Mercurial > repos > devteam > picard
annotate picard_FastqToSam.xml @ 9:5eaa8a968300 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
| author | devteam |
|---|---|
| date | Fri, 09 Oct 2015 17:43:13 -0400 |
| parents | 3a3234d7a2e8 |
| children | 05087b27692a |
| rev | line source |
|---|---|
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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1 <tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>convert Fastq data into unaligned BAM</description> |
| 3 <macros> | |
| 4 <import>picard_macros.xml</import> | |
| 5 </macros> | |
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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6 <expand macro="requirements" /> |
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5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
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7 <stdio> |
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5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
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8 <exit_code range="1:" level="fatal"/> |
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5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
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|
9 </stdio> |
| 5 | 10 <command> |
| 11 @java_options@ | |
| 12 | |
| 13 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 14 FastqToSam | |
| 15 | |
| 16 #if str( $input_type.input_type_selector ) == "se": | |
| 17 FASTQ="${input_type.fastq}" | |
| 18 #elif str( $input_type.input_type_selector ) == "pe": | |
| 19 FASTQ="${input_type.fastq}" | |
| 20 FASTQ2="${input_type.fastq2}" | |
| 21 #else | |
| 22 FASTQ="${input_type.fastq.forward}" | |
| 23 FASTQ2="${input_type.fastq.reverse}" | |
| 0 | 24 #end if |
| 5 | 25 |
| 26 QUALITY_FORMAT="${quality_format}" | |
| 27 OUTPUT="${outFile}" | |
| 0 | 28 READ_GROUP_NAME="${read_group_name}" |
| 5 | 29 SAMPLE_NAME="${sample_name}" