# HG changeset patch
# User stef
# Date 1419948573 18000
# Node ID fbe7fe47991f0976b3b0459a2be310b9ea989397
# Parent  831c62364275c753aac4c0af1c08e8161f1b54c0
Uploaded

diff -r 831c62364275 -r fbe7fe47991f QDNAseq.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/QDNAseq.xml	Tue Dec 30 09:09:33 2014 -0500
@@ -0,0 +1,297 @@
+<tool id="QDNAseq" name="QDNAseq" version="0.0.2" force_history_refresh="True">
+  
+  <requirements>
+    
+    <requirement type="package" version="0.1.18">samtools</requirement>
+    <!-- R 3.1.0 dependency will be used instead when available, now default R is used, see command -->
+    <!-- <requirement type="package" version="3.1.0">R</requirement> -->
+    <!-- <requirement type="package" version="1.0.5">qdnaseq</requirement> -->
+    <requirement type="set_environment">QDNASEQ_PATH</requirement>
+    
+  </requirements>
+
+  <description>Quantitative copy number abberation detection</description>
+
+  <!-- change to /full/path/to/Rscript if required (eg /ccagc/lib/R/R-3.1.0/bin/Rscript) -->
+  <command interpreter="Rscript"> 
+    QDNAseq.R 
+    $qdnaseq_cfg
+    \$QDNASEQ_PATH
+  </command>
+
+  <stdio>
+    <!-- Anything higher than 0 means the R script didnt finish (correctly) -->
+    <!-- Because different R packages deal with err/warn differently unable to waterproof this -->
+    <exit_code range="1:" level="fatal" description="R script didnt finish correctly, check log" />
+  </stdio>
+  
+  <inputs>
+    
+    <!-- ==================== -->
+    <!-- General inputs -->
+    <!-- ==================== -->
+    
+    <!-- Job name: must contain non-whitespace chars -->
+    <param name="jobName" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain" value="TEST">
+      <validator type="empty_field" />
+      <validator type="regex" message="This field should contain some non-whitespace character">.*\S</validator>
+    </param>
+
+    <!-- Bin Size: only certain sizes are supported by QDNAseq package -->
+    <param name="binSizes" type="select" optional="false" multiple="true" label="Select bin-sizes to use (kb)" help="Larger bin sizes provide faster analysis but lower resolution">
+      <option value="1000" selected="true">1Mb</option>
+      <option value="100" selected="true">100kb</option>
+      <option value="30">30kb</option>
+      <option value="15" selected="true">15kb</option>
+      <option value="5">5kb</option>
+      <option value="1">1kb</option>
+    </param>
+
+    <!-- Experiment type: only one type (SR50) supported now, maybe more in the future-->
+    <param name="experimentType" type="select" label="Type of sequencing data" help="Currently only single end reads of lenght 50 are supported within galaxy">
+      <option value="SR50">Single Reads of 50bp</option>
+      <!-- <option value="PE1000">PairedEnd1000</option> -->
+    </param>
+
+    <!-- ==================== -->
+    <!-- Input BAMs -->
+    <!-- ==================== -->
+    <param name="bams" type="data" multiple="true" optional="True" format="bam" label="Input BAMs" help="Select the BAM files to analyze" />
+
+    <!-- ==================== -->
+    <!-- Optional segmenting -->
+    <!-- ==================== -->
+    <param name="doSegment" type="select" label="Also perform segmentation" help="Segmentation collects bins with similar ratio into regions">
+      <option value="TRUE">yes</option>
+      <option value="FALSE">no</option>
+    </param>
+
+    <!-- ==================== -->
+    <!-- Option to use your own bin annotations file -->
+    <!-- ==================== -->
+    <conditional name="binannotations_source">
+      <param name="show" type="select" label="Bin annotations to use" help="Default bin-annotations are for GRCh37/hg19 and tuned for 50bp reads (single end)">
+        <option value="default">Default</option>
+        <option value="history">From history</option>
+      </param>
+      <when value="history">
+        <param name="binannotation_file" type="data" multiple="false" label="R data structure file (*.rds) with bin-annotations" help="If you made your own bin-annotations with the QDNAseq bioconductor package you can upload them to your history and select here" />
+      </when>
+      <when value="default">
