# HG changeset patch
# User jeremie
# Date 1404915465 14400
# Node ID 077a2dbd906aee40bef1f19f5a423c86ca09bb89
# Parent  4e22c03bff6225c74385fa263e2f66fec2f81621
Uploaded

diff -r 4e22c03bff62 -r 077a2dbd906a pindel.xml
--- a/pindel.xml	Tue Jul 08 05:28:06 2014 -0400
+++ b/pindel.xml	Wed Jul 09 10:17:45 2014 -0400
@@ -13,7 +13,7 @@
 		-s $insertSize
 		<!-- -o1 $outputRaw -->
 		-o2 $outputVcfFile
-		-n $sampleTag
+		-t $sampleTag
 
 		<!-- optional -->
 
@@ -98,7 +98,7 @@
 		<!-- required -->
 		<param format="fasta" name="inputReferenceFile" type="data" label="reference file" help="" />
 		<param format="bam" name="inputBamFile" type="data" label="bam file" help="" />
-		<param name="insertSize" type="integer" label="Insert size" help="insert size of the reads" value="500" />
+		<param name="insertSize" type="integer" label="Insert size" help="insert size of the reads" value="" />
 		<param name="sampleTag" type="text" label="Tag" help="tag for this sample" value="sample" />
 
 		<!-- optional -->
@@ -130,13 +130,16 @@
 				<param name="reportDuplications" type="boolean" label="Report duplications" checked="true"/>
 				<param name="reportLongInsertions" type="boolean" label="Report long insertions" checked="true"/>
 				<param name="reportBreakpoints" type="boolean" label="Report breakpoints" checked="true"/>
-
+				<param name="report_only_close_mapped_reads" type="boolean" label="Report only close mapped reads" help="do not search for SVs, only report reads of which only one end (the one closest to the mapped read of the paired-end read) could be mapped (the output file can then be used as an input file for another run of pindel, which may save size if you need to transfer files)." checked="false" />
+				<param name="report_interchromosomal_events" type="boolean" label="Report interchromosomal events" help="search for interchromosomal events. Note: will require the computer to have at least 4 GB of memory" checked="false" />
+				<param name="min_inversion_size" type="integer" value="50" label="min inversion size" help="only report inversions greater than this number of bases" />
 				<conditional name="options_DD">
 					<param name="options_DD_selector" type="select" label="Display paramters affecting Dispersed Duplications">
-						<option value="yes" selected="True">yes</option>
-						<option value="no">no</option>
+						<option value="yes">yes</option>
+						<option value="no" selected="True">no</option>
 					</param>
 					<when value="yes">
+						<!-- <param name="detect_DD" type="boolean" label="Flag indicating whether to detect dispersed duplications" checked="false" /> -->
 						<param name="MAX_DD_BREAKPOINT_DISTANCE" type="integer" value="350" label="MAX DD BREAKPOINT DISTANCE" help="Maximum distance between dispersed duplication breakpoints to assume they refer to the same event" />
 						<param name="MAX_DISTANCE_CLUSTER_READS" type="integer" value="100" label="MAX DISTANCE CLUSTER READS" help="Maximum distance between reads for them to provide evidence for a single breakpoint for dispersed duplications" />
 						<param name="MIN_DD_CLUSTER_SIZE" type="integer" value="3" label="MIN DD CLUSTER SIZE" help="Minimum number of reads needed for calling a breakpoint for dispersed duplications" />
@@ -155,43 +158,12 @@
 			</when>
 		</conditional>
 
-		<conditional name="options_sensel">
-			<param name="options_sensel_selector" type="select" label="Display paramters affecting runtime and memory usage">
-				<option value="yes" selected="True">yes</option>
-				<option value="no">no</option>
-			</param>
-			<when value="yes">
-				<param name="detect_DD" type="boolean" label="Flag indicating whether to detect dispersed duplications" checked="false" />
-
-				<param name="MAX_DD_BREAKPOINT_DISTANCE" type="integer" value="350" label="MAX DD BREAKPOINT DISTANCE" help="Maximum distance between dispersed duplication breakpoints to assume they refer to the same event" />
-
-				<param name="MAX_DISTANCE_CLUSTER_READS" type="integer" value="100" label="MAX DISTANCE CLUSTER READS" help="Maximum distance between reads for them to provide evidence for a single breakpoint for dispersed duplications" />
-
-				<param name="MIN_DD_CLUSTER_SIZE" type="integer" value="3" label="MIN DD CLUSTER SIZE" help="Minimum number of reads needed for calling a breakpoint for dispersed duplications" />
-
-				<param name="MIN_DD_BREAKPOINT_SUPPORT" type="integer" value="3" label="MIN DD BREAKPOINT SUPPORT" help="Minimum number of split reads for calling an exact breakpoint for dispersed duplications" />
-
-				<param name="MIN_DD_MAP_DISTANCE" type="integer" value="8000" label="MIN DD MAP DISTANCE" help="Minimum mapping distance of read pairs for them to be considered discordant" />
-
-				<param name="DD_REPORT_DUPLICATION_READS" type="boolean" label="DD REPORT DUPLICATION READS" checked="false" help="Report discordant sequences and positions for mates of reads mapping inside dispersed duplications"/>
-				<param name="report_close_mapped_reads" type="boolean" label="Report close mapped reads" help="report reads of which only one end (the one closest to the mapped read of the paired-end read) could be mapped." checked="false" />
-
-
-				<param name="report_only_close_mapped_reads" type="boolean" label="Report only close mapped reads" help="do not search for SVs, only report reads of which only one end (the one closest to the mapped read of the paired-end read) could be mapped (the output file can then be used as an input file for another run of pindel, which may save size if you need to transfer files)." checked="false" />
-
-				<param name="report_interchromosomal_events" type="boolean" label="Report interchromosomal events" help="search for interchromosomal events. Note: will require the computer to have at least 4 GB of memory" checked="false" />
-				<param name="min_inversion_size" type="integer" value="50" label="min inversion size" help="only report inversions greater than this number of bases" />
-			</when>
-			<when value="no">
-				<!-- Do nothing here -->
-			</when>
-		</conditional>
 
 		<!-- Parameters affecting sensitivity and selectivity -->
 		<conditional name="options_sensel">
 			<param name="options_sensel_selector" type="select" label="Display paramters affecting runtime and memory usage">
-				<option value="yes" selected="True">yes</option>
-				<option value="no">no</option>
+				<option value="yes">yes</option>
+				<option value="no" selected="True">no</option>
 			</param>
 			<when value="yes">
 				<param name="sequencing_error_rate" type="float" value="0.01" label="Sequencing error rate" help="the expected fraction of sequencing errors"/>
@@ -218,8 +190,8 @@
 		<!-- Miscellaneous parameters -->
 		<conditional name="options_miscellaneous">
 			<param name="options_miscellaneous_selector" type="select" label="Display miscellaneous paramters">
-				<option value="yes" selected="True">yes</option>
-				<option value="no">no</option>
+				<option value="yes">yes</option>
+				<option value="no" selected="True">no</option>
 			</param>
 			<when value="yes">
 				<conditional name="breakdancer">