picard: picard_ValidateSamFile.xml annotate

annotate picard_ValidateSamFile.xml @ 27:a1f0b3f4b781 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 11b94d7cd69b919f16feb10bd4b830a963334ab8"

author	iuc
date	Wed, 19 Feb 2020 14:27:00 -0500
parents	2a17c789e0a5
children	881d7645d1bf

rev	line source
19 5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73 iuc parents: 14 diff changeset	1 <tool name="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	2 <description>assess validity of SAM/BAM dataset</description>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	3 <macros>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	4 <import>picard_macros.xml</import>
20 2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a iuc parents: 19 diff changeset	5 <token name="@WRAPPER_VERSION@">1</token>
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	6 </macros>
8 3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty devteam parents: 7 diff changeset	7 <expand macro="requirements" />
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	8 <stdio>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	9 <exit_code range="1:" level="warning"/>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	10 </stdio>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	11 <command><![CDATA[
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	12
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	13 ##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
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	14
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	15 [ `ulimit -Hn` = unlimited ] && ulimit -Sn 4096 \|\| ulimit -Sn `ulimit -Hn`
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	16
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	17 &&
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	18
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	19 ##set up input files
13 7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e devteam parents: 12 diff changeset	20 @symlink_element_identifier@
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	21 #set $reference_fasta_filename = "localref.fa"
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	22
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	23 #if str( $reference_source.reference_source_selector ) == "history":
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	24 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	25 #else:
3d4f1fa26f0e Uploaded devteam parents: diff changeset	26 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
3d4f1fa26f0e Uploaded devteam parents: diff changeset	27 #end if
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	28
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	29 @java_options@
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	30
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	31 picard
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	32 ValidateSamFile
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	33
14 465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f devteam parents: 13 diff changeset	34 INPUT='$escaped_element_identifier'
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	35 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	36 MODE="${mode}"
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	37
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	38 #if str( $ignore ) != "None":
3d4f1fa26f0e Uploaded devteam parents: diff changeset	39 #for $element in str( $ignore ).split(','): ## See trello card https://trello.com/c/9nW02Zhd
3d4f1fa26f0e Uploaded devteam parents: diff changeset	40 IGNORE="${element}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	41 #end for
3d4f1fa26f0e Uploaded devteam parents: diff changeset	42 #end if
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	43
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	44 MAX_OUTPUT="${max_output}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	45 REFERENCE_SEQUENCE="${reference_fasta_filename}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	46 IGNORE_WARNINGS="${ignore_warnings}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	47 IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
3d4f1fa26f0e Uploaded devteam parents: diff changeset	48 MAX_OPEN_TEMP_FILES=`ulimit -Sn`
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	49
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	50 VERBOSITY=ERROR
20 2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a iuc parents: 19 diff changeset	51 @TMPDIR_OPTION@
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	52 QUIET=true
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	53
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	54 ]]></command>
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	55 <inputs>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	56 <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." />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	57 <conditional name="reference_source">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	58 <param name="reference_source_selector" type="select" label="Load reference genome from">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	59 <option value="cached">Local cache</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	60 <option value="history">History</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	61 </param>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	62 <when value="cached">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	63 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	64 <options from_data_table="picard_indexes">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	65 <filter type="sort_by" column="2" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	66 <validator type="no_options" message="No indexes are available" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	67 </options>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	68 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	69 </param>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	70 </when>
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	71 <when value="history">
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	72 <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" />
3d4f1fa26f0e Uploaded devteam parents: diff changeset	73 </when>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	74 </conditional>
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	75
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	76 <param name="mode" type="select" label="Select output mode" help="MODE">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	77 <option value="VERBOSE">Verbose</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	78 <option value="SUMMARY">Summary</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	79 </param>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	80 <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE">