+        <param name="binannotation_file" type="hidden" value="" />
+      </when>
+      
+    </conditional> 
+
+    <!-- ==================== -->
+    <!-- Optional advanced options -->
+    <!-- ==================== -->
+    <conditional name="advanced">
+      <param name="show" type="select" label="Use advanced options" help="Select yes to show and use filter and output options">
+        <option value="no">no</option>
+        <option value="yes">yes</option>
+      </param>
+      <when value="yes">
+        
+        <param name="copynumbers_igv" type="select" label="Also output copynumber IGV file to history">
+          <option value="FALSE">no</option>
+          <option value="TRUE">yes</option>
+        </param>
+
+        <param name="undo_splits" type="select" label="undoSplits" help="If set to sdundo, see undoSD below">
+          <option value="sdundo">sdundo</option>
+          <option value="prune">prune</option>
+          <option value="none">none</option>
+        </param>
+
+        <param name="undoSD" size="10" type="float" value="1" label="undoSD" help='The number of SDs between means to keep a split if undo.splits="sdundo".' />
+          
+        <param name="blacklist" type="select" label="Filter blacklisted bins (blacklist)" help="Will exclude all blacklisted bins in the binannotation if set">
+          <option value="TRUE">yes</option>
+          <option value="FALSE">no</option>
+        </param>
+
+        <param name="mappability" type="integer" value="0" min="0" max="100" label="Filter bins with lower mappability" help="Will exclude all bins will lower mappability than this number (0-100)" />
+      
+        <!-- ==================== -->
+        <!-- Optional graphical/plotting options -->
+        <!-- ==================== -->
+        <param name="plot_width" size="3" type="integer" value="1440" label="Width of the png image produced" />
+        <param name="plot_height" size="3" type="integer" value="720" label="Height of the png image produced" />
+        <param name="exclude_chrs" type="select" multiple="true" label="Hide these chromosomes in plots" help="Currently only standard human chromosomes supported. NOTE: other filters might also exclude chromosomes">
+          <option value="1">1</option><option value="2">2</option>
+          <option value="3">3</option><option value="4">4</option>
+          <option value="5">5</option><option value="6">6</option>
+          <option value="7">7</option><option value="8">8</option>
+          <option value="9">9</option><option value="10">10</option>
+          <option value="11">11</option><option value="12">12</option>
+          <option value="13">13</option><option value="14">14</option>
+          <option value="15">15</option><option value="16">16</option>
+          <option value="17">17</option><option value="18">18</option>
+          <option value="19">19</option><option value="20">20</option>
+          <option value="21">21</option><option value="22">22</option>
+          <option value="X" selected="true">X</option>
+          <option value="Y" selected="true">Y</option>
+        </param>
+      </when>
+
+      <!-- need to set defaults because params are passed to R regardless of conditional opened/closed -->
+      <when value="no">
+        <param name="copynumbers_igv" type="hidden" value="FALSE" />
+        <param name="undoSD" type="hidden" value="1" />
+        <param name="undo_splits" type="hidden" value="sdundo" />
+        <param name="blacklist" type="hidden" value="TRUE" />
+        <param name="mappability" type="hidden" value="0" />
+        <param name="plot_width" type="hidden" value="1440" />
+        <param name="plot_height" type="hidden" value="720" />
+        <param name="exclude_chrs" type="hidden" value="X,Y" />
+      </when>
+    </conditional>
+
+    <!-- ==================== -->
+    <!-- Option to perform a test run with built in data -->
+    <!-- ==================== -->
+    <param name="debug" type="select" label="Run with test data" help="Use inbuilt LGG150 data instead of input BAMs">
+      <option value="FALSE">no</option>
+      <option value="TRUE">yes</option>
+    </param>
+    
+  </inputs>
