# HG changeset patch
# User iuc
# Date 1630483137 0
# Node ID 4740a2548206582427b38fb02c283e41643a714a
# Parent  81de93de916fbfda630177bed2ba4227993bf46e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

diff -r 81de93de916f -r 4740a2548206 picard_FastqToSam.xml
--- a/picard_FastqToSam.xml	Wed Feb 19 19:26:15 2020 +0000
+++ b/picard_FastqToSam.xml	Wed Sep 01 07:58:57 2021 +0000
@@ -1,11 +1,14 @@
 <tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
-  <description>convert Fastq data into unaligned BAM</description>
-  <macros>
-    <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
-  </macros>
-  <expand macro="requirements" />
-  <command detect_errors="exit_code"><![CDATA[
+    <description>convert Fastq data into unaligned BAM</description>
+    <xrefs>
+        <xref type="bio.tools">picard_fastqtosam</xref>
+    </xrefs>
+    <macros>
+        <import>picard_macros.xml</import>
+        <token name="@WRAPPER_VERSION@">1</token>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
     @java_options@
     picard
     FastqToSam
diff -r 81de93de916f -r 4740a2548206 picard_ReorderSam.xml
--- a/picard_ReorderSam.xml	Wed Feb 19 19:26:15 2020 +0000
+++ b/picard_ReorderSam.xml	Wed Sep 01 07:58:57 2021 +0000
@@ -1,11 +1,14 @@
 <tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
-  <description>reorder reads to match ordering in reference sequences</description>
-  <macros>
-    <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
-  </macros>
-  <expand macro="requirements" />
-  <command detect_errors="exit_code"><![CDATA[
+    <description>reorder reads to match ordering in reference sequences</description>
+    <xrefs>
+        <xref type="bio.tools">picard_reordersam</xref>
+    </xrefs>
+    <macros>
+        <import>picard_macros.xml</import>
+        <token name="@WRAPPER_VERSION@">1</token>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
     @java_options@
     @symlink_element_identifier@
     #set $picard_dict = "localref.dict"
diff -r 81de93de916f -r 4740a2548206 picard_ReplaceSamHeader.xml
--- a/picard_ReplaceSamHeader.xml	Wed Feb 19 19:26:15 2020 +0000
+++ b/picard_ReplaceSamHeader.xml	Wed Sep 01 07:58:57 2021 +0000
@@ -1,11 +1,14 @@
 <tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
-  <description>replace header in a SAM/BAM dataset</description>
-  <macros>
-    <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
-  </macros>
-  <expand macro="requirements" />
-  <command detect_errors="exit_code"><![CDATA[
+    <description>replace header in a SAM/BAM dataset</description>
+    <xrefs>
+        <xref type="bio.tools">picard_replacesamheader</xref>
+    </xrefs>
+    <macros>
+        <import>picard_macros.xml</import>
+        <token name="@WRAPPER_VERSION@">1</token>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
     @java_options@
     @symlink_element_identifier@
 
diff -r 81de93de916f -r 4740a2548206 picard_SamToFastq.xml
--- a/picard_SamToFastq.xml	Wed Feb 19 19:26:15 2020 +0000
+++ b/picard_SamToFastq.xml	Wed Sep 01 07:58:57 2021 +0000
@@ -1,11 +1,14 @@
 <tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
-  <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>
-  </macros>
-  <expand macro="requirements" />
-  <command detect_errors="exit_code"><![CDATA[
+    <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description>
+    <xrefs>
+        <xref type="bio.tools">picard_samtofastq</xref>
+    </xrefs>
+    <macros>
+        <import>picard_macros.xml</import>
+        <token name="@WRAPPER_VERSION@">2</token>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
 
     @java_options@
     @symlink_element_identifier@