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annotate picard_MergeBamAlignment.xml @ 8:3a3234d7a2e8 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
| author | devteam |
|---|---|
| date | Thu, 16 Jul 2015 15:53:10 -0400 |
| parents | 3d4f1fa26f0e |
| children | 5eaa8a968300 |
| rev | line source |
|---|---|
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8
3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
5
diff
changeset
|
1 <tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>merge alignment data with additional info stored in an unmapped BAM dataset</description> |
| 3 <macros> | |
| 4 <import>picard_macros.xml</import> | |
| 5 </macros> | |
|
8
3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
5
diff
changeset
|
6 <expand macro="requirements" /> |
| 5 | 7 <command> |
| 8 @java_options@ | |
| 9 #set $picard_dict = "localref.dict" | |
| 10 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension | |
| 11 | |
| 12 ln -s "${reference_source.ref_file}" "${ref_fasta}" && | |
| 13 | |
| 14 #if str( $reference_source.reference_source_selector ) == "history": | |
| 15 | |
| 16 java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" | |
| 17 QUIET=true | |
| 18 VERBOSITY=ERROR | |
| 19 | |
| 20 && | |
| 21 | |
| 22 #else: | |
| 23 | |
| 24 #set $ref_fasta = str( $reference_source.ref_file.fields.path ) | |
| 25 | |
| 26 #end if | |
| 27 | |
| 28 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 29 MergeBamAlignment | |
| 30 UNMAPPED_BAM="${unmapped_bam}" | |
| 31 | |
| 32 PAIRED_RUN=true ##This argument is ignored and will be removed. Required. Possible values: {true, false} | |
| 33 | |
| 34 #if str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_one_file": | |
| 35 #for $dataset in $aligned_or_read1_and_read2.aligned_bams: | |
| 36 ALIGNED_BAM="${dataset.aligned_bam}" | |
| 37 #end for | |
| 38 #elif str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_two_files": | |
| 39 #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams: | |
| 40 READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}" | |
| 41 #end for | |
| 42 #for $dataset in $aligned_or_read1_and_read2.read2_aligned_bams: | |
|
8
3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
5
diff
changeset
|
43 READ2_ALIGNED_BAM="${dataset.read2_aligned_bam}" |
| 5 | 44 #end for |
| 45 #else | |
| 46 #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams: | |
| 47 READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}" | |
| 48 #end for | |
| 49 #end if | |
| 50 | |
| 51 OUTPUT="${outFile}" | |
| 52 REFERENCE_SEQUENCE="${ref_fasta}" | |
| 53 | |
| 54 CLIP_ADAPTERS="${clip_adapters}" | |
| 55 IS_BISULFITE_SEQUENCE="${is_bisulfite_sequence}" | |
| 56 ALIGNED_READS_ONLY="${aligned_reads_only}" | |
| 57 MAX_INSERTIONS_OR_DELETIONS="${max_insertions_or_deletions}" | |
| 58 | |
| 59 #for $attribute in $attributes_to_retain: | |
| 60 ATTRIBUTES_TO_RETAIN="${$attribute.attribute}" | |
| 61 #end for | |
| 62 | |
| 63 #for $attribute in $attributes_to_remove: | |
| 64 ATTRIBUTES_TO_REMOVE="${$attribute.attribute}" | |
| 65 #end for | |
| 66 | |
| 67 READ1_TRIM="${read1_trim}" | |
| 68 READ2_TRIM="${read2_trim}" | |
| 69 | |
| 70 #if str( $orientations ) != "None": | |
| 71 #for $orientation in str( $orientations ).split(','): ## See trello card https://trello.com/c/9nW02Zhd | |
| 72 EXPECTED_ORIENTATIONS="${orientation}" | |
| 73 #end for | |
| 74 #end if | |
| 75 | |
| 76 ALIGNER_PROPER_PAIR_FLAGS="${aligner_proper_pair_flags}" | |
| 77 PRIMARY_ALIGNMENT_STRATEGY="${primary_alignment_strategy}" | |
| 78 CLIP_OVERLAPPING_READS="${clip_overlapping_reads}" | |
| 79 INCLUDE_SECONDARY_ALIGNMENTS="${include_secondary_alignments}" | |
