Oncoprintplus

packages/package_boutroslab_plotting_general_5_3_4/tool_dependencies.xml

@@ -11,24 +11,24 @@
             <package name="R" version="3.2.1" />
           </repository>
           <package>https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz</package>
-          <package>https://cran.r-project.org/src/contrib/lattice_0.20-33.tar.gz</package>
+          <package>https://cran.r-project.org/src/contrib/Archive/lattice/lattice_0.20-33.tar.gz</package>
           <package>https://cran.r-project.org/src/contrib/Archive/latticeExtra/latticeExtra_0.6-26.tar.gz</package>
           <package>https://cran.r-project.org/src/contrib/Archive/R.methodsS3/R.methodsS3_1.7.0.tar.gz</package>
-          <package>https://cran.r-project.org/src/contrib/hexbin_1.27.1.tar.gz</package>
+          <package>https://cran.r-project.org/src/contrib/Archive/hexbin/hexbin_1.27.0.tar.gz</package>
           <package>http://bpg.oicr.on.ca/src/contrib/BoutrosLab.plotting.general_5.3.4.tar.gz</package>
-          <package>https://cran.r-project.org/src/contrib/proto_0.3-10.tar.gz</package>
+          <package>https://cran.r-project.org/src/contrib/Archive/proto/proto_0.3-10.tar.gz</package>
           <package>https://cran.r-project.org/src/contrib/findpython_1.0.1.tar.gz</package>
           <package>https://cran.r-project.org/src/contrib/getopt_1.20.0.tar.gz</package>
           <package>https://cran.r-project.org/src/contrib/rjson_0.2.15.tar.gz</package>
-          <package>https://cran.r-project.org/src/contrib/argparse_1.0.1.tar.gz</package>
+          <package>https://cran.r-project.org/src/contrib/Archive/argparse/argparse_1.0.1.tar.gz</package>
           <package>https://cran.r-project.org/src/contrib/assertthat_0.1.tar.gz</package>
-          <package>https://cran.r-project.org/src/contrib/R6_2.1.3.tar.gz</package>
-          <package>https://cran.r-project.org/src/contrib/Rcpp_0.12.6.tar.gz</package>
+          <package>https://cran.r-project.org/src/contrib/Archive/R6/R6_2.1.3.tar.gz</package>
+          <package>https://cran.r-project.org/src/contrib/Archive/Rcpp/Rcpp_0.12.6.tar.gz</package>
           <package>https://cran.r-project.org/src/contrib/lazyeval_0.2.0.tar.gz</package>
-          <package>https://cran.r-project.org/src/contrib/tibble_1.1.tar.gz</package>
+          <package>https://cran.r-project.org/src/contrib/Archive/tibble/tibble_1.1.tar.gz</package>
           <package>https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz</package>
-          <package>https://cran.r-project.org/src/contrib/DBI_0.5.tar.gz</package>
-          <package>https://cran.r-project.org/src/contrib/BH_1.60.0-2.tar.gz</package>
+          <package>https://cran.r-project.org/src/contrib/Archive/DBI/DBI_0.5.tar.gz</package>
+          <package>https://cran.r-project.org/src/contrib/Archive/BH/BH_1.60.0-1.tar.gz</package>
           <package>https://cran.r-project.org/src/contrib/dplyr_0.5.0.tar.gz</package>
         </action>
       </actions>

tools/maftools/.shed.yml

@@ -0,0 +1,7 @@
+categories:
+- Variant Analysis
+description: MAFTools - a suite of visualizations for summarizing MAF files 
+name: maftools
+owner: morinlab
+remote_repository_url: https://github.com/morinlab/tools-morinlab/tree/master/tools/maftools
+type: unrestricted

tools/maftools/all_fasta.loc.sample

@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>      <dbkey> <display_name>  <file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3        apiMel3 Honeybee (Apis mellifera): apiMel3      /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon      hg19    Human (Homo sapiens): hg19 Canonical    /path/to/genome/hg19/hg19canon.fa
+#hg19full       hg19    Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#

