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comparison picard_ValidateSamFile.xml @ 0:5166ed57b1c4 draft

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Uploaded version 1.135
author avowinkel
date Mon, 06 Jul 2015 14:46:32 -0400
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1 <tool name="ValidateSamFile" id="picard_ValidateSamFile" version="1.135">
2 <description>assess validity of SAM/BAM dataset</description>
3 <macros>
4 <import>picard_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>
8
9 ##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
10
11 [ `ulimit -Hn` = unlimited ] &amp;&amp; ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn`
12
13 &amp;&amp;
14
15 ##set up input files
16
17 #set $reference_fasta_filename = "localref.fa"
18
19 #if str( $reference_source.reference_source_selector ) == "history":
20 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
21 #else:
22 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
23 #end if
24
25 @java_options@
26
27 java -jar \$JAVA_JAR_PATH/picard.jar
28 ValidateSamFile
29
30 INPUT="${inputFile}"
31 OUTPUT="${outFile}"
32 MODE="${mode}"
33
34 #if str( $ignore ) != "None":
35 #for $element in str( $ignore ).split(','): ## See trello card https://trello.com/c/9nW02Zhd
36 IGNORE="${element}"
37 #end for
38 #end if
39
40 MAX_OUTPUT="${max_output}"
41 REFERENCE_SEQUENCE="${reference_fasta_filename}"
42 IGNORE_WARNINGS="${ignore_warnings}"
43 IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
44 MAX_OPEN_TEMP_FILES=`ulimit -Sn`
45
46 VERBOSITY=ERROR
47 QUIET=true
48
49 </command>
50 <inputs>
51 <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." />
52 <conditional name="reference_source">
53 <param name="reference_source_selector" type="select" label="Load reference genome from">
54 <option value="cached">Local cache</option>
55 <option value="history">History</option>
56 </param>
57 <when value="cached">
58 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
59 <options from_data_table="picard_indexes">
60 <filter type="sort_by" column="2" />
61 <validator type="no_options" message="No indexes are available" />
62 </options>
63 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
64 </param>
65 </when>
66 <when value="history">
67 <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" />
68 </when>
69 </conditional>
70
71 <param name="mode" type="select" label="Select output mode" help="MODE">
72 <option value="VERBOSE">Verbose</option>
73 <option value="SUMMARY">Summary</option>
74 </param>
75 <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE">
76 <option value="INVALID_QUALITY_FORMAT">INVALID_QUALITY_FORMAT</option>
77 <option value="INVALID_FLAG_PROPER_PAIR">INVALID_FLAG_PROPER_PAIR</option>
78 <option value="INVALID_FLAG_MATE_UNMAPPED"/>
79 <option value="MISMATCH_FLAG_MATE_UNMAPPED"/>
80 <option value="INVALID_FLAG_MATE_NEG_STRAND"/>
81 <option value="MISMATCH_FLAG_MATE_NEG_STRAND"/>
82 <option value="INVALID_FLAG_FIRST_OF_PAIR"/>
83 <option value="INVALID_FLAG_SECOND_OF_PAIR"/>
84 <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND"/>
85 <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT"/>
86 <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT"/>
87 <option value="INVALID_FLAG_READ_UNMAPPED"/>
88 <option value="INVALID_INSERT_SIZE"/>
89 <option value="INVALID_MAPPING_QUALITY"/>
90 <option value="INVALID_CIGAR"/>
91 <option value="ADJACENT_INDEL_IN_CIGAR"/>
92 <option value="INVALID_MATE_REF_INDEX"/>
93 <option value="MISMATCH_MATE_REF_INDEX"/>
94 <option value="INVALID_REFERENCE_INDEX"/>
95 <option value="INVALID_ALIGNMENT_START"/>
96 <option value="MISMATCH_MATE_ALIGNMENT_START"/>
97 <option value="MATE_FIELD_MISMATCH"/>
98 <option value="INVALID_TAG_NM"/>
99 <option value="MISSING_TAG_NM"/>
100 <option value="MISSING_HEADER"/>
101 <option value="MISSING_SEQUENCE_DICTIONARY"/>
102 <option value="MISSING_READ_GROUP"/>
103 <option value="RECORD_OUT_OF_ORDER"/>
104 <option value="READ_GROUP_NOT_FOUND"/>
105 <option value="RECORD_MISSING_READ_GROUP"/>
106 <option value="INVALID_INDEXING_BIN"/>
107 <option value="MISSING_VERSION_NUMBER"/>
108 <option value="INVALID_VERSION_NUMBER"/>
109 <option value="TRUNCATED_FILE"/>
110 <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH"/>
111 <option value="EMPTY_READ"/>
112 <option value="CIGAR_MAPS_OFF_REFERENCE"/>
113 <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH"/>
114 <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH"/>
115 <option value="E2_BASE_EQUALS_PRIMARY_BASE"/>
116 <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK"/>
117 <option value="UNRECOGNIZED_HEADER_TYPE"/>
118 <option value="POORLY_FORMATTED_HEADER_TAG"/>
119 <option value="HEADER_TAG_MULTIPLY_DEFINED"/>
120 <option value="HEADER_RECORD_MISSING_REQUIRED_TAG"/>
121 <option value="INVALID_DATE_STRING"/>
122 <option value="TAG_VALUE_TOO_LARGE"/>
123 <option value="INVALID_INDEX_FILE_POINTER"/>
124 <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE"/>
125 <option value="DUPLICATE_READ_GROUP_ID"/>
126 <option value="MISSING_PLATFORM_VALUE"/>
127 <option value="INVALID_PLATFORM_VALUE"/>
128 <option value="DUPLICATE_PROGRAM_GROUP_ID"/>
129 <option value="MATE_NOT_FOUND"/>
130 <option value="MATES_ARE_SAME_END"/>
131 <option value="MISMATCH_MATE_CIGAR_STRING"/>
132 <option value="MATE_CIGAR_STRING_INVALID_PRESENCE"/>
133 </param>
134 <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/>
135 <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/>
136 <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"/>
137 <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"/>
138
139 </inputs>
140
141 <outputs>
142 <data format="txt" name="outFile" label="${tool.name} on ${on_string}: BAM validation summary"/>
143 </outputs>
144
145 <tests>
146 <test>
147 <param name="inputFile" value="picard_ValidateSamFile.bam" ftype="bam"/>
148 <param name="reference_source_selector" value="history"/>
149 <param name="ref_file" value="picard_ValidateSamFile_ref.fa"/>
150 <param name="mode" value="VERBOSE"/>
151 <param name="ignore" value="INVALID_QUALITY_FORMAT,INVALID_FLAG_PROPER_PAIR"/>