| 80 ADD_MATE_CIGAR="${add_mate_cigar}" | |
| 81 | |
| 82 VALIDATION_STRINGENCY="${validation_stringency}" | |
| 83 | |
| 84 SORT_ORDER=coordinate | |
| 85 QUIET=true | |
| 86 VERBOSITY=ERROR | |
| 87 | |
| 88 </command> | |
| 89 | |
| 90 <inputs> | |
| 91 | |
| 92 <conditional name="reference_source"> | |
| 93 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
| 94 <option value="cached">Local cache</option> | |
| 95 <option value="history">History</option> | |
| 96 </param> | |
| 97 <when value="cached"> | |
| 98 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> | |
| 99 <options from_data_table="picard_indexes"> | |
| 100 <filter type="sort_by" column="2" /> | |
| 101 <validator type="no_options" message="No indexes are available" /> | |
| 102 </options> | |
| 103 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> | |
| 104 </param> | |
| 105 </when> | |
| 106 <when value="history"> | |
| 107 <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" /> | |
| 108 </when> | |
| 109 </conditional> | |
| 110 | |
| 111 <param format="sam,bam" name="unmapped_bam" type="data" label="Selected unaligned SAM or BAM with original reads" help="UNMAPPED_BAM; This dataset must be sorted in queryname order (use picard_SortSam to do this)" /> | |
| 112 <conditional name="aligned_or_read1_and_read2"> | |
| 113 <param name="aligned_or_read1_and_read2_selector" type="select" label="What type of aligned data do you have?"> | |
| 114 <option value="paired_one_file">Paired data in a single BAM file (ALIGNED_BAM)</option> | |
| 115 <option value="paired_two_files">Paired data in separate files (READ1_ALIGNED_BAM and READ2_ALIGNED_BAM)</option> | |
| 116 <option value="single_file">Singe end data (READ1_ALIGNED_BAM)</option> | |
| 117 </param> | |
| 118 <when value="paired_one_file"> | |
| 119 <repeat name="aligned_bams" title="Aligned SAM or BAM dataset" min="1" help="You can provide multiple datasets"> | |
| 120 <param name="aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data" help="ALIGNED_BAM"/> | |
| 121 </repeat> | |
| 122 </when> | |
| 123 <when value="paired_two_files"> | |
| 124 <repeat name="read1_aligned_bams" title="Aligned SAM or BAM dataset for Read 1" min="1" help="You can provide multiple datasets"> | |
| 125 <param name="read1_aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data for Read1" help="READ1_ALIGNED_BAM"/> | |
| 126 </repeat> | |
| 127 <repeat name="read2_aligned_bams" title="Aligned SAM or BAM dataset for Read 2" min="1" help="You can provide multiple datasets"> | |
| 128 <param name="read2_aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data for Read2" help="READ2_ALIGNED_BAM"/> | |
| 129 </repeat> | |
| 130 </when> | |
| 131 <when value="single_file"> | |
| 132 <repeat name="read1_aligned_bams" title="Aligned SAM or BAM dataset for Single Reads" min="1" help="You can provide multiple datasets"> | |
| 133 <param name="read1_aligned_bam" type="data" format="sam,bam" label="SAM or BAM dataset(s) with alignment data" help="READ1_ALIGNED_BAM"/> | |
| 134 </repeat> | |
| 135 </when> | |
| 136 </conditional> | |
| 137 | |
| 138 <param name="clip_adapters" type="boolean" checked="true" label="Whether to clip adapters where identified" help="CLIP_ADAPTERS; default=True"/> | |
| 139 <param name="is_bisulfite_sequence" type="boolean" label="Whether the data is from bisulfite sequencing (used when caculating the NM tag)" help="IS_BISULFITE_SEQUENCE; default=False"/> | |
| 140 <param name="aligned_reads_only" type="boolean" label="Whether to output only aligned reads" help="ALIGNED_READS_ONLY; default=False"/> | |
