# HG changeset patch
# User stef
# Date 1402666896 14400
# Node ID 75d96e0555d1f36f0d32ebd7fa277dd09925f00a
# Parent  e81046cbc191576008931acdef0d904f248822a4
Uploaded

diff -r e81046cbc191 -r 75d96e0555d1 QDNAseq.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/QDNAseq.xml	Fri Jun 13 09:41:36 2014 -0400
@@ -0,0 +1,328 @@
+<tool id="QDNAseq" name="QDNAseq" version="0.0.1">
+  
+  <requirements>
+    <!-- <requirement type="set_environment">QDNASEQ_SCRIPT_PATH</requirement> -->
+    <requirement type="package" version="3.0.3">R</requirement>
+  </requirements>
+
+  <description>Quantitative copy number abberation detection</description>
+  
+  <command interpreter="Rscript">
+    QDNAseq.R 
+    $qdnaseq_cfg <!-- use a tmp config file to pass all params to R by source() -->
+  </command>
+
+  <stdio>
+    <!-- Anything higher than 0 means the R script didnt finish -->
+    <!-- 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 -->
+    <!-- ==================== -->
+    <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>
+      <!-- <validator type="expression" message="Window Size must be even">value % 2 ==0</validator> -->
+    </param>
+    <param name="binSize" type="select" label="Select bin-size to use (kb)" help="Larger bin sizes provide faster analysis but lower resolution">
+      <option value="1000">1Mb</option>
+      <option value="100">100kb</option>
+      <option value="30">30kb</option>
+      <option value="15">15kb</option>
+      <option value="5">5kb</option>
+      <option value="1">1kb</option>
+    </param>
+    <param name="doCall" type="select" label="Also segment and call with CGHcall" help="This setting will be set to yes if called output is requested (see additional history outputs)">
+      <option value="TRUE">yes</option>
+      <option value="FALSE">no</option>
+    </param>
+    <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 Read 50bp</option>
+      <!-- <option value="PE1000">PairedEnd1000</option> -->
+    </param>
+    
+    <!--
+    <param name="excludeChrs" type="select" multiple="true" label="Exclude certain Chromosomes">
+      <option value="X">X</option>
+      <option value="Y">Y</option>
+    </param>
+    -->
+
+    <!-- ==================== -->
+    <!-- Input BAMs -->
+    <!-- ==================== -->
+    <param name="bams" type="data" multiple="true" optional="false" format="bam" label="Input BAMs" help="Select all BAM files to include in the analysis" />
+
+    <!-- ==================== -->
+    <!-- This section contains galaxy history output settings -->
+    <!-- ==================== -->
+    <conditional name="extra_history_outputs">
+      <param name="show" type="select" label="Show additional history outputs">
+        <option value="NO">Only output Report to history</option>
+        <option value="YES">Select additional history outputs</option>
+      </param>
+      <when value="YES">
+        <param name="readcounts_rds" type="select" label="Also output readcounts RDS (R object) to history">
+          <option value="FALSE">no</option>
+          <option value="TRUE">yes</option>
+        </param>
+        <param name="copynumbers_rds" type="select" label="Also output copynumbers RDS (R object) to history">
+          <option value="FALSE">no</option>
+          <option value="TRUE">yes</option>
+        </param>
+        <param name="calls_rds" type="select" label="Also output called segments RDS (R object) to history">
+          <option value="FALSE">no</option>
+          <option value="TRUE">yes</option>
+        </param>
+      </when>
+      <when value="NO">
+        <param name="readcounts_rds" type="hidden" value="FALSE" />
+        <param name="copynumbers_rds" type="hidden" value="FALSE" />
+        <param name="calls_rds" type="hidden" value="FALSE" />
+      </when>
+    </conditional>
+
+    <!-- ==================== -->
+    <!-- Option to use your own bin annotations -->
+    <!-- ==================== -->
+    <conditional name="use_own_binannotation">
+      <param name="show" type="select" label="Use your own bin annotations from history">
+        <option value="no">no</option>
+        <option value="yes">yes</option>
+      </param>
+      <when value="yes">
+        <param name="binannotation_file" type="data" multiple="false" format="rds" label="R data structure file 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="no">
+        <param name="binannotation_file" type="hidden" value="" />
+      </when>
+    </conditional> 
+    <!-- ==================== -->
+    <!-- Optional advanced options -->
+    <!-- ==================== -->
+    <conditional name="advanced">
+      <param name="show" type="select" label="Show advanced options">
+        <option value="no">no</option>
+        <option value="yes">yes</option>
+      </param>
+      <when value="yes">
+        
+        <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)" />
+
+        <param name="debug" type="select" label="DEBUG" help="Uses the inbuilt LGG data instead of input BAMs">
+          <option value="FALSE">no</option>
+          <option value="TRUE">yes</option>
+        </param>
+      </when>