3d4f1fa26f0e Uploaded devteam parents: diff changeset	81 <option value="INVALID_QUALITY_FORMAT">INVALID_QUALITY_FORMAT</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	82 <option value="INVALID_FLAG_PROPER_PAIR">INVALID_FLAG_PROPER_PAIR</option>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	83 <option value="INVALID_FLAG_MATE_UNMAPPED"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	84 <option value="MISMATCH_FLAG_MATE_UNMAPPED"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	85 <option value="INVALID_FLAG_MATE_NEG_STRAND"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	86 <option value="MISMATCH_FLAG_MATE_NEG_STRAND"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	87 <option value="INVALID_FLAG_FIRST_OF_PAIR"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	88 <option value="INVALID_FLAG_SECOND_OF_PAIR"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	89 <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	90 <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	91 <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	92 <option value="INVALID_FLAG_READ_UNMAPPED"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	93 <option value="INVALID_INSERT_SIZE"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	94 <option value="INVALID_MAPPING_QUALITY"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	95 <option value="INVALID_CIGAR"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	96 <option value="ADJACENT_INDEL_IN_CIGAR"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	97 <option value="INVALID_MATE_REF_INDEX"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	98 <option value="MISMATCH_MATE_REF_INDEX"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	99 <option value="INVALID_REFERENCE_INDEX"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	100 <option value="INVALID_ALIGNMENT_START"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	101 <option value="MISMATCH_MATE_ALIGNMENT_START"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	102 <option value="MATE_FIELD_MISMATCH"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	103 <option value="INVALID_TAG_NM"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	104 <option value="MISSING_TAG_NM"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	105 <option value="MISSING_HEADER"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	106 <option value="MISSING_SEQUENCE_DICTIONARY"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	107 <option value="MISSING_READ_GROUP"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	108 <option value="RECORD_OUT_OF_ORDER"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	109 <option value="READ_GROUP_NOT_FOUND"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	110 <option value="RECORD_MISSING_READ_GROUP"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	111 <option value="INVALID_INDEXING_BIN"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	112 <option value="MISSING_VERSION_NUMBER"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	113 <option value="INVALID_VERSION_NUMBER"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	114 <option value="TRUNCATED_FILE"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	115 <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	116 <option value="EMPTY_READ"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	117 <option value="CIGAR_MAPS_OFF_REFERENCE"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	118 <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	119 <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	120 <option value="E2_BASE_EQUALS_PRIMARY_BASE"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	121 <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	122 <option value="UNRECOGNIZED_HEADER_TYPE"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	123 <option value="POORLY_FORMATTED_HEADER_TAG"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	124 <option value="HEADER_TAG_MULTIPLY_DEFINED"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	125 <option value="HEADER_RECORD_MISSING_REQUIRED_TAG"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	126 <option value="INVALID_DATE_STRING"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	127 <option value="TAG_VALUE_TOO_LARGE"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	128 <option value="INVALID_INDEX_FILE_POINTER"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	129 <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	130 <option value="DUPLICATE_READ_GROUP_ID"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	131 <option value="MISSING_PLATFORM_VALUE"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	132 <option value="INVALID_PLATFORM_VALUE"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	133 <option value="DUPLICATE_PROGRAM_GROUP_ID"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	134 <option value="MATE_NOT_FOUND"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	135 <option value="MATES_ARE_SAME_END"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	136 <option value="MISMATCH_MATE_CIGAR_STRING"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	137 <option value="MATE_CIGAR_STRING_INVALID_PRESENCE"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	138 </param>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	139 <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	140 <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	141 <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"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	142 <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"/>
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	143
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	144 </inputs>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	145
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	146 <outputs>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	147 <data format="txt" name="outFile" label="${tool.name} on ${on_string}: BAM validation summary"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	148 </outputs>
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	149
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	150 <tests>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	151 <test>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	152 <param name="inputFile" value="picard_ValidateSamFile.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	153 <param name="reference_source_selector" value="history"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	154 <param name="ref_file" value="picard_ValidateSamFile_ref.fa"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	155 <param name="mode" value="VERBOSE"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	156 <param name="ignore" value="INVALID_QUALITY_FORMAT,INVALID_FLAG_PROPER_PAIR"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	157 <param name="max_output" value="100"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	158 <param name="ignore_warnings" value="Fasle"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	159 <param name="validate_index" value="True"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	160 <param name="is_bisulfite_sequenced" value="False"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	161 <output name="outFile" file="picard_ValidateSamFile_test1.txt" ftype="txt"/>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	162 </test>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	163 </tests>