152 <param name="max_output" value="100"/>
153 <param name="ignore_warnings" value="Fasle"/>
154 <param name="validate_index" value="True"/>
155 <param name="is_bisulfite_sequenced" value="False"/>
156 <output name="outFile" file="picard_ValidateSamFile_test1.txt" ftype="txt"/>
157 </test>
158 </tests>
159
160 <stdio>
161 <exit_code range="1:" level="warning"/>
162 </stdio>
163
164 <help>
165
166 **Purpose**
167
168 Reads a SAM/BAM dataset and report on its validity.
169
170 @dataset_collections@
171
172 @description@
173
174 MODE=Mode
175 M=Mode Mode of output Default value: VERBOSE. This option can be set to 'null' to clear the
176 default value. Possible values: {VERBOSE, SUMMARY}
177
178 IGNORE=Type List of validation error types to ignore. Possible values: {INVALID_QUALITY_FORMAT,
179 INVALID_FLAG_PROPER_PAIR, INVALID_FLAG_MATE_UNMAPPED, MISMATCH_FLAG_MATE_UNMAPPED,
180 INVALID_FLAG_MATE_NEG_STRAND, MISMATCH_FLAG_MATE_NEG_STRAND, INVALID_FLAG_FIRST_OF_PAIR,
181 INVALID_FLAG_SECOND_OF_PAIR, PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND,
182 INVALID_FLAG_NOT_PRIM_ALIGNMENT, INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT,
183 INVALID_FLAG_READ_UNMAPPED, INVALID_INSERT_SIZE, INVALID_MAPPING_QUALITY, INVALID_CIGAR,
184 ADJACENT_INDEL_IN_CIGAR, INVALID_MATE_REF_INDEX, MISMATCH_MATE_REF_INDEX,
185 INVALID_REFERENCE_INDEX, INVALID_ALIGNMENT_START, MISMATCH_MATE_ALIGNMENT_START,
186 MATE_FIELD_MISMATCH, INVALID_TAG_NM, MISSING_TAG_NM, MISSING_HEADER,
187 MISSING_SEQUENCE_DICTIONARY, MISSING_READ_GROUP, RECORD_OUT_OF_ORDER,
188 READ_GROUP_NOT_FOUND, RECORD_MISSING_READ_GROUP, INVALID_INDEXING_BIN,
189 MISSING_VERSION_NUMBER, INVALID_VERSION_NUMBER, TRUNCATED_FILE,
190 MISMATCH_READ_LENGTH_AND_QUALS_LENGTH, EMPTY_READ, CIGAR_MAPS_OFF_REFERENCE,
191 MISMATCH_READ_LENGTH_AND_E2_LENGTH, MISMATCH_READ_LENGTH_AND_U2_LENGTH,
192 E2_BASE_EQUALS_PRIMARY_BASE, BAM_FILE_MISSING_TERMINATOR_BLOCK, UNRECOGNIZED_HEADER_TYPE,
193 POORLY_FORMATTED_HEADER_TAG, HEADER_TAG_MULTIPLY_DEFINED,
194 HEADER_RECORD_MISSING_REQUIRED_TAG, INVALID_DATE_STRING, TAG_VALUE_TOO_LARGE,
195 INVALID_INDEX_FILE_POINTER, INVALID_PREDICTED_MEDIAN_INSERT_SIZE,
196 DUPLICATE_READ_GROUP_ID, MISSING_PLATFORM_VALUE, INVALID_PLATFORM_VALUE,
197 DUPLICATE_PROGRAM_GROUP_ID, MATE_NOT_FOUND, MATES_ARE_SAME_END,
198 MISMATCH_MATE_CIGAR_STRING, MATE_CIGAR_STRING_INVALID_PRESENCE} This option may be
199 specified 0 or more times.
200
201 MAX_OUTPUT=Integer
202 MO=Integer The maximum number of lines output in verbose mode Default value: 100. This option can
203 be set to 'null' to clear the default value.
204
205 REFERENCE_SEQUENCE=File
206 R=File Reference sequence file, the NM tag check will be skipped if this is missing Default
207 value: null.
208
209 IGNORE_WARNINGS=Boolean If true, only report errors and ignore warnings. Default value: false. This option can
210 be set to 'null' to clear the default value. Possible values: {true, false}
211
212 VALIDATE_INDEX=Boolean If true and input is a BAM file with an index file, also validates the index. Default
213 value: true. This option can be set to 'null' to clear the default value. Possible
214 values: {true, false}
215
216 IS_BISULFITE_SEQUENCED=Boolean
217 BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not
218 counted as an error in computing the value of the NM tag. Default value: false. This
219 option can be set to 'null' to clear the default value. Possible values: {true, false}
220
221 @more_info@
222
223 </help>
224 </tool>
225
226