| 141 <param name="max_insertions_or_deletions" type="integer" value="1" label="The maximum number of insertions or deletions permitted for an alignment to be included" help="MAX_INSERTIONS_OR_DELETIONS; Alignments with more than this many insertions or deletions will be ignored. Set to -1 to allow any number of insertions or deletions. default=1"/> | |
| 142 | |
| 143 <repeat name="attributes_to_retain" title="Retain the following alignment attribute" min="0" help="You can provide multiple attributes"> | |
| 144 <param name="attribute" type="text" size="4" label="Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over from the alignment data when merging" help="ATTRIBUTES_TO_RETAIN; example: XA"/> | |
| 145 </repeat> | |
| 146 | |
| 147 <repeat name="attributes_to_remove" title="Remove the following alignment attribute" min="0" help="You can provide multiple attributes"> | |
| 148 <param name="attribute" type="text" size="4" label="Attributes from the alignment record that should be removed when merging." help="ATTRIBUTES_TO_REMOVE; This overrides ATTRIBUTES_TO_RETAIN if they share common tags"/> | |
| 149 </repeat> | |
| 150 | |
| 151 <param name="read1_trim" type="integer" value="0" label="The number of bases trimmed from the beginning of read 1 prior to alignment" help="READ1_TRIM; default=0"/> | |
| 152 <param name="read2_trim" type="integer" value="0" label="The number of bases trimmed from the beginning of read 2 prior to alignment" help="READ2_TRIM; default=0"/> | |
| 153 | |
| 154 <param name="orientations" type="select" multiple="True" display="checkboxes" label="The expected orientation of proper read pairs" help="EXPECTED_ORIENTATIONS; multiple orinetations can be selected"> | |
| 155 <option value="FR">Forward/Reverse (FR)</option> | |
| 156 <option value="RF">Reverse/Forward (RF)</option> | |
| 157 <option value="TANDEM">Tandem</option> | |
| 158 </param> | |
| 159 | |
| 160 | |
| 161 <param name="aligner_proper_pair_flags" type="boolean" label="Use the aligner's idea of what a proper pair is rather than computing in this program" help="ALIGNER_PROPER_PAIR_FLAGS; default=False"/> | |
| 162 | |
| 163 <param name="primary_alignment_strategy" type="select" label="Strategy for selecting primary alignment when the aligner has provided more than one alignment for a pair or fragments" help="PRIMARY_ALIGNMENT_STRATEGY; see help below for more info; default=BestMapq"> | |
| 164 <option value="BestMapq" selected="True">BestMapq</option> | |
| 165 <option value="EarliestFragment">EarliestFragment</option> | |
| 166 <option value="BestEndMapq">BestEndMapq</option> | |
| 167 <option value="MostDistant">MostDistant</option> | |
| 168 </param> | |
| 169 | |
| 170 <param name="clip_overlapping_reads" type="boolean" checked="True" label="For paired reads, soft clip the 3' end of each read if necessary so that it does not extend past the 5' end of its mate" help="CLIP_OVERLAPPING_READS; default=True"/> | |
| 171 <param name="include_secondary_alignments" type="boolean" checked="True" label="If false, do not write secondary alignments to output" help="INCLUDE_SECONDARY_ALIGNMENTS; default=True"/> | |
| 172 <param name="add_mate_cigar" type="boolean" checked="True" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/> | |
| 173 <expand macro="VS" /> | |
| 174 </inputs> | |
| 175 <outputs> | |
| 176 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with merged alignments"/> | |
| 177 </outputs> | |
| 178 <tests> | |
| 179 <test> | |
| 180 <param name="reference_source_selector" value="history" /> | |
| 181 <param name="ref_file" value="picard_MergeBamAlignment_ref.fa" ftype="fasta" /> | |
| 182 <param name="unmapped_bam" value="picard_MergeBamAlignment_unaligned.bam" ftype="bam"/> | |