+  <!-- ==================== -->
+  <!-- Config file to pass params to R script -->
+  <!-- ==================== -->
+  <configfiles>
+    <configfile name="qdnaseq_cfg">
+## Desc: this file was sourced in QDNAseq R wrapper script
+##  as means to pass all galaxy params to R
+
+## -----
+## required params
+## -----
+TRUE -> inGalaxy 
+"${binSizes}" -> binSizesString
+"${experimentType}" -> experimentType
+"${jobName}" -> outputName
+
+## -----
+## extra main params
+## -----
+"${htmlFile}" -> outputHtml
+"${htmlFile.id}" -> outputId
+"${__new_file_path__}" -> newFilePath
+
+"${htmlFile.files_path}" -> outputPath
+as.logical( "${doSegment}" ) -> doSegment
+as.logical( "${debug}" ) -> debug
+
+## -----
+## own bin-annotations file options
+## -----
+"${binannotations_source.binannotation_file}" -> binAnnotations
+
+## -----
+## advanced options
+## -----
+as.double( "${advanced.undoSD}" ) -> undoSD
+as.logical( "${advanced.blacklist}" ) -> filterBlacklistedBins
+as.integer( "${advanced.mappability}" ) -> mappabilityCutoff
+"${advanced.undo_splits}" -> undoSplits
+as.logical( "${advanced.copynumbers_igv}" ) -> doOutputCopynumbersIgv
+
+## #for binSize in $binSizes}.split(",")# 
+## "${binSize}kbp_${igvCopyNumbers}" -> copyNumbersIgvDatasetFile
+## #end for
+
+## -----
+## plot options
+## -----
+as.integer( "${advanced.plot_width}" ) -> PLOT_WIDTH
+as.integer( "${advanced.plot_height}" ) -> PLOT_HEIGHT
+"${advanced.exclude_chrs}" -> excludeChrsString
+  
+## -----
+## input BAMs init
+## -----
+c() -> bamsPaths
+c() -> bamsNames
+
+#for bam in $bams# 
+c( bamsPaths, "${bam}" ) -> bamsPaths
+c( bamsNames, "${bam.name}" ) -> bamsNames
+#end for
+
+    </configfile>
+  </configfiles>
+
+  <!-- ==================== -->
+  <!-- Main output is an html based report -->
+  <!-- ==================== -->
+  <outputs>
+
+    <!-- main output is a html report -->
+    <!-- ...but there can be more outputs using the id of the htmlFile output -->
+    <data format="html" name="htmlFile" label="QDNAseq: ${jobName}" />
+
+  </outputs>
+
+  <!-- ==================== -->
+  <!-- Tests still to be done -->
+  <!-- ==================== -->
+
+  <!-- 
+  <tests>
+    <test>
+      <param name="input1" value="input1" />   
+      <param name="input2" value="input2" />   
+    </test>
+  </tests>
+  -->
+
+  <help>
+.. class:: infomark
+
+**Introduction**
+
+This tool is a wrapper for the R Bioconductor package QDNAseq_
+
+.. _QDNAseq: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html
+
+It determines the copy number state of human chromosomes 1 - 22 for (shallow coverage) whole genome sequencing data.
+
+For questions/remarks about the galaxy part of this tool, see contact form here_
+
+.. _here: http://www.stefs.nl/wp/contact
+
+You can **test this tool** with built-in data by selecting the option "Run with test data" and press execute.
+
+-----
+
+.. class:: warningmark
+
+As there is no R 3.1.0 galaxy-package yet (a requirement for QDNAseq), the **dependencies** need to be installed by hand and available to the user under which galaxy runs: R (3.1.0) and bioconductor package QDNAseq (>= 1.0.5). In case the default R is not 3.1.0, also the wrapper xml must be updated to include the correct path during installation of this tool.
+
+.. class:: warningmark
+
+The input BAMs are expected to be **single end reads of 50bp length** mapped to GRCh37/hg19 genome build. Other experiment setups are currently not tested or supported within galaxy. See the documentation of QDNAseq at bioconductor on how to deal with different setups (or keep fingers crossed ;) )
+
+.. class:: warningmark
+
+Requires **internet access** for downloading bin-annotations from bitbucket and to show some styling (css) of the final report
+
+-----
+
+**Citation**
+
+For the underlying QDNAseq R package please cite: 
+Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG and Ylstra B (2014). “DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly.” Genome Research. doi:10.1101/gr.175141.114.
+
+See also the bioconductor package_ documentation.
+
+.. _package: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html
+
+.. image:: LGG150_copynumber.png
+.. image:: LGG150_copynumberSegmented.png
+
+  </help>
+
+</tool>