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changeset 28:881d7645d1bf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
author iuc
date Sat, 15 Jan 2022 12:39:30 +0000
parents a1f0b3f4b781
children 1aac2a13842a
files picard_FastqToSam.xml picard_MarkDuplicates.xml picard_MarkDuplicatesWithMateCigar.xml picard_ReorderSam.xml picard_ReplaceSamHeader.xml picard_SamToFastq.xml picard_ValidateSamFile.xml read_group_macros.xml test-data/picard_MarkDuplicates_test1.bam test-data/picard_MarkDuplicates_test2.bam
diffstat 10 files changed, 99 insertions(+), 86 deletions(-) [+]
line wrap: on
line diff
--- a/picard_FastqToSam.xml	Wed Feb 19 14:27:00 2020 -0500
+++ b/picard_FastqToSam.xml	Sat Jan 15 12:39:30 2022 +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>
+    <macros>
+        <import>picard_macros.xml</import>
+        <token name="@WRAPPER_VERSION@">1</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">picard_fastqtosam</xref>
+    </xrefs>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
     @java_options@
     picard
     FastqToSam
--- a/picard_MarkDuplicates.xml	Wed Feb 19 14:27:00 2020 -0500
+++ b/picard_MarkDuplicates.xml	Sat Jan 15 12:39:30 2022 +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[
@@ -34,6 +34,7 @@
     #end if
 
     VALIDATION_STRINGENCY='${validation_stringency}'
+    TAGGING_POLICY=All
     QUIET=true
     VERBOSITY=ERROR
     @TMPDIR_OPTION@
--- a/picard_MarkDuplicatesWithMateCigar.xml	Wed Feb 19 14:27:00 2020 -0500
+++ b/picard_MarkDuplicatesWithMateCigar.xml	Sat Jan 15 12:39:30 2022 +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@">1</token>
+    <token name="@WRAPPER_VERSION@">2</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
--- a/picard_ReorderSam.xml	Wed Feb 19 14:27:00 2020 -0500
+++ b/picard_ReorderSam.xml	Sat Jan 15 12:39:30 2022 +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>
+    <macros>
+        <import>picard_macros.xml</import>
+        <token name="@WRAPPER_VERSION@">1</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">picard_reordersam</xref>
+    </xrefs>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
     @java_options@
     @symlink_element_identifier@
     #set $picard_dict = "localref.dict"
--- a/picard_ReplaceSamHeader.xml	Wed Feb 19 14:27:00 2020 -0500
+++ b/picard_ReplaceSamHeader.xml	Sat Jan 15 12:39:30 2022 +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>
+    <macros>
+        <import>picard_macros.xml</import>
+        <token name="@WRAPPER_VERSION@">1</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">picard_replacesamheader</xref>
+    </xrefs>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
     @java_options@
     @symlink_element_identifier@
 
--- a/picard_SamToFastq.xml	Wed Feb 19 14:27:00 2020 -0500
+++ b/picard_SamToFastq.xml	Sat Jan 15 12:39:30 2022 +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>
+    <macros>
+        <import>picard_macros.xml</import>
+        <token name="@WRAPPER_VERSION@">2</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">picard_samtofastq</xref>
+    </xrefs>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
 
     @java_options@
     @symlink_element_identifier@
--- a/picard_ValidateSamFile.xml	Wed Feb 19 14:27:00 2020 -0500
+++ b/picard_ValidateSamFile.xml	Sat Jan 15 12:39:30 2022 +0000
@@ -80,61 +80,61 @@
     <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE">
       <option value="INVALID_QUALITY_FORMAT">INVALID_QUALITY_FORMAT</option>
       <option value="INVALID_FLAG_PROPER_PAIR">INVALID_FLAG_PROPER_PAIR</option>
-      <option value="INVALID_FLAG_MATE_UNMAPPED"/>
-      <option value="MISMATCH_FLAG_MATE_UNMAPPED"/>
-      <option value="INVALID_FLAG_MATE_NEG_STRAND"/>
-      <option value="MISMATCH_FLAG_MATE_NEG_STRAND"/>
-      <option value="INVALID_FLAG_FIRST_OF_PAIR"/>
-      <option value="INVALID_FLAG_SECOND_OF_PAIR"/>
-      <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND"/>