+      <!-- need to set defaults because params are passed to R anyway -->
+      <when value="no">
+        <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="debug" type="hidden" value="FALSE" />
+      </when>
+    </conditional> 
+
+    <!-- ==================== -->
+    <!-- Optional graphical/plotting options -->
+    <!-- ==================== -->
+    <conditional name="plot_options">
+      <param name="show" type="select" label="Show graphical options">
+        <option value="no">no</option>
+        <option value="yes">yes</option>
+      </param>
+      <when value="yes">
+        <param name="plot_width" size="3" type="integer" value="960" label="Plot width" />
+        <param name="plot_height" size="3" type="integer" value="480" label="Plot height" />
+        <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>
+      <when value="no">
+        <param name="plot_width" type="hidden" value="960" />
+        <param name="plot_height" type="hidden" value="480" />
+        <param name="exclude_chrs" type="hidden" value="X,Y" />
+      </when>
+    </conditional>
+  </inputs>
+  <!-- ==================== -->
+  <!-- This config is sourced in R code -->
+  <!-- ==================== -->
+  <configfiles>
+    <configfile name="qdnaseq_cfg">
+## this file was sourced in QDNAseq R wrapper script
+## in this way all galaxy params are passes to R
+
+## required params
+as.integer( "${binSize}" ) -> binSize
+"${experimentType}" -> experimentType
+"${jobName}" -> outputName
+
+## extra params
+as.logical( "${doCall}" ) -> doCall
+"${htmlFile}" -> outputHtml
+"${htmlFile.files_path}" -> outputPath
+"${use_own_binannotation.binannotation_file}" -> binAnnotations
+
+## advanced options
+as.double( "${advanced.undoSD}" ) -> undoSD
+as.logical( "${advanced.debug}" ) -> debug
+as.logical( "${advanced.blacklist}" ) -> filterBlacklistedBins
+as.integer( "${advanced.mappability}" ) -> mappabilityCutoff
+"${advanced.undo_splits}" -> undoSplits
+
+## history output params
+as.logical( "${extra_history_outputs.readcounts_rds}" ) -> doOutputReadcountsRds
+as.logical( "${extra_history_outputs.copynumbers_rds}" ) -> doOutputCopynumbersRds
+as.logical( "${extra_history_outputs.calls_rds}" ) -> doOutputCallsRds
+"${rdsReadCounts}" -> readCountsDatasetFile
+"${rdsCopyNumbers}" -> copyNumbersDatasetFile
+"${rdsCalls}" -> calledSegmentsDatasetFile
+
+## plotting params
+as.integer( "${plot_options.plot_width}" ) -> PLOT_WIDTH
+as.integer( "${plot_options.plot_height}" ) -> PLOT_HEIGHT
+"${plot_options.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, additional on request -->
+  <!-- ==================== -->
+  <outputs>
+
+    <data format="html" name="htmlFile" label="QDNAseq Report ${binSize}kb (${jobName})" />
+    
+    <data format="rds" name="rdsReadCounts" label="${jobName}_readCounts_${binSize}kb.rds">
+      <filter> extra_history_outputs['readcounts_rds'] == "TRUE" </filter><!-- <filter>("readcounts_rds" in outputs)</filter> -->
+    </data>
+
+    <data format="rds" name="rdsCopyNumbers" label="${jobName}_copyNumbers_${binSize}kb.rds">
+      <filter> extra_history_outputs['copynumbers_rds'] == "TRUE" </filter>
+    </data>
+
+    <data format="rds" name="rdsCalls" label="${jobName}_calls_${binSize}kb.rds">
+      <filter> extra_history_outputs['calls_rds'] == "TRUE" </filter>
+    </data>
+
+  </outputs>
+
+  <!-- ==================== -->
+  <!-- Tests still to be done -->
+  <!-- ==================== -->
+
+  <!-- 
+  <tests>
+    <test>
+      <param name="input1" value="5.bed" />
+      <param name="distance" value="1" />
+      <param name="minregions" value="2" />
+      <param name="returntype" value="1" />
+      <output name="output" file="gops-cluster-1.bed" />     
+    </test>
+  </tests>
+  -->
+  <!-- <requirements>
+      <requirement type="package">ucsc_tools</requirement>
+  </requirements>
+-->
+
+  <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.
+
+-----
+
+.. class:: warningmark
+
+Requires internet access for downloading bin-annotations from bitbucket and to show css styling of the final report
+
+.. class:: warningmark
+
+All R stderr is rerouted to stdout due to limitations in R. This means the tool might be marked succesful (green) while it actually isn't, closer inspection of the stdout output is required in that case.
+
+.. class:: warningmark
+
+The smaller the binsize, the longer the analysis takes
+
+.. class:: warningmark
+
+If the data is noisy, a **larger binsize** should be chosen
+
+.. 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 supported within galaxy. See the documentation of QDNAseq at bioconductor on how to deal with different setups.
+
+-----
+
+**Example**
+
+To be done
+
+-----
+
+**Citation**
+
+For the underlying tool please cite: llari Scheinin, Daoud Sie et al. DNA copy number analysis of fresh and formalin-fixed specimens by whole-genome sequencing: improved correction of systematic biases and exclusion of problematic regions, (submitted). See also the bioconductor package_ documentation.
+
+.. _package: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html
+  </help>
+
+</tool>
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