Mercurial > repos > devteam > picard
diff picard_ValidateSamFile.xml @ 12:05087b27692a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
| author | devteam |
|---|---|
| date | Sun, 27 Nov 2016 15:11:50 -0500 |
| parents | 3a3234d7a2e8 |
| children | 7e6fd3d0f16e |
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--- a/picard_ValidateSamFile.xml Wed Nov 11 12:23:17 2015 -0500 +++ b/picard_ValidateSamFile.xml Sun Nov 27 15:11:50 2016 -0500 @@ -4,49 +4,52 @@ <import>picard_macros.xml</import> </macros> <expand macro="requirements" /> - <command> - + <stdio> + <exit_code range="1:" level="warning"/> + </stdio> + <command><![CDATA[ + ##set the maximum number of open file to hard maximum or 4096 if on a mac (mac gives 'unlimited' as output of `ulimit -Hn` command - - [ `ulimit -Hn` = unlimited ] && ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn` - - && - + + [ `ulimit -Hn` = unlimited ] && ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn` + + && + ##set up input files #set $reference_fasta_filename = "localref.fa" - + #if str( $reference_source.reference_source_selector ) == "history": - ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && #else: #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) #end if - + @java_options@ - - java -jar \$JAVA_JAR_PATH/picard.jar + + picard ValidateSamFile - + INPUT="${inputFile}" OUTPUT="${outFile}" MODE="${mode}" - + #if str( $ignore ) != "None": #for $element in str( $ignore ).split(','): ## See trello card https://trello.com/c/9nW02Zhd IGNORE="${element}" #end for #end if - + MAX_OUTPUT="${max_output}" REFERENCE_SEQUENCE="${reference_fasta_filename}" IGNORE_WARNINGS="${ignore_warnings}" IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}" MAX_OPEN_TEMP_FILES=`ulimit -Sn` - + VERBOSITY=ERROR QUIET=true - - </command> + + ]]></command> <inputs> <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset." /> <conditional name="reference_source"> @@ -63,11 +66,11 @@ <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> </param> </when> - <when value="history"> + <when value="history"> <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" /> </when> </conditional> - + <param name="mode" type="select" label="Select output mode" help="MODE"> <option value="VERBOSE">Verbose</option> <option value="SUMMARY">Summary</option> @@ -135,13 +138,13 @@ <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/> <param name="validate_index" type="boolean" checked="True" label="If true and input is a BAM file with an index file, also validates the index" help="VALIDATE_INDEX; default=True"/> <param name="is_bisulfite_sequenced" type="boolean" label="Whether the SAM or BAM file consists of bisulfite sequenced reads" help="IS_BISULFITE_SEQUENCED; If so, C->T is not counted as an error in computing the value of the NM tag; default=False"/> - - </inputs> - + + </inputs> + <outputs> <data format="txt" name="outFile" label="${tool.name} on ${on_string}: BAM validation summary"/> </outputs> - + <tests> <test> <param name="inputFile" value="picard_ValidateSamFile.bam" ftype="bam"/> @@ -156,11 +159,7 @@ <output name="outFile" file="picard_ValidateSamFile_test1.txt" ftype="txt"/> </test> </tests> - - <stdio> - <exit_code range="1:" level="warning"/> - </stdio> - + <help> **Purpose** @@ -172,52 +171,52 @@ @description@ MODE=Mode - M=Mode Mode of output Default value: VERBOSE. This option can be set to 'null' to clear the - default value. Possible values: {VERBOSE, SUMMARY} - - IGNORE=Type List of validation error types to ignore. Possible values: {INVALID_QUALITY_FORMAT, - INVALID_FLAG_PROPER_PAIR, INVALID_FLAG_MATE_UNMAPPED, MISMATCH_FLAG_MATE_UNMAPPED, - INVALID_FLAG_MATE_NEG_STRAND, MISMATCH_FLAG_MATE_NEG_STRAND, INVALID_FLAG_FIRST_OF_PAIR, - INVALID_FLAG_SECOND_OF_PAIR, PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND, - INVALID_FLAG_NOT_PRIM_ALIGNMENT, INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT, - INVALID_FLAG_READ_UNMAPPED, INVALID_INSERT_SIZE, INVALID_MAPPING_QUALITY, INVALID_CIGAR, - ADJACENT_INDEL_IN_CIGAR, INVALID_MATE_REF_INDEX, MISMATCH_MATE_REF_INDEX, - INVALID_REFERENCE_INDEX, INVALID_ALIGNMENT_START, MISMATCH_MATE_ALIGNMENT_START, - MATE_FIELD_MISMATCH, INVALID_TAG_NM, MISSING_TAG_NM, MISSING_HEADER, - MISSING_SEQUENCE_DICTIONARY, MISSING_READ_GROUP, RECORD_OUT_OF_ORDER, - READ_GROUP_NOT_FOUND, RECORD_MISSING_READ_GROUP, INVALID_INDEXING_BIN, - MISSING_VERSION_NUMBER, INVALID_VERSION_NUMBER, TRUNCATED_FILE, - MISMATCH_READ_LENGTH_AND_QUALS_LENGTH, EMPTY_READ, CIGAR_MAPS_OFF_REFERENCE, - MISMATCH_READ_LENGTH_AND_E2_LENGTH, MISMATCH_READ_LENGTH_AND_U2_LENGTH, - E2_BASE_EQUALS_PRIMARY_BASE, BAM_FILE_MISSING_TERMINATOR_BLOCK, UNRECOGNIZED_HEADER_TYPE, - POORLY_FORMATTED_HEADER_TAG, HEADER_TAG_MULTIPLY_DEFINED, - HEADER_RECORD_MISSING_REQUIRED_TAG, INVALID_DATE_STRING, TAG_VALUE_TOO_LARGE, - INVALID_INDEX_FILE_POINTER, INVALID_PREDICTED_MEDIAN_INSERT_SIZE, - DUPLICATE_READ_GROUP_ID, MISSING_PLATFORM_VALUE, INVALID_PLATFORM_VALUE, - DUPLICATE_PROGRAM_GROUP_ID, MATE_NOT_FOUND, MATES_ARE_SAME_END, - MISMATCH_MATE_CIGAR_STRING, MATE_CIGAR_STRING_INVALID_PRESENCE} This