-      <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT"/>
-      <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT"/>
-      <option value="INVALID_FLAG_READ_UNMAPPED"/>
-      <option value="INVALID_INSERT_SIZE"/>
-      <option value="INVALID_MAPPING_QUALITY"/>
-      <option value="INVALID_CIGAR"/>
-      <option value="ADJACENT_INDEL_IN_CIGAR"/>
-      <option value="INVALID_MATE_REF_INDEX"/>
-      <option value="MISMATCH_MATE_REF_INDEX"/>
-      <option value="INVALID_REFERENCE_INDEX"/>
-      <option value="INVALID_ALIGNMENT_START"/>
-      <option value="MISMATCH_MATE_ALIGNMENT_START"/>
-      <option value="MATE_FIELD_MISMATCH"/>
-      <option value="INVALID_TAG_NM"/>
-      <option value="MISSING_TAG_NM"/>
-      <option value="MISSING_HEADER"/>
-      <option value="MISSING_SEQUENCE_DICTIONARY"/>
-      <option value="MISSING_READ_GROUP"/>
-      <option value="RECORD_OUT_OF_ORDER"/>
-      <option value="READ_GROUP_NOT_FOUND"/>
-      <option value="RECORD_MISSING_READ_GROUP"/>
-      <option value="INVALID_INDEXING_BIN"/>
-      <option value="MISSING_VERSION_NUMBER"/>
-      <option value="INVALID_VERSION_NUMBER"/>
-      <option value="TRUNCATED_FILE"/>
-      <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH"/>
-      <option value="EMPTY_READ"/>
-      <option value="CIGAR_MAPS_OFF_REFERENCE"/>
-      <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH"/>
-      <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH"/>
-      <option value="E2_BASE_EQUALS_PRIMARY_BASE"/>
-      <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK"/>
-      <option value="UNRECOGNIZED_HEADER_TYPE"/>
-      <option value="POORLY_FORMATTED_HEADER_TAG"/>
-      <option value="HEADER_TAG_MULTIPLY_DEFINED"/>
-      <option value="HEADER_RECORD_MISSING_REQUIRED_TAG"/>
-      <option value="INVALID_DATE_STRING"/>
-      <option value="TAG_VALUE_TOO_LARGE"/>
-      <option value="INVALID_INDEX_FILE_POINTER"/>
-      <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE"/>
-      <option value="DUPLICATE_READ_GROUP_ID"/>
-      <option value="MISSING_PLATFORM_VALUE"/>
-      <option value="INVALID_PLATFORM_VALUE"/>
-      <option value="DUPLICATE_PROGRAM_GROUP_ID"/>
-      <option value="MATE_NOT_FOUND"/>
-      <option value="MATES_ARE_SAME_END"/>
-      <option value="MISMATCH_MATE_CIGAR_STRING"/>
-      <option value="MATE_CIGAR_STRING_INVALID_PRESENCE"/>
+      <option value="INVALID_FLAG_MATE_UNMAPPED">INVALID_FLAG_MATE_UNMAPPED</option>
+      <option value="MISMATCH_FLAG_MATE_UNMAPPED">MISMATCH_FLAG_MATE_UNMAPPED</option>
+      <option value="INVALID_FLAG_MATE_NEG_STRAND">INVALID_FLAG_MATE_NEG_STRAND</option>
+      <option value="MISMATCH_FLAG_MATE_NEG_STRAND">MISMATCH_FLAG_MATE_NEG_STRAND</option>
+      <option value="INVALID_FLAG_FIRST_OF_PAIR">INVALID_FLAG_FIRST_OF_PAIR</option>
+      <option value="INVALID_FLAG_SECOND_OF_PAIR">INVALID_FLAG_SECOND_OF_PAIR</option>
+      <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND">PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND</option>
+      <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT">INVALID_FLAG_NOT_PRIM_ALIGNMENT</option>
+      <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT">INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT</option>
+      <option value="INVALID_FLAG_READ_UNMAPPED">INVALID_FLAG_READ_UNMAPPED</option>
+      <option value="INVALID_INSERT_SIZE">INVALID_INSERT_SIZE</option>
+      <option value="INVALID_MAPPING_QUALITY">INVALID_MAPPING_QUALITY</option>
+      <option value="INVALID_CIGAR">INVALID_CIGAR</option>
+      <option value="ADJACENT_INDEL_IN_CIGAR">ADJACENT_INDEL_IN_CIGAR</option>
+      <option value="INVALID_MATE_REF_INDEX">INVALID_MATE_REF_INDEX</option>
+      <option value="MISMATCH_MATE_REF_INDEX">MISMATCH_MATE_REF_INDEX</option>
+      <option value="INVALID_REFERENCE_INDEX">INVALID_REFERENCE_INDEX</option>
+      <option value="INVALID_ALIGNMENT_START">INVALID_ALIGNMENT_START</option>
+      <option value="MISMATCH_MATE_ALIGNMENT_START">MISMATCH_MATE_ALIGNMENT_START</option>
+      <option value="MATE_FIELD_MISMATCH">MATE_FIELD_MISMATCH</option>
+      <option value="INVALID_TAG_NM">INVALID_TAG_NM</option>
+      <option value="MISSING_TAG_NM">MISSING_TAG_NM</option>
+      <option value="MISSING_HEADER">MISSING_HEADER</option>
+      <option value="MISSING_SEQUENCE_DICTIONARY">MISSING_SEQUENCE_DICTIONARY</option>
+      <option value="MISSING_READ_GROUP">MISSING_READ_GROUP</option>
+      <option value="RECORD_OUT_OF_ORDER">RECORD_OUT_OF_ORDER</option>
+      <option value="READ_GROUP_NOT_FOUND">READ_GROUP_NOT_FOUND</option>
+      <option value="RECORD_MISSING_READ_GROUP">RECORD_MISSING_READ_GROUP</option>
+      <option value="INVALID_INDEXING_BIN">INVALID_INDEXING_BIN</option>
+      <option value="MISSING_VERSION_NUMBER">MISSING_VERSION_NUMBER</option>
+      <option value="INVALID_VERSION_NUMBER">INVALID_VERSION_NUMBER</option>
+      <option value="TRUNCATED_FILE">TRUNCATED_FILE</option>
+      <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH">MISMATCH_READ_LENGTH_AND_QUALS_LENGTH</option>
+      <option value="EMPTY_READ">EMPTY_READ</option>
+      <option value="CIGAR_MAPS_OFF_REFERENCE">CIGAR_MAPS_OFF_REFERENCE</option>
+      <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH">MISMATCH_READ_LENGTH_AND_E2_LENGTH</option>
+      <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH">MISMATCH_READ_LENGTH_AND_U2_LENGTH</option>
+      <option value="E2_BASE_EQUALS_PRIMARY_BASE">E2_BASE_EQUALS_PRIMARY_BASE</option>
+      <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK">BAM_FILE_MISSING_TERMINATOR_BLOCK</option>
+      <option value="UNRECOGNIZED_HEADER_TYPE">UNRECOGNIZED_HEADER_TYPE</option>
+      <option value="POORLY_FORMATTED_HEADER_TAG">POORLY_FORMATTED_HEADER_TAG</option>
+      <option value="HEADER_TAG_MULTIPLY_DEFINED">HEADER_TAG_MULTIPLY_DEFINED</option>
+      <option value="HEADER_RECORD_MISSING_REQUIRED_TAG">HEADER_RECORD_MISSING_REQUIRED_TAG</option>
+      <option value="INVALID_DATE_STRING">INVALID_DATE_STRING</option>
+      <option value="TAG_VALUE_TOO_LARGE">TAG_VALUE_TOO_LARGE</option>
+      <option value="INVALID_INDEX_FILE_POINTER">INVALID_INDEX_FILE_POINTER</option>
+      <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE">INVALID_PREDICTED_MEDIAN_INSERT_SIZE</option>
+      <option value="DUPLICATE_READ_GROUP_ID">DUPLICATE_READ_GROUP_ID</option>
+      <option value="MISSING_PLATFORM_VALUE">MISSING_PLATFORM_VALUE</option>
+      <option value="INVALID_PLATFORM_VALUE">INVALID_PLATFORM_VALUE</option>
+      <option value="DUPLICATE_PROGRAM_GROUP_ID">DUPLICATE_PROGRAM_GROUP_ID</option>
+      <option value="MATE_NOT_FOUND">MATE_NOT_FOUND</option>
+      <option value="MATES_ARE_SAME_END">MATES_ARE_SAME_END</option>
+      <option value="MISMATCH_MATE_CIGAR_STRING">MISMATCH_MATE_CIGAR_STRING</option>
+      <option value="MATE_CIGAR_STRING_INVALID_PRESENCE">MATE_CIGAR_STRING_INVALID_PRESENCE</option>
     </param>
     <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/>
     <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/>
--- a/read_group_macros.xml	Wed Feb 19 14:27:00 2020 -0500
+++ b/read_group_macros.xml	Sat Jan 15 12:39:30 2022 +0000
@@ -23,7 +23,7 @@
         #import itertools
         #set $input_name1 = $clean($identifier_or_name($input1))
         #set $input_name2 = $clean($identifier_or_name($input2))
-        #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), itertools.izip(*[$input_name1, $input_name2]))])
+        #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), zip(*[$input_name1, $input_name2]))])
         #if len($common_prefix) > 3
             #return $common_prefix
         #else
Binary file test-data/picard_MarkDuplicates_test1.bam has changed
Binary file test-data/picard_MarkDuplicates_test2.bam has changed