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changeset 21:6f9c0884a3e7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 78c3dea7dcd0c854fe7e6dc1d2b2349956167661
author iuc
date Tue, 16 Oct 2018 11:49:10 -0400
parents 2a17c789e0a5
children f6ced08779c4
files picard_EstimateLibraryComplexity.xml picard_MarkDuplicates.xml picard_MarkDuplicatesWithMateCigar.xml picard_macros.xml
diffstat 4 files changed, 17 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- a/picard_EstimateLibraryComplexity.xml	Tue Jun 19 11:28:49 2018 -0400
+++ b/picard_EstimateLibraryComplexity.xml	Tue Oct 16 11:49:10 2018 -0400
@@ -18,8 +18,7 @@
     MAX_DIFF_RATE="${max_diff_rate}"
     MIN_MEAN_QUALITY="${min_mean_quality}"
     MAX_GROUP_RATIO="${max_group_ratio}"
-    #import pipes
-    READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
+    READ_NAME_REGEX='${ str( $read_name_regex ) }'
     OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"
 
     VALIDATION_STRINGENCY="${validation_stringency}"
@@ -36,10 +35,7 @@
     <param name="max_group_ratio" type="integer" value="500" label="Do not process self-similar groups that are this many times over the mean expected group size" help="MAX_GROUP_RATIO; I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then the mean expected group size would be approximately 10 reads; default-500"/>
 
     <param name="read_name_regex" type="text" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.">
-      <sanitizer>
-        <valid initial="string.printable">
-        </valid>
-      </sanitizer>
+      <expand macro="sanitize_query" />
     </param>
     <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>
 
--- a/picard_MarkDuplicates.xml	Tue Jun 19 11:28:49 2018 -0400
+++ b/picard_MarkDuplicates.xml	Tue Oct 16 11:49:10 2018 -0400
@@ -24,9 +24,8 @@
 
     DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}'
 
-    #import pipes
     #if $read_name_regex:
-      READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) }
+      READ_NAME_REGEX='${ str( $read_name_regex ) }'
     #end if
     OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}'
 
@@ -55,11 +54,7 @@
     </param>
 
     <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default='' (uses : separation)">
-
-      <sanitizer>
-        <valid initial="string.printable">
-        </valid>
-      </sanitizer>
+      <expand macro="sanitize_query" />
     </param>
     <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>
 
--- a/picard_MarkDuplicatesWithMateCigar.xml	Tue Jun 19 11:28:49 2018 -0400
+++ b/picard_MarkDuplicatesWithMateCigar.xml	Tue Oct 16 11:49:10 2018 -0400
@@ -26,8 +26,7 @@
 
     DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}"
 
-    #import pipes
-    READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
+    READ_NAME_REGEX='${ str( $read_name_regex ) }'
     OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"
 
 
@@ -54,10 +53,7 @@
 
 
     <param name="read_name_regex" type="text" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.">
-      <sanitizer>
-        <valid initial="string.printable">
-        </valid>
-      </sanitizer>
+      <expand macro="sanitize_query" />
     </param>
     <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>
 
--- a/picard_macros.xml	Tue Jun 19 11:28:49 2018 -0400
+++ b/picard_macros.xml	Tue Oct 16 11:49:10 2018 -0400
@@ -9,6 +9,17 @@
         </param>
     </xml>
 
+    <xml name="sanitize_query">
+        <sanitizer>
+            <valid initial="string.printable">
+                <remove value="&apos;" />
+            </valid>
+            <mapping initial="none">
+                <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
+            </mapping>
+       </sanitizer>
+    </xml>
+
     <token name="@TOOL_VERSION@">2.18.2</token>
 
     <xml name="requirements">