_gene_ensembl' &&
+      tar zcvf sleuth_shiny.tar.gz data/app.R data/so.rds
+    ]]>
+  </command>
+  <inputs>
+    <param name="input_files" type="data" format="h5" label="Select Abundance(HDF5) Datasets" min="2" multiple="True"/>
+    <param name="metadata" type="data" format="txt,tsv,tabular" label="Metadata file"/>
+    <param name="full_model" type="text" value="condition" label="Full model"/>
+    <param name="reduced_model" type="text" value="1" label="Reduced model"/>
+    <param name="gene_anno_name" type="select" label="BioMart dataset">
+      <option value="hsapiens_gene_ensembl" selected="true">homo_sapiens</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="output" format="tar" label="${tool.name} on ${on_string}: R Shiny app" from_work_dir="sleuth_shiny.tar.gz"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_files" value="SRR1867792.h5,SRR1909613.h5,SRR1909637.h5"/>
+      <param name="metadata" value="metadata.txt"/>
+      <output name="output" file="sleuth_shiny.tar.gz" ftype="tar"/>
+    </test>
+  </tests>
+  <help>
+<![CDATA[
+This is a Galaxy wrapper for the Sleuth package.
+
+**Input file format of metadata**
+
+sample      condition
+---------------------
+SRR1867792  ESC
+SRR1909613  BM-MSC
+SRR1909637  BM-MSC
+
+**Output**
+
+This wrapper script generates Shiny web application files for RStudio.
+Unzip sleuth_shiny.tar.gz file, then run app.R file in RStudio.
+]]>
+  </help>
+  <citations>
+    <citation type="bibtex">
+      @misc{githubsleuth,
+      title = {sleuth},
+      publisher = {GitHub},
+      journal = {GitHub repository},
+      url = {https://pachterlab.github.io/sleuth/},
+      }
+    </citation>
+  </citations>
+</tool>
diff -r 527c214feb7d -r a049d0d5a05e test-data/SRR1867792.h5
Binary file test-data/SRR1867792.h5 has changed
diff -r 527c214feb7d -r a049d0d5a05e test-data/SRR1909613.h5
Binary file test-data/SRR1909613.h5 has changed
diff -r 527c214feb7d -r a049d0d5a05e test-data/SRR1909637.h5
Binary file test-data/SRR1909637.h5 has changed
diff -r 527c214feb7d -r a049d0d5a05e test-data/metadata.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metadata.txt	Fri Dec 08 22:15:41 2017 -0500
@@ -0,0 +1,4 @@
+sample	condition
+SRR1867792	ESC
+SRR1909613	BM-MSC
+SRR1909637	BM-MSC