# HG changeset patch
# User devteam
# Date 1444753669 14400
# Node ID 2589e6207cb415533feeb5f94884e52f75adde09
# Parent  52fdfc45590ad322883fdafeec43816ba173f871
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

diff -r 52fdfc45590a -r 2589e6207cb4 picard_AddCommentsToBam.xml
--- a/picard_AddCommentsToBam.xml	Thu Jul 16 15:32:31 2015 -0400
+++ b/picard_AddCommentsToBam.xml	Tue Oct 13 12:27:49 2015 -0400
@@ -21,7 +21,7 @@
   <inputs>
     <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
     <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
-          <param name="comment" type="text" size="50" label="Add this comment to BAM dataset" help="COMMENT"/>
+          <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
     </repeat>
 
     <expand macro="VS" />
diff -r 52fdfc45590a -r 2589e6207cb4 picard_CollectAlignmentSummaryMetrics.xml
--- a/picard_CollectAlignmentSummaryMetrics.xml	Thu Jul 16 15:32:31 2015 -0400
+++ b/picard_CollectAlignmentSummaryMetrics.xml	Tue Oct 13 12:27:49 2015 -0400
@@ -1,21 +1,24 @@
-<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.0">
+<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.1">
   <description>writes a file containing summary alignment metrics</description>
   <macros>
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
   <command>
     @java_options@
     ##set up input files
 
     #set $reference_fasta_filename = "localref.fa"
-    
+
     #if str( $reference_source.reference_source_selector ) == "history":
         ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
-    
+
     java -jar \$JAVA_JAR_PATH/picard.jar
     CollectAlignmentSummaryMetrics
     INPUT="${inputFile}"
@@ -24,11 +27,13 @@
     #for $sequence in $adapters:
         ADAPTER_SEQUENCE="${sequence.adapter}"
     #end for
-    METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
+    #for $level in str($metric_accumulation_level).split(','):
+        METRIC_ACCUMULATION_LEVEL="${level}"
+    #end for
     IS_BISULFITE_SEQUENCED="${bisulphite}"
-    
+
     REFERENCE_SEQUENCE="${reference_fasta_filename}"
-    
+
     ASSUME_SORTED="${assume_sorted}"
 
     VALIDATION_STRINGENCY="${validation_stringency}"
@@ -63,23 +68,15 @@
     <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
     <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/>
     <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences">
-          <param name="adapter" type="text" size="50" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/>
+          <param name="adapter" type="text" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/>
     </repeat>
-    <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" size="20" help="MAX_INSERT_SIZE"/>
-    
+    <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/>
     <expand macro="VS" />
-    
+
   </inputs>
-  
   <outputs>
     <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
   </outputs>
-  
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
-  
-  
   <tests>
     <test>
       <param name="bisulphite" value="false" />
@@ -92,7 +89,6 @@
       <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/>
     </test>
   </tests>
-  
   <help>
 
 .. class:: infomark
diff -r 52fdfc45590a -r 2589e6207cb4 picard_CollectRnaSeqMetrics.xml
--- a/picard_CollectRnaSeqMetrics.xml	Thu Jul 16 15:32:31 2015 -0400
+++ b/picard_CollectRnaSeqMetrics.xml	Tue Oct 13 12:27:49 2015 -0400
@@ -83,7 +83,7 @@
       </param>
       <param name="minimum_length" type="integer" value="500" label="When calculating coverage based values use only use transcripts of this length or greater" help="MINIMUM_LENGTH; default=500"/>
       <repeat name="ignore_list" title="Sequences to ignore" min="0" help="You can provide multiple sequences by clicking the button below">
-          <param name="sequence" type="text" size="80" label="Ignore reads matching this sequence"/>
+          <param name="sequence" type="text" label="Ignore reads matching this sequence"/>
       </repeat>
       <param name="rrna_fragment_percentage" type="float" value="0.8" label="This percentage of the length of a fragment must overlap one of the ribosomal intervals for a read or read pair to be considered rRNA." help="RRNA_FRAGMENT_PERCENTAGE; default=0.8"/>
       <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
diff -r 52fdfc45590a -r 2589e6207cb4 picard_DownsampleSam.xml
--- a/picard_DownsampleSam.xml	Thu Jul 16 15:32:31 2015 -0400
+++ b/picard_DownsampleSam.xml	Tue Oct 13 12:27:49 2015 -0400
@@ -19,8 +19,8 @@
   </command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset" />
-    <param name="probability" type="float" size="4" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
-    <param name="seed" type="integer" size="5" label="Random seed value" help="RANDOM_SEED; default=1" value="1" />
+    <param name="probability" type="float" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
+    <param name="seed" type="integer" label="Random seed value" help="RANDOM_SEED; default=1" value="1" />
     
