diff QDNAseq-plot.xml @ 27:f89205f51e27 draft default tip

Uploaded

--- a/QDNAseq-plot.xml	Mon Jul 06 05:38:44 2015 -0400
+++ b/QDNAseq-plot.xml	Mon Jul 06 05:41:08 2015 -0400
@@ -16,6 +16,8 @@
     $cfg
   </command>
 
+  <version_command interpreter="Rscript">QDNAseq-version.R</version_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 -->
@@ -57,7 +59,57 @@
       
     </conditional> 
     -->
-    <param name="sample_index" type="integer" required="True" value="1" label="Sample-index (integer)" help="The RDS input object can contain data from multiple individuals, this number tells the script which one to plot. Plotting multiple at the same time is not supported." />
+    <param name="sample_index" type="integer" required="True" value="1" label="Sample-index (integer)" help="The RDS input object can contain data from multiple samples, this index tells the script which one to plot. Plotting multiple samples at the same time is not supported." />
+
+    <conditional name="subset_selection">
+      <param name="what_to_plot" type="select" label="What to plot" help="Instead of plotting everything in the object you can also select certain chromosomes or set a genomic region">
+        <option value="everything">Everything</option>
+        <option value="chromosomes">Selected chromosomes</option>
+        <option value="region">Genomic region</option>
+      </param>
+      <when value="everything">
+        <!-- ==================== -->
+        <param name="chr_name" type="hidden" value="NA" />
+        <param name="chr_start" type="hidden" value="NA" />
+        <param name="chr_end" type="hidden" value="NA" />
+        <param name="chromosomes" type="hidden" value="NA" />
+      </when>
+      <when value="chromosomes">
+        <!-- ==================== -->
+        <param name="chromosomes" type="select" multiple="true" optional="false" label="Select chromosomes to plot" help="To zoom in on a particular chromosome you can select one or more here">
+          <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>
+        <param name="chr_name" type="hidden" value="NA" />
+        <param name="chr_start" type="hidden" value="NA" />
+        <param name="chr_end" type="hidden" value="NA" />
+      </when>
+      <when value="region">
+        <!-- ==================== -->
+        <!--
+        <param name="genomic_region" type="text" optional="false" label="Genomic region" help="Supply a genomic region in format chr1:12345-23456" value="chr1:12345-23456" size="30">
+          <validator type="regex" message="No whitespace characters allowed">^[^\s\\]*$</validator>
+          <validator type="regex" message="String is not of correct format">^chr\d+\:\d+\-\d+$</validator>
+        </param>
+        -->
+        <param name="chr_name" size="2" type="integer" optional="false" value="" label="Chromosome" />
+        <param name="chr_start" size="15" type="integer" optional="false" value="" label="Start position on chromosome" />
+        <param name="chr_end" size="15" type="integer" optional="false" value="" label="End position on chromosome" />
+        <param name="chromosomes" type="hidden" value="NA" />
+      </when>
+
+    </conditional>
 
     <!-- ==================== -->
     <!-- Optional advanced options -->
@@ -98,6 +150,11 @@
 "${outputPng}" -> outputPngPath
 "${rdsFile}" -> rdsFilePath
 as.integer( "${sample_index}" ) -> SAMPLE_INDEX
+"${subset_selection.what_to_plot}" -> whatToPlot
+"${subset_selection.chromosomes}" -> chromosomesToPlotString
+as.integer( "${subset_selection.chr_name}" ) -> chrName
+as.integer( "${subset_selection.chr_start}" ) -> chrStart
+as.integer( "${subset_selection.chr_end}" ) -> chrEnd
 
 ## -----
 ## extra options