# HG changeset patch
# User iuc
# Date 1677357174 0
# Node ID fdca9493e09bae593ac7e2109a51239a90081f8a
# Parent  fc3866ddc7b6c74b189d9d5e782be339f28b6158
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 70d2a66c405be58d4413753792bcadf212a4da84

diff -r fc3866ddc7b6 -r fdca9493e09b picard_CollectAlignmentSummaryMetrics.xml
--- a/picard_CollectAlignmentSummaryMetrics.xml	Mon Aug 22 09:54:37 2022 +0000
+++ b/picard_CollectAlignmentSummaryMetrics.xml	Sat Feb 25 20:32:54 2023 +0000
@@ -2,7 +2,7 @@
   <description>writes a file containing summary alignment metrics</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@WRAPPER_VERSION@">2</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
@@ -71,13 +71,15 @@
 
   </inputs>
   <outputs>
-    <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
+    <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: tablular"/>
   </outputs>
   <tests>
     <test>
       <param name="bisulphite" value="false" />
-      <param name="sorted" value="true" />
-      <param name="adaptors" value="" />
+      <param name="assume_sorted" value="true" />
+      <repeat name="adapters">
+        <param name="adapter" value = ""/>
+      </repeat>
       <param name="maxinsert" value="100000" />
       <param name="reference_source_selector" value="history" />
       <param name="ref_file" value="picard_CASM_ref.fa" />
diff -r fc3866ddc7b6 -r fdca9493e09b picard_CollectBaseDistributionByCycle.xml
--- a/picard_CollectBaseDistributionByCycle.xml	Mon Aug 22 09:54:37 2022 +0000
+++ b/picard_CollectBaseDistributionByCycle.xml	Sat Feb 25 20:32:54 2023 +0000
@@ -2,7 +2,7 @@
   <description>charts the nucleotide distribution per cycle in a SAM or BAM dataset</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@WRAPPER_VERSION@">2</token>
   </macros>
   <expand macro="requirements">
     <requirement type="package" version="3.4.1">r-base</requirement>
@@ -59,8 +59,8 @@
   </inputs>
 
   <outputs>
-    <data format="tabular" name="outFile"/>
-    <data format="pdf" name="pdfFile"/>
+    <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: tabular"/>
+    <data format="pdf" name="pdfFile"  label="${tool.name} on ${on_string}: PDF"/>
   </outputs>
 
   <tests>
diff -r fc3866ddc7b6 -r fdca9493e09b picard_CollectInsertSizeMetrics.xml
--- a/picard_CollectInsertSizeMetrics.xml	Mon Aug 22 09:54:37 2022 +0000
+++ b/picard_CollectInsertSizeMetrics.xml	Sat Feb 25 20:32:54 2023 +0000
@@ -2,7 +2,7 @@
   <description>plots distribution of insert sizes</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@WRAPPER_VERSION@">2</token>
   </macros>
   <expand macro="requirements">
     <requirement type="package" version="3.4.1">r-base</requirement>
@@ -72,8 +72,8 @@
   </inputs>
 
   <outputs>
-    <data format="tabular" name="outFile"/>
-    <data format="pdf" name="histFile"/>
+    <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: tabular"/>
+    <data format="pdf" name="histFile" label="${tool.name} on ${on_string}: PDF"/>
   </outputs>
 
   <tests>
diff -r fc3866ddc7b6 -r fdca9493e09b picard_MarkDuplicates.xml
--- a/picard_MarkDuplicates.xml	Mon Aug 22 09:54:37 2022 +0000
+++ b/picard_MarkDuplicates.xml	Sat Feb 25 20:32:54 2023 +0000
@@ -2,7 +2,7 @@
   <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">3</token>
+    <token name="@WRAPPER_VERSION@">4</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
@@ -56,7 +56,7 @@
     <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)">
       <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"/>
+    <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="5000" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>
 
     <param name="barcode_tag" type="text" optional="True" label="Barcode Tag" help="Barcode SAM tag. This tag can be utilized when you have data from an assay that includes Unique Molecular Indices. Typically 'RX' "/>
 
@@ -65,8 +65,8 @@
   </inputs>
 
   <outputs>
-    <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/>
-    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/>
+    <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: tabular"/>
+    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM"/>
   </outputs>
 