     <expand macro="VS" />
     
diff -r 52fdfc45590a -r 2589e6207cb4 picard_EstimateLibraryComplexity.xml
--- a/picard_EstimateLibraryComplexity.xml	Thu Jul 16 15:32:31 2015 -0400
+++ b/picard_EstimateLibraryComplexity.xml	Tue Oct 13 12:27:49 2015 -0400
@@ -33,7 +33,7 @@
     <param name="min_mean_quality" type="integer" min="0" max="93" value="20" label="The minimum mean quality of the bases in a read pair for the read to be analyzed" help="MIN_MEAN_QUALITY; Reads with lower average quality are filtered out and not considered in any calculations; default=20"/>
     <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" size="40" 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]+).*.">
+    <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>
diff -r 52fdfc45590a -r 2589e6207cb4 picard_FastqToSam.xml
--- a/picard_FastqToSam.xml	Thu Jul 16 15:32:31 2015 -0400
+++ b/picard_FastqToSam.xml	Tue Oct 13 12:27:49 2015 -0400
@@ -4,6 +4,9 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
+  <stdio>
+    <exit_code range="1:" level="fatal"/>
+  </stdio>
   <command>
     @java_options@
     
@@ -83,7 +86,7 @@
         <param name="fastq2" type="data" format="fastq" label="Input fastq file for the second read of paired end data" help="FASTQ2"/>
       </when>
       <when value="pc">
-        <param name="fastq" type="data_collection" collection_type="paired" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/>
+        <param name="fastq" type="data_collection" collection_type="paired" format="fastq" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/>
       </when>
     </conditional>
       
@@ -93,16 +96,16 @@
       <option value="Solexa">Solexa (+66)</option>
     </param>
 
-    <param name="read_group_name" type="text" size="20" value="A" label="Read group name" help="READ_GROUP_NAME"/>
-    <param name="sample_name" type="text" size="20" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
-    <param name="library_name" type="text" size="20" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
-    <param name="platform_unit" type="text" size="20" optional="True"  label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
-    <param name="platform" type="text" size="20" optional="True"  label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/>
-    <param name="sequencing_center" type="text" size="20" optional="True"  label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/>
+    <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/>
+    <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
+    <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
+    <param name="platform_unit" type="text" optional="True"  label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
+    <param name="platform" type="text" optional="True"  label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/>
+    <param name="sequencing_center" type="text" optional="True"  label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/>
 
     <param name="predicted_insert_size" type="integer" min="0" max="100000" optional="True" label="Predicted median insert size, to insert into the read group header" help="PREDICTED_INSERT_SIZE; Optional"/>
-    <param name="comment" type="text" size="20" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/>
-    <param name="description" type="text" size="20" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/>
+    <param name="comment" type="text" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/>
+    <param name="description" type="text" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/>
     <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/>
     <param name="min_q" type="integer" value="0" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MIN_Q; An exception will be thrown if a quality is less than this value; default=0"/>
     <param name="max_q" type="integer" value="93" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MAX_Q; An exception will be thrown if a quality is greater than this value; default=93"/>
@@ -142,10 +145,6 @@
     </test> 
   </tests>
   