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	164
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	165 <help>
3d4f1fa26f0e Uploaded devteam parents: diff changeset	166
3d4f1fa26f0e Uploaded devteam parents: diff changeset	167 Purpose
3d4f1fa26f0e Uploaded devteam parents: diff changeset	168
3d4f1fa26f0e Uploaded devteam parents: diff changeset	169 Reads a SAM/BAM dataset and report on its validity.
3d4f1fa26f0e Uploaded devteam parents: diff changeset	170
3d4f1fa26f0e Uploaded devteam parents: diff changeset	171 @dataset_collections@
3d4f1fa26f0e Uploaded devteam parents: diff changeset	172
3d4f1fa26f0e Uploaded devteam parents: diff changeset	173 @description@
3d4f1fa26f0e Uploaded devteam parents: diff changeset	174
3d4f1fa26f0e Uploaded devteam parents: diff changeset	175 MODE=Mode
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	176 M=Mode Mode of output Default value: VERBOSE. This option can be set to 'null' to clear the
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	177 default value. Possible values: {VERBOSE, SUMMARY}
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	178
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	179 IGNORE=Type List of validation error types to ignore. Possible values: {INVALID_QUALITY_FORMAT,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	180 INVALID_FLAG_PROPER_PAIR, INVALID_FLAG_MATE_UNMAPPED, MISMATCH_FLAG_MATE_UNMAPPED,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	181 INVALID_FLAG_MATE_NEG_STRAND, MISMATCH_FLAG_MATE_NEG_STRAND, INVALID_FLAG_FIRST_OF_PAIR,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	182 INVALID_FLAG_SECOND_OF_PAIR, PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	183 INVALID_FLAG_NOT_PRIM_ALIGNMENT, INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	184 INVALID_FLAG_READ_UNMAPPED, INVALID_INSERT_SIZE, INVALID_MAPPING_QUALITY, INVALID_CIGAR,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	185 ADJACENT_INDEL_IN_CIGAR, INVALID_MATE_REF_INDEX, MISMATCH_MATE_REF_INDEX,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	186 INVALID_REFERENCE_INDEX, INVALID_ALIGNMENT_START, MISMATCH_MATE_ALIGNMENT_START,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	187 MATE_FIELD_MISMATCH, INVALID_TAG_NM, MISSING_TAG_NM, MISSING_HEADER,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	188 MISSING_SEQUENCE_DICTIONARY, MISSING_READ_GROUP, RECORD_OUT_OF_ORDER,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	189 READ_GROUP_NOT_FOUND, RECORD_MISSING_READ_GROUP, INVALID_INDEXING_BIN,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	190 MISSING_VERSION_NUMBER, INVALID_VERSION_NUMBER, TRUNCATED_FILE,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	191 MISMATCH_READ_LENGTH_AND_QUALS_LENGTH, EMPTY_READ, CIGAR_MAPS_OFF_REFERENCE,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	192 MISMATCH_READ_LENGTH_AND_E2_LENGTH, MISMATCH_READ_LENGTH_AND_U2_LENGTH,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	193 E2_BASE_EQUALS_PRIMARY_BASE, BAM_FILE_MISSING_TERMINATOR_BLOCK, UNRECOGNIZED_HEADER_TYPE,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	194 POORLY_FORMATTED_HEADER_TAG, HEADER_TAG_MULTIPLY_DEFINED,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	195 HEADER_RECORD_MISSING_REQUIRED_TAG, INVALID_DATE_STRING, TAG_VALUE_TOO_LARGE,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	196 INVALID_INDEX_FILE_POINTER, INVALID_PREDICTED_MEDIAN_INSERT_SIZE,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	197 DUPLICATE_READ_GROUP_ID, MISSING_PLATFORM_VALUE, INVALID_PLATFORM_VALUE,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	198 DUPLICATE_PROGRAM_GROUP_ID, MATE_NOT_FOUND, MATES_ARE_SAME_END,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	199 MISMATCH_MATE_CIGAR_STRING, MATE_CIGAR_STRING_INVALID_PRESENCE} This option may be
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	200 specified 0 or more times.
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	201
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	202 MAX_OUTPUT=Integer
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	203 MO=Integer The maximum number of lines output in verbose mode Default value: 100. This option can
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	204 be set to 'null' to clear the default value.
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	205
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	206 REFERENCE_SEQUENCE=File
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	207 R=File Reference sequence file, the NM tag check will be skipped if this is missing Default
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	208 value: null.
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	209
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	210 IGNORE_WARNINGS=Boolean If true, only report errors and ignore warnings. Default value: false. This option can
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	211 be set to 'null' to clear the default value. Possible values: {true, false}
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	212
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	213 VALIDATE_INDEX=Boolean If true and input is a BAM file with an index file, also validates the index. Default
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	214 value: true. This option can be set to 'null' to clear the default value. Possible
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	215 values: {true, false}
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	216
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	217 IS_BISULFITE_SEQUENCED=Boolean
12 05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	218 BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	219 counted as an error in computing the value of the NM tag. Default value: false. This
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	220 option can be set to 'null' to clear the default value. Possible values: {true, false}
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92 devteam parents: 8 diff changeset	221
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	222 @more_info@
3d4f1fa26f0e Uploaded devteam parents: diff changeset	223
3d4f1fa26f0e Uploaded devteam parents: diff changeset	224 </help>
19 5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73 iuc parents: 14 diff changeset	225 <expand macro="citations" />
5 3d4f1fa26f0e Uploaded devteam parents: diff changeset	226 </tool>

Mercurial > repos > devteam > picard

annotate picard_ValidateSamFile.xml @ 27:a1f0b3f4b781 draft