tools/maftools/gene_cloud.R

@@ -0,0 +1,33 @@
+require(maftools);
+library(argparse);
+
+###
+
+parser <- ArgumentParser(description="Create a Gene Lollipop using Maftools");
+
+parser$add_argument(
+    "--input_maf", "-maf",
+    required="True",
+    help="Input Variants in MAF format"
+    );
+
+parser$add_argument(
+    "--min_mutations", "-m",
+    required="True",
+    help="Minimum number of mutations for each included gene"
+    )
+
+parser$add_argument(
+    "--output_pdf", "-o",
+    required="True",
+    help="Output PDF"
+    )
+
+args <- parser$parse_args();
+
+###
+
+laml = read.maf(maf = args$input_maf, removeSilent = T, useAll = T)
+pdf(args$output_pdf)
+geneCloud(input = laml, minMut = args$min_mutations)
+dev.off()

tools/maftools/gene_cloud.xml

@@ -0,0 +1,25 @@
+<tool id="gene_cloud" name="Gene Cloud Plot" version="0.9.30">
+
+  <description>
+    creates a cloud plot where gene names are sized by mutation rate
+  </description>
+
+  <command detect_errors="aggressive">
+
+      Rscript $__tool_directory__/gene_cloud.R
+        --input_maf $input_maf
+        --min_mutations $min_mutations
+        --output_pdf $output
+
+  </command>
+
+  <inputs>
+    <param type="data" format="maf" name="input_maf" label="MAF File"/>
+    <param type="integer" min="1" value="3" name="min_mutations" label="Minimum mutation count to include gene"/>
+  </inputs>
+
+  <outputs>
+    <data format="pdf" name="output"/>
+  </outputs>
+
+</tool>    

tools/maftools/lollipop.R

@@ -0,0 +1,39 @@
+require(maftools);
+library(argparse);
+
+###
+
+parser <- ArgumentParser(description="Create a Gene Lollipop using Maftools");
+
+parser$add_argument(
+    "--input_maf", "-maf",
+    required="True",
+    help="Input Variants in MAF format"
+    );
+
+parser$add_argument(
+    "--gene_list", "-gl",
+    required="True",
+    help="Input gene list with separated by newline"
+    );
+
+parser$add_argument(
+   "--output_directory", "-o",
+   required="True",
+   help="Output directory to store gene plots"
+   )
+
+args <- parser$parse_args();
+
+###
+
+all_genes <- read.table(args$gene_list, stringsAsFactors=FALSE)[,1]
+laml = read.maf(maf = args$input_maf, removeSilent = T, useAll = T)
+count = 1
+for (gene in all_genes) {
+    output_name = paste(args$output_directory, paste("samp", count, ".pdf", sep=""), sep="/")
+    pdf(output_name)
+    lollipopPlot(maf = laml, gene = gene, AACol = 'amino_acid_change', labelPos = 'all')
+    dev.off()
+    count <- count + 1
+    }

tools/maftools/lollipop.xml

@@ -0,0 +1,46 @@
+<tool id="lollipop" name="Lollipop Plot" version="0.9.30">
+
+  <description>
+    gene summary plots
+  </description>
+
+  <command detect_errors="aggressive">
+
+      mkdir outputs;
+      touch gene_list.txt;
+      #if $gene_input_type.gene_input_type_selector.value == "other":
+        echo $gene_input_type.gene > gene_list.txt;
+      #else:
+        cat $gene_input_type.gene_file > gene_list.txt;
+      #end if
+
+      Rscript $__tool_directory__/lollipop.R
+        --input_maf $input_maf
+        --gene_list gene_list.txt
+        --output_directory \$(pwd)/outputs;
+
+  </command>
+
+  <inputs>
+    <param type="data" format="maf" name="input_maf" label="MAF File"/>
+    <conditional name="gene_input_type">
+      <param name="gene_input_type_selector" type="select" label="Choose how to input genes">
+        <option value="file" selected="True">Gene File</option>
+        <option value="other">Other</option>
+      </param>
+      <when value="file">
+        <param name="gene_file" type="data" format="txt" label="Gene File"  help="list of genes separated by newlines" />
+      </when>
+      <when value="other">
+        <param name="gene" type="text" value="TP53" label="Gene" help="type the single gene" />
+      </when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <collection name="list_output" type="list" description="Gene Lollipop Plots">
+      <discover_datasets pattern="__name_and_ext__" directory="outputs"/>
+    </collection>
+  </outputs>
+
+</tool>    