| 183 <param name="aligned_or_read1_and_read2_selector" value="paired_one_file"/> | |
| 184 <param name="aligned_bam" value="picard_MergeBamAlignment_aligned.bam" ftype="bam"/> | |
| 185 <param name="clip_adapters" value="True"/> | |
| 186 <param name="is_bisulfite_sequence" value="False"/> | |
| 187 <param name="aligned_reads_only" value="False"/> | |
| 188 <param name="max_insertions_or_deletions" value="1"/> | |
| 189 <param name="read1_trim" value="0"/> | |
| 190 <param name="read2_trim" value="0"/> | |
| 191 <param name="orientation" value="FR"/> | |
| 192 <param name="aligner_proper_pair_flags" value="False"/> | |
| 193 <param name="primary_alignment_strategy" value="BestMapq"/> | |
| 194 <param name="clip_overlapping_reads" value="True"/> | |
| 195 <param name="include_secondary_alignments" value="True"/> | |
| 196 <param name="add_mate_cigar" value="True"/> | |
| 197 <output name="outFile" file="picard_MergeBamAlignment_test1.bam" ftype="bam" lines_diff="2"/> | |
| 198 </test> | |
| 199 </tests> | |
| 200 | |
| 201 <stdio> | |
| 202 <exit_code range="1:" level="fatal"/> | |
| 203 </stdio> | |
| 204 | |
| 205 <help> | |
| 206 | |
| 207 .. class:: infomark | |
| 208 | |
| 209 **Purpose** | |
| 210 | |
| 211 Merges alignment data from a SAM or BAM dataset with additional data stored in an unmapped BAM dataset and produces a third SAM or BAM dataset of aligned and unaligned reads. | |
| 212 | |
| 213 @dataset_collections@ | |
| 214 | |
| 215 @description@ | |
| 216 | |
| 217 UNMAPPED_BAM=File | |
| 218 UNMAPPED=File Original SAM or BAM file of unmapped reads, which must be in queryname order. Required. | |
| 219 | |
| 220 ALIGNED_BAM=File | |
| 221 ALIGNED=File SAM or BAM file(s) with alignment data. This option may be specified 0 or more times. | |
| 222 Cannot be used in conjuction with option(s) READ1_ALIGNED_BAM (R1_ALIGNED) | |
| 223 READ2_ALIGNED_BAM (R2_ALIGNED) | |
| 224 | |
| 225 READ1_ALIGNED_BAM=File | |
| 226 R1_ALIGNED=File SAM or BAM file(s) with alignment data from the first read of a pair. This option may be | |
| 227 specified 0 or more times. Cannot be used in conjuction with option(s) ALIGNED_BAM | |
| 228 (ALIGNED) | |
| 229 | |
| 230 READ2_ALIGNED_BAM=File | |
| 231 R2_ALIGNED=File SAM or BAM file(s) with alignment data from the second read of a pair. This option may | |
| 232 be specified 0 or more times. Cannot be used in conjuction with option(s) ALIGNED_BAM | |
| 233 (ALIGNED) | |
| 234 | |
| 235 PAIRED_RUN=Boolean | |
| 236 PE=Boolean This argument is ignored and will be removed. Required. Possible values: {true, false} | |
| 237 | |
| 238 JUMP_SIZE=Integer | |
| 239 JUMP=Integer The expected jump size (required if this is a jumping library). Deprecated. Use | |
| 240 EXPECTED_ORIENTATIONS instead Default value: null. Cannot be used in conjuction with | |
| 241 option(s) EXPECTED_ORIENTATIONS (ORIENTATIONS) | |
| 242 | |
| 243 CLIP_ADAPTERS=Boolean Whether to clip adapters where identified. Default value: true. Possible values: {true, false} | |
| 244 | |
| 245 IS_BISULFITE_SEQUENCE=Boolean Whether the lane is bisulfite sequence (used when caculating the NM tag). Default value: | |
| 246 false. Possible values: {true, false} | |
| 247 | |
| 248 ALIGNED_READS_ONLY=Boolean Whether to output only aligned reads. Default value: false. Possible values: {true, false} | |
| 249 | |
| 250 MAX_INSERTIONS_OR_DELETIONS=Integer | |
| 251 MAX_GAPS=Integer The maximum number of insertions or deletions permitted for an alignment to be included. | |
| 252 Alignments with more than this many insertions or deletions will be ignored. Set to -1 to | |
| 253 allow any number of insertions or deletions. Default value: 1. | |
| 254 | |