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
-  
   <help>
 
 .. class:: infomark
@@ -221,6 +220,6 @@
 @more_info@
 
   </help>
+  <citations>
+  </citations>
 </tool>
-
-
diff -r 52fdfc45590a -r 2589e6207cb4 picard_MarkDuplicates.xml
--- a/picard_MarkDuplicates.xml	Thu Jul 16 15:32:31 2015 -0400
+++ b/picard_MarkDuplicates.xml	Tue Oct 13 12:27:49 2015 -0400
@@ -34,7 +34,7 @@
   <inputs>
     <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
     <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
-      <param name="comment" type="text" size="50" label="Add this comment to BAM dataset"/>
+      <param name="comment" type="text" label="Add this comment to BAM dataset"/>
     </repeat>
     <param name="remove_duplicates" type="boolean" label="If true do not write duplicates to the output file instead of writing them with appropriate flags set" help="REMOVE_DUPLICATES; default=False"/>
     <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/>
@@ -45,7 +45,7 @@
     </param>
 
 
-    <param name="read_name_regex" type="text" size="40" 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]+).*.">
+    <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>
diff -r 52fdfc45590a -r 2589e6207cb4 picard_MarkDuplicatesWithMateCigar.xml
--- a/picard_MarkDuplicatesWithMateCigar.xml	Thu Jul 16 15:32:31 2015 -0400
+++ b/picard_MarkDuplicatesWithMateCigar.xml	Tue Oct 13 12:27:49 2015 -0400
@@ -38,7 +38,7 @@
   </command>
   <inputs>
     <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
-      <param name="comment" type="text" size="50" label="Add this comment to BAM dataset"/>
+      <param name="comment" type="text" label="Add this comment to BAM dataset"/>
     
     <param name="minimum_distance" type="integer" value="-1" label="The minimum distance to buffer records to account for clipping on the 5' end of the records" help="MINIMUM_DISTANCE; Set this number to -1 to use twice the first read's read length (or 100, whichever is smaller); default=-1"/>
     <param name="skip_pairs_with_no_mate_cigar" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Skip record pairs with no mate cigar and include them in the output" help="SKIP_PAIRS_WITH_NO_MATE_CIGAR; default=True"/>
@@ -51,7 +51,7 @@
     </param>
 
 
-    <param name="read_name_regex" type="text" size="40" 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]+).*.">
+    <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>
diff -r 52fdfc45590a -r 2589e6207cb4 picard_MergeBamAlignment.xml
--- a/picard_MergeBamAlignment.xml	Thu Jul 16 15:32:31 2015 -0400
+++ b/picard_MergeBamAlignment.xml	Tue Oct 13 12:27:49 2015 -0400
@@ -141,11 +141,11 @@
     <param name="max_insertions_or_deletions" type="integer" value="1" label="The maximum number of insertions or deletions permitted for an alignment to be included" help="MAX_INSERTIONS_OR_DELETIONS; Alignments with more than this many insertions or deletions will be ignored. Set to -1 to allow any number of insertions or deletions. default=1"/>
  
     <repeat name="attributes_to_retain" title="Retain the following alignment attribute" min="0" help="You can provide multiple attributes">
-      <param name="attribute" type="text" size="4" label="Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over from the alignment data when merging" help="ATTRIBUTES_TO_RETAIN; example: XA"/>
+      <param name="attribute" type="text" label="Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over from the alignment data when merging" help="ATTRIBUTES_TO_RETAIN; example: XA"/>
     </repeat>
     
     <repeat name="attributes_to_remove" title="Remove the following alignment attribute" min="0" help="You can provide multiple attributes">
-      <param name="attribute" type="text" size="4" label="Attributes from the alignment record that should be removed when merging." help="ATTRIBUTES_TO_REMOVE; This overrides ATTRIBUTES_TO_RETAIN if they share common tags"/>
+      <param name="attribute" type="text" label="Attributes from the alignment record that should be removed when merging." help="ATTRIBUTES_TO_REMOVE; This overrides ATTRIBUTES_TO_RETAIN if they share common tags"/>
     </repeat>
     
     <param name="read1_trim" type="integer" value="0" label="The number of bases trimmed from the beginning of read 1 prior to alignment" help="READ1_TRIM; default=0"/>
diff -r 52fdfc45590a -r 2589e6207cb4 picard_MergeSamFiles.xml
--- a/picard_MergeSamFiles.xml	Thu Jul 16 15:32:31 2015 -0400
+++ b/picard_MergeSamFiles.xml	Tue Oct 13 12:27:49 2015 -0400
@@ -35,7 +35,7 @@
     <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/>
 