tools/maftools/maf_summary.R

@@ -0,0 +1,27 @@
+require(maftools);
+library(argparse);
+
+###
+
+parser <- ArgumentParser(description="Create a Gene Lollipop using Maftools");
+
+parser$add_argument(
+    "--input_maf", "-maf",
+    required="True",
+    help="Input Variants in MAF format"
+    );
+
+parser$add_argument(
+   "--output_pdf", "-o",
+   required="True",
+   help="Output directory to store gene plots"
+   )
+
+args <- parser$parse_args();
+
+###
+
+laml = read.maf(maf = args$input_maf, removeSilent = T, useAll = T)
+pdf(args$output_pdf)
+plotmafSummary(maf = laml, rmOutlier = T, addStat = 'median', dashboard = TRUE)
+dev.off()

tools/maftools/maf_summary.xml

@@ -0,0 +1,23 @@
+<tool id="maf_summary" name="MAF Summary Plot" version="0.9.30">
+
+  <description>
+    summarizes maf statistics into single multiplot
+  </description>
+
+  <command detect_error="aggressive">
+
+      Rscript $__tool_directory__/maf_summary.R
+        --input_maf $input_maf
+        --output_pdf $output;
+
+  </command>
+
+  <inputs>
+    <param type="data" format="maf" name="input_maf" label="MAF File"/>
+  </inputs>
+
+  <outputs>
+    <data format="pdf" name="output"/>
+  </outputs>
+
+</tool>    

tools/maftools/oncoplot.R

@@ -0,0 +1,33 @@
+require(maftools);
+library(argparse);
+
+###
+
+parser <- ArgumentParser(description="Create a Gene Lollipop using Maftools");
+
+parser$add_argument(
+    "--input_maf", "-maf",
+    required="True",
+    help="Input Variants in MAF format"
+    );
+
+parser$add_argument(
+   "--top", "-t",
+   required="True",
+   help="The Top [val] genes to include in plot"
+   )
+
+parser$add_argument(
+   "--output_pdf", "-o",
+   required="True",
+   help="Output directory to store gene plots"
+   )
+
+args <- parser$parse_args();
+
+###
+
+laml = read.maf(maf = args$input_maf, removeSilent = T, useAll = T)
+pdf(args$output_pdf)
+oncoplot(maf = laml, top=args$top)
+dev.off()

tools/maftools/oncoplot.xml

@@ -0,0 +1,25 @@
+<tool id="oncoplot" name="MAF Oncoplot" version="0.9.30">
+
+  <description>
+    summarizes top mutated genes by mutual exclusivity
+  </description>
+
+  <command detect_errors="aggressive">
+
+      Rscript $__tool_directory__/oncoplot.R
+        --input_maf $input_maf
+        --top $top
+        --output_pdf $output;
+
+  </command>
+
+  <inputs>
+    <param type="data" format="maf" name="input_maf" label="MAF File"/>
+    <param type="integer" min="1" value="10" name="top" label="Top Gene Count"/>
+  </inputs>
+
+  <outputs>
+    <data format="pdf" name="output"/>
+  </outputs>
+
+</tool>    

tools/maftools/rainfall.R

@@ -0,0 +1,39 @@
+require(maftools);
+library(argparse);
+
+###
+
+parser <- ArgumentParser(description="Create a Gene Lollipop using Maftools");
+
+parser$add_argument(
+    "--input_maf", "-maf",
+    required="True",
+    help="Input Variants in MAF format"
+    );
+
+parser$add_argument(
+    "--sample_list", "-sl",
+    required="True",
+    help="Input sample list separated by newline"
+    );
+
+parser$add_argument(
+   "--output_directory", "-o",
+   required="True",
+   help="Output directory to store rainfall plots"
+   )
+
+args <- parser$parse_args();
+
+###
+
+all_samples <- read.table(args$sample_list, stringsAsFactors=FALSE)[,1]
+laml = read.maf(maf = args$input_maf, removeSilent = T, useAll = T)
+count = 1
+for (sample in all_samples) {
+    output_name = paste(args$output_directory, paste("samp", count, ".pdf", sep=""), sep="/")
+    pdf(output_name)
+    rainfallPlot(maf = laml, tsb = sample)
+    dev.off()
+    count <- count + 1
+    }