   <tests>
diff -r fc3866ddc7b6 -r fdca9493e09b picard_MarkDuplicatesWithMateCigar.xml
--- a/picard_MarkDuplicatesWithMateCigar.xml	Mon Aug 22 09:54:37 2022 +0000
+++ b/picard_MarkDuplicatesWithMateCigar.xml	Sat Feb 25 20:32:54 2023 +0000
@@ -2,7 +2,7 @@
   <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">2</token>
+    <token name="@WRAPPER_VERSION@">3</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
@@ -55,15 +55,15 @@
     <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]+).*.">
       <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"/>
+    <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="5000" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>
 
    <expand macro="VS" />
 
   </inputs>
 
   <outputs>
-    <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/>
-    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/>
+    <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: metrics"/>
+    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM"/>
   </outputs>
 
   <tests>
diff -r fc3866ddc7b6 -r fdca9493e09b picard_MergeBamAlignment.xml
--- a/picard_MergeBamAlignment.xml	Mon Aug 22 09:54:37 2022 +0000
+++ b/picard_MergeBamAlignment.xml	Sat Feb 25 20:32:54 2023 +0000
@@ -2,7 +2,7 @@
   <description>merge alignment data with additional info stored in an unmapped BAM dataset</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@WRAPPER_VERSION@">2</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
@@ -176,7 +176,7 @@
     <expand macro="VS" />
   </inputs>
   <outputs>
-    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with merged alignments"/>
+    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM"/>
   </outputs>
   <tests>
     <test>
@@ -191,7 +191,7 @@
       <param name="max_insertions_or_deletions" value="1"/>
       <param name="read1_trim" value="0"/>
       <param name="read2_trim" value="0"/>
-      <param name="orientation" value="FR"/>
+      <param name="orientations" value="FR"/>
       <param name="aligner_proper_pair_flags" value="False"/>
       <param name="primary_alignment_strategy" value="BestMapq"/>
       <param name="clip_overlapping_reads" value="True"/>
diff -r fc3866ddc7b6 -r fdca9493e09b picard_SamToFastq.xml
--- a/picard_SamToFastq.xml	Mon Aug 22 09:54:37 2022 +0000
+++ b/picard_SamToFastq.xml	Sat Feb 25 20:32:54 2023 +0000
@@ -2,7 +2,7 @@
     <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description>
     <macros>
         <import>picard_macros.xml</import>
-        <token name="@WRAPPER_VERSION@">2</token>
+        <token name="@WRAPPER_VERSION@">3</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">picard_samtofastq</xref>
@@ -107,7 +107,6 @@
     <test>
       <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
       <param name="single_or_paired" value="pe_interleaved" />
-      <param name="output_per_rg" value="false"/>
       <param name="re_reverse" value="true"/>
       <param name="include_non_pf_reads" value="false"/>
       <param name="clipping_attribute" value="" />
@@ -122,7 +121,6 @@
     <test>
       <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
       <param name="single_or_paired" value="pe_sep" />
-      <param name="output_per_rg" value="false"/>
       <param name="re_reverse" value="true"/>
       <param name="include_non_pf_reads" value="false"/>
       <param name="clipping_attribute" value="" />
@@ -139,7 +137,6 @@
     <test>
       <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/>
       <param name="single_or_paired" value="se" />
-      <param name="output_per_rg" value="false"/>
       <param name="re_reverse" value="true"/>
       <param name="include_non_pf_reads" value="false"/>
       <param name="clipping_attribute" value="" />
@@ -164,34 +161,21 @@
 
 .. class:: warningmark
 
-**DANGER: Multiple Outputs**
-
-Generating per readgroup fastq (setting **OUTPUT_PER_RG** to True) may produce very large numbers of outputs. Know what you are doing!
-
 @dataset_collections@
 
 @description@
 
   FASTQ=File
   F=File                        Output fastq file (single-end fastq or, if paired, first end of the pair fastq).
-                                Required.  Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
+                                Required.
 
   SECOND_END_FASTQ=File
   F2=File                       Output fastq file (if paired, second end of the pair fastq).  Default value: null.
-                                Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
+                                
 
   UNPAIRED_FASTQ=File
   FU=File                       Output fastq file for unpaired reads; may only be provided in paired-fastq mode  Default
-                                value: null.  Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
-
-  OUTPUT_PER_RG=Boolean
-  OPRG=Boolean                  Output a fastq file per read group (two fastq files per read group if the group is
-                                paired).  Default value: false. Possible values: {true, false}  Cannot be used in
-                                conjuction with option(s) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F)
-
-  OUTPUT_DIR=File
-  ODIR=File                     Directory in which to output the fastq file(s).  Used only when OUTPUT_PER_RG is true.
-                                Default value: null.
+                                value: null.
 
   RE_REVERSE=Boolean
   RC=Boolean                    Re-reverse bases and qualities of reads with negative strand flag set before writing them