# HG changeset patch
# User youyuh48
# Date 1528840727 14400
# Node ID 172091d47f5a51ee33648815103075a116eaf01b
# Parent  a049d0d5a05e240e6b815491f332538504c180a1
planemo upload for repository https://github.com/youyuh48/galaxy-sleuth/tree/master/ commit 8d9ff6181e933951e015e67f1719588bab2b3ab5-dirty

diff -r a049d0d5a05e -r 172091d47f5a r-sleuth.R
--- a/r-sleuth.R	Fri Dec 08 22:15:41 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,87 +0,0 @@
-#!/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 a049d0d5a05e -r 172091d47f5a r-sleuth.xml
--- a/r-sleuth.xml	Fri Dec 08 22:15:41 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-<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 a049d0d5a05e -r 172091d47f5a sleuth.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sleuth.R	Tue Jun 12 17:58:47 2018 -0400
@@ -0,0 +1,101 @@
+#!/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
+# https://github.com/nturaga/bioc-galaxy-integration/blob/master/README.md
+
+## Command to run tool:
+## Rscript sleuth.R --indir test-rscript --metadata test-rscript/metadata.txt
+## --full_model '~condition' --reduced_model '~1'
+## --gene_anno_name 'hsapiens_gene_ensembl'
+
+# 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)
+
+cat("Successfully finished script.\n")
diff -r a049d0d5a05e -r 172091d47f5a sleuth.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sleuth.xml	Tue Jun 12 17:58:47 2018 -0400
@@ -0,0 +1,83 @@
+<tool id="sleuth" name="sleuth" version="0.30.0">
+  <description>Sleuth is an R library for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto.</description>
+  <requirements>
+    <container type="docker">youyuh48/sleuth:0.30.0</container>
+  </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 '${__tool_directory__}/sleuth.R'
+        --indir 'data'
+        --metadata '$metadata'
+        --full_model '~${full_model}'
+        --reduced_model '~${reduced_model}'
+        #if $anno.biomart == "Yes"
+        --gene_anno_name '$anno.gene_anno_name'
+        #end if
+      && 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"/>
+    <conditional name="anno">
+      <param name="biomart" type="select" label="Use BioMart?" help="">
+        <option value="Yes">Yes</option>
+        <option value="No">No</option>
+      </param>
+      <when value="Yes">
+        <param name="gene_anno_name" type="select" label="BioMart dataset">
+          <option value="hsapiens_gene_ensembl" selected="true">homo_sapiens</option>
+        </param>
+      </when>
+      <when value="No"></when>
+    </conditional>
+  </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 a049d0d5a05e -r 172091d47f5a test-data/SRR1867792.h5
diff -r a049d0d5a05e -r 172091d47f5a test-data/SRR1909613.h5
diff -r a049d0d5a05e -r 172091d47f5a test-data/SRR1909637.h5
diff -r a049d0d5a05e -r 172091d47f5a test-data/metadata.txt