     <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
-      <param name="comment" type="text" size="50" label="Add this comment to BAM dataset" help="COMMENT"/>
+      <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
     </repeat>
     
     <expand macro="VS" />
diff -r 52fdfc45590a -r 2589e6207cb4 picard_RevertSam.xml
--- a/picard_RevertSam.xml	Thu Jul 16 15:32:31 2015 -0400
+++ b/picard_RevertSam.xml	Tue Oct 13 12:27:49 2015 -0400
@@ -38,12 +38,12 @@
     <param name="remove_duplicate_information" type="boolean" checked="True" label="Remove duplicate read flags from all reads" help="REMOVE_DUPLICATE_INFORMATION; Note that if this is true and REMOVE_ALIGNMENT_INFORMATION is set to False, the output may have the unusual but sometimes desirable trait of having unmapped reads that are marked as duplicates; default=True"/>
     <param name="remove_alignment_information" type="boolean" checked="True" label="Remove all alignment information from the file" help="REMOVE_ALIGNMENT_INFORMATION; default=True"/>
     <repeat name="attributes_to_clear" title="Clear attribute" min="0" help="You can provide multiple attributes">
-      <param name="attribute" type="text" size="10" label="When removing alignment information, specify optional tags to remove (e.g., XM)" help="ATTRIBUTE_TO_CLEAR"/>
+      <param name="attribute" type="text" label="When removing alignment information, specify optional tags to remove (e.g., XM)" help="ATTRIBUTE_TO_CLEAR"/>
     </repeat>
     <param name="sanitize" type="boolean" label="Discard reads in order to produce a consistent output BAM" help="SANITIZE; WARNING: This option is potentially destructive. Reads discarded include (but are not limited to) paired reads with missing mates, duplicated records, records with mismatches in length of bases and qualities. This option can only be enabled if the output sort order is queryname and will always cause sorting to occur; default=False"/>
     <param name="max_discard_fraction" value="0.01" type="float" min="0.0" max="1.0" label="If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to sanitization then the program will exit with an Exception instead of exiting cleanly" help="MAX_DISCARD_FRACTION; default=0.01"/>
-    <param name="sample_alias" type="text" size="40" value="null" label="The sample alias to use in the reverted output file. This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same sample alias" help="SAMPLE_ALIAS; default=Null"/>
-    <param name="library_name" type="text" size="40" value="null" label="The library name to use in the reverted output file. This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same sample alias" help="LIBRARY_NAME; default=Null"/>
+    <param name="sample_alias" type="text" value="null" label="The sample alias to use in the reverted output file. This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same sample alias" help="SAMPLE_ALIAS; default=Null"/>
+    <param name="library_name" type="text" value="null" label="The library name to use in the reverted output file. This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same sample alias" help="LIBRARY_NAME; default=Null"/>
     <param name="sort_order" type="select" label="The sort order to create the reverted output file with" help="SORT_ORDER; Picard default=queryname; Galaxy default=coordinate">
       <option value="coordinate" selected="True">Coordinate</option>
       <option value="queryname">Queryname</option>
diff -r 52fdfc45590a -r 2589e6207cb4 picard_SamToFastq.xml
--- a/picard_SamToFastq.xml	Thu Jul 16 15:32:31 2015 -0400
+++ b/picard_SamToFastq.xml	Tue Oct 13 12:27:49 2015 -0400
@@ -58,8 +58,8 @@
     <param name="re_reverse" type="boolean" checked="True" label="Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq" help="RE_REVERSE; default=True"/>
     <param name="interleave" type="boolean" label="Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe which end it came from" help="INTERLEAVE; default=False"/>
     <param name="include_non_pf_reads" type="boolean" label="Include non-PF reads from the SAM/BAM dataset into the output FASTQ" help="INCLUDE_NON_PF_READS; PF means 'passes filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads; default=False"/>
-    <param name="clipping_attribute" type="text" size="4" value="null" label="The attribute that stores the position at which the SAM/BAM record should be clipped" help="CLIPPING_ATTRIBUTE; default=null"/>
-    <param name="clipping_action" type="text" size="10" value="null" label="The action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region" help="CLIPPING_ACTION; default=null"/>
+    <param name="clipping_attribute" type="text" value="null" label="The attribute that stores the position at which the SAM/BAM record should be clipped" help="CLIPPING_ATTRIBUTE; default=null"/>