option may be - specified 0 or more times. - + M=Mode Mode of output Default value: VERBOSE. This option can be set to 'null' to clear the + default value. Possible values: {VERBOSE, SUMMARY} + + IGNORE=Type List of validation error types to ignore. Possible values: {INVALID_QUALITY_FORMAT, + INVALID_FLAG_PROPER_PAIR, INVALID_FLAG_MATE_UNMAPPED, MISMATCH_FLAG_MATE_UNMAPPED, + INVALID_FLAG_MATE_NEG_STRAND, MISMATCH_FLAG_MATE_NEG_STRAND, INVALID_FLAG_FIRST_OF_PAIR, + INVALID_FLAG_SECOND_OF_PAIR, PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND, + INVALID_FLAG_NOT_PRIM_ALIGNMENT, INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT, + INVALID_FLAG_READ_UNMAPPED, INVALID_INSERT_SIZE, INVALID_MAPPING_QUALITY, INVALID_CIGAR, + ADJACENT_INDEL_IN_CIGAR, INVALID_MATE_REF_INDEX, MISMATCH_MATE_REF_INDEX, + INVALID_REFERENCE_INDEX, INVALID_ALIGNMENT_START, MISMATCH_MATE_ALIGNMENT_START, + MATE_FIELD_MISMATCH, INVALID_TAG_NM, MISSING_TAG_NM, MISSING_HEADER, + MISSING_SEQUENCE_DICTIONARY, MISSING_READ_GROUP, RECORD_OUT_OF_ORDER, + READ_GROUP_NOT_FOUND, RECORD_MISSING_READ_GROUP, INVALID_INDEXING_BIN, + MISSING_VERSION_NUMBER, INVALID_VERSION_NUMBER, TRUNCATED_FILE, + MISMATCH_READ_LENGTH_AND_QUALS_LENGTH, EMPTY_READ, CIGAR_MAPS_OFF_REFERENCE, + MISMATCH_READ_LENGTH_AND_E2_LENGTH, MISMATCH_READ_LENGTH_AND_U2_LENGTH, + E2_BASE_EQUALS_PRIMARY_BASE, BAM_FILE_MISSING_TERMINATOR_BLOCK, UNRECOGNIZED_HEADER_TYPE, + POORLY_FORMATTED_HEADER_TAG, HEADER_TAG_MULTIPLY_DEFINED, + HEADER_RECORD_MISSING_REQUIRED_TAG, INVALID_DATE_STRING, TAG_VALUE_TOO_LARGE, + INVALID_INDEX_FILE_POINTER, INVALID_PREDICTED_MEDIAN_INSERT_SIZE, + DUPLICATE_READ_GROUP_ID, MISSING_PLATFORM_VALUE, INVALID_PLATFORM_VALUE, + DUPLICATE_PROGRAM_GROUP_ID, MATE_NOT_FOUND, MATES_ARE_SAME_END, + MISMATCH_MATE_CIGAR_STRING, MATE_CIGAR_STRING_INVALID_PRESENCE} This option may be + specified 0 or more times. + MAX_OUTPUT=Integer - MO=Integer The maximum number of lines output in verbose mode Default value: 100. This option can - be set to 'null' to clear the default value. - + MO=Integer The maximum number of lines output in verbose mode Default value: 100. This option can + be set to 'null' to clear the default value. + REFERENCE_SEQUENCE=File - R=File Reference sequence file, the NM tag check will be skipped if this is missing Default - value: null. - - IGNORE_WARNINGS=Boolean If true, only report errors and ignore warnings. Default value: false. This option can - be set to 'null' to clear the default value. Possible values: {true, false} - - VALIDATE_INDEX=Boolean If true and input is a BAM file with an index file, also validates the index. Default - value: true. This option can be set to 'null' to clear the default value. Possible - values: {true, false} - + R=File Reference sequence file, the NM tag check will be skipped if this is missing Default + value: null. + + IGNORE_WARNINGS=Boolean If true, only report errors and ignore warnings. Default value: false. This option can + be set to 'null' to clear the default value. Possible values: {true, false} + + VALIDATE_INDEX=Boolean If true and input is a BAM file with an index file, also validates the index. Default + value: true. This option can be set to 'null' to clear the default value. Possible + values: {true, false} + IS_BISULFITE_SEQUENCED=Boolean - BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not - counted as an error in computing the value of the NM tag. Default value: false. This - option can be set to 'null' to clear the default value. Possible values: {true, false} - + BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not + counted as an error in computing the value of the NM tag. Default value: false. This + option can be set to 'null' to clear the default value. Possible values: {true, false} + @more_info@ </help>