| 255 ATTRIBUTES_TO_RETAIN=String Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over | |
| 256 from the alignment data when merging. This option may be specified 0 or more times. | |
| 257 | |
| 258 ATTRIBUTES_TO_REMOVE=String Attributes from the alignment record that should be removed when merging. This overrides | |
| 259 ATTRIBUTES_TO_RETAIN if they share common tags. This option may be specified 0 or more | |
| 260 times. | |
| 261 | |
| 262 READ1_TRIM=Integer | |
| 263 R1_TRIM=Integer The number of bases trimmed from the beginning of read 1 prior to alignment Default | |
| 264 value: 0. | |
| 265 | |
| 266 READ2_TRIM=Integer | |
| 267 R2_TRIM=Integer The number of bases trimmed from the beginning of read 2 prior to alignment Default | |
| 268 value: 0. | |
| 269 | |
| 270 EXPECTED_ORIENTATIONS=PairOrientation | |
| 271 ORIENTATIONS=PairOrientation The expected orientation of proper read pairs. Replaces JUMP_SIZE Possible values: {FR, | |
| 272 RF, TANDEM} This option may be specified 0 or more times. Cannot be used in conjuction | |
| 273 with option(s) JUMP_SIZE (JUMP) | |
| 274 | |
| 275 ALIGNER_PROPER_PAIR_FLAGS=Boolean | |
| 276 Use the aligner's idea of what a proper pair is rather than computing in this program. | |
| 277 Default value: false. Possible values: {true, false} | |
| 278 | |
| 279 SORT_ORDER=SortOrder | |
| 280 SO=SortOrder The order in which the merged reads should be output. Default value: coordinate. | |
| 281 Possible values: {unsorted, queryname, coordinate} | |
| 282 | |
| 283 PRIMARY_ALIGNMENT_STRATEGY=PrimaryAlignmentStrategy | |
| 284 Strategy for selecting primary alignment when the aligner has provided more than one | |
| 285 alignment for a pair or fragment, and none are marked as primary, more than one is marked | |
| 286 as primary, or the primary alignment is filtered out for some reason. BestMapq expects | |
| 287 that multiple alignments will be correlated with HI tag, and prefers the pair of | |
| 288 alignments with the largest MAPQ, in the absence of a primary selected by the aligner. | |
| 289 EarliestFragment prefers the alignment which maps the earliest base in the read. Note | |
| 290 that EarliestFragment may not be used for paired reads. BestEndMapq is appropriate for | |
| 291 cases in which the aligner is not pair-aware, and does not output the HI tag. It simply | |
| 292 picks the alignment for each end with the highest MAPQ, and makes those alignments | |
| 293 primary, regardless of whether the two alignments make sense together.MostDistant is also | |
| 294 for a non-pair-aware aligner, and picks the alignment pair with the largest insert size. | |
| 295 If all alignments would be chimeric, it picks the alignments for each end with the best | |
| 296 MAPQ. For all algorithms, ties are resolved arbitrarily. Default value: BestMapq. | |
| 297 Possible values: {BestMapq, EarliestFragment, BestEndMapq, MostDistant} | |
| 298 | |
| 299 CLIP_OVERLAPPING_READS=BooleanFor paired reads, soft clip the 3' end of each read if necessary so that it does not | |
| 300 extend past the 5' end of its mate. Default value: true. Possible values: {true, false} | |
| 301 | |
| 302 INCLUDE_SECONDARY_ALIGNMENTS=Boolean | |
| 303 If false, do not write secondary alignments to output. Default value: true. | |
| 304 Possible values: {true, false} | |
| 305 | |
| 306 ADD_MATE_CIGAR=Boolean | |
| 307 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Possible values: {true, false} | |
| 308 | |
| 309 | |
| 310 | |
| 311 | |
| 312 @more_info@ | |
| 313 </help> | |
| 314 </tool> | |
| 315 | |
| 316 | |
| 317 | |
| 318 | |
| 319 | |
| 320 | |
| 321 | |
| 322 | |
| 323 | |
| 324 | |
| 325 | |
| 326 | |
| 327 |