+    <param name="clipping_action" type="text" value="null" label="The action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region" help="CLIPPING_ACTION; default=null"/>
     <param name="read1_trim" type="integer" value="0" min="0" label="The number of bases to trim from the beginning of read 1" help="READ1_TRIM; default=0"/>
     <param name="read1_max_bases_to_write" type="integer" value="-1" label="The maximum number of bases to write from read 1 after trimming" help="READ1_MAX_BASES_TO_WRITE; If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written; default=null (-1)"/>
     <param name="read2_trim" type="integer" value="0" min="0" label="The number of bases to trim from the beginning of read 2" help="READ2_TRIM; default=0"/>
diff -r 52fdfc45590a -r 2589e6207cb4 read_group_macros.xml
--- a/read_group_macros.xml	Thu Jul 16 15:32:31 2015 -0400
+++ b/read_group_macros.xml	Tue Oct 13 12:27:49 2015 -0400
@@ -146,7 +146,7 @@
         </when>
     </xml>
     <xml name="read_group_id_param">
-        <param name="ID" type="text" value="" size="20" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false">
+        <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false">
             <validator type="empty_field" />
         </param>
     </xml>
@@ -158,7 +158,7 @@
         </conditional>
     </xml>
     <xml name="read_group_sm_param">
-        <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" />
+        <param name="SM" type="text" value="" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" />
     </xml>
     <xml name="read_group_sm_conditional">
         <conditional name="read_group_sm_conditional">
@@ -171,7 +171,7 @@
          as per Picard.
     -->
     <xml name="read_group_sm_param_required">
-        <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced">
+        <param name="SM" type="text" value="" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced">
             <validator type="empty_field" />
         </param>
     </xml>
@@ -194,7 +194,7 @@
         </param>
     </xml>
     <xml name="read_group_lb_param">
-        <param name="LB" type="text" size="25" label="Library name (LB)" optional="true" />
+        <param name="LB" type="text" label="Library name (LB)" optional="true" />
     </xml>
     <xml name="read_group_lb_conditional">
         <conditional name="read_group_lb_conditional">
@@ -204,7 +204,7 @@
         </conditional>
     </xml>
     <xml name="read_group_lb_required_param">
-        <param name="LB" type="text" size="25" label="Library name (LB)" optional="false">
+        <param name="LB" type="text" label="Library name (LB)" optional="false">
             <validator type="empty_field" />
         </param>
     </xml>
@@ -216,33 +216,33 @@
         </conditional>
     </xml>
     <xml name="read_group_cn_param">
-        <param name="CN" type="text" size="25" label="Sequencing center that produced the read (CN)" />
+        <param name="CN" type="text" label="Sequencing center that produced the read (CN)" />
     </xml>
     <xml name="read_group_ds_param">
-        <param name="DS" type="text" size="25" label="Description (DS)" />
+        <param name="DS" type="text" label="Description (DS)" />
     </xml>
     <xml name="read_group_dt_param">
-        <param name="DT" type="text" size="25" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />
+        <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />
     </xml>
     <xml name="read_group_fo_param">
-        <param name="FO" type="text" size="25" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/">
+        <param name="FO" type="text" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/">
           <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator>
         </param>
     </xml>
     <xml name="read_group_ks_param">
-        <param name="KS" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" />
+        <param name="KS" type="text" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" />
     </xml>
     <xml name="read_group_pg_param">
-        <param name="PG" type="text" size="25" label="Programs used for processing the read group (PG)" />
+        <param name="PG" type="text" label="Programs used for processing the read group (PG)" />
     </xml>
     <xml name="read_group_pi_param">
         <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" />
     </xml>
     <xml name="read_group_pu_param">
-        <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />
+        <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />
     </xml>
     <xml name="read_group_pu_required_param">
-        <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
+        <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
     </xml>
     <!-- Only ID is required - all groups available -->
     <xml name="read_group_inputs_spec">