| Previous changeset 27:a1f0b3f4b781 (2020-02-19) Next changeset 29:1aac2a13842a (2022-03-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130" |
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modified:
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 |
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| diff -r a1f0b3f4b781 -r 881d7645d1bf picard_FastqToSam.xml --- a/picard_FastqToSam.xml Wed Feb 19 14:27:00 2020 -0500 +++ b/picard_FastqToSam.xml Sat Jan 15 12:39:30 2022 +0000 |
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| @@ -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 |
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| diff -r a1f0b3f4b781 -r 881d7645d1bf picard_MarkDuplicates.xml --- a/picard_MarkDuplicates.xml Wed Feb 19 14:27:00 2020 -0500 +++ b/picard_MarkDuplicates.xml Sat Jan 15 12:39:30 2022 +0000 |
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| @@ -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@ |
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| diff -r a1f0b3f4b781 -r 881d7645d1bf picard_MarkDuplicatesWithMateCigar.xml --- a/picard_MarkDuplicatesWithMateCigar.xml Wed Feb 19 14:27:00 2020 -0500 +++ b/picard_MarkDuplicatesWithMateCigar.xml Sat Jan 15 12:39:30 2022 +0000 |
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| @@ -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[ |
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| diff -r a1f0b3f4b781 -r 881d7645d1bf picard_ReorderSam.xml --- a/picard_ReorderSam.xml Wed Feb 19 14:27:00 2020 -0500 +++ b/picard_ReorderSam.xml Sat Jan 15 12:39:30 2022 +0000 |
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| @@ -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" |
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| diff -r a1f0b3f4b781 -r 881d7645d1bf picard_ReplaceSamHeader.xml --- a/picard_ReplaceSamHeader.xml Wed Feb 19 14:27:00 2020 -0500 +++ b/picard_ReplaceSamHeader.xml Sat Jan 15 12:39:30 2022 +0000 |
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| @@ -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@ |
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| diff -r a1f0b3f4b781 -r 881d7645d1bf picard_SamToFastq.xml --- a/picard_SamToFastq.xml Wed Feb 19 14:27:00 2020 -0500 +++ b/picard_SamToFastq.xml Sat Jan 15 12:39:30 2022 +0000 |
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| @@ -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@ |
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| diff -r a1f0b3f4b781 -r 881d7645d1bf picard_ValidateSamFile.xml --- a/picard_ValidateSamFile.xml Wed Feb 19 14:27:00 2020 -0500 +++ b/picard_ValidateSamFile.xml Sat Jan 15 12:39:30 2022 +0000 |
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| @@ -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"/> |
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| diff -r a1f0b3f4b781 -r 881d7645d1bf read_group_macros.xml --- 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 |
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| @@ -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 |
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| diff -r a1f0b3f4b781 -r 881d7645d1bf test-data/picard_MarkDuplicates_test1.bam |
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| Binary file test-data/picard_MarkDuplicates_test1.bam has changed |
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| diff -r a1f0b3f4b781 -r 881d7645d1bf test-data/picard_MarkDuplicates_test2.bam |
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| Binary file test-data/picard_MarkDuplicates_test2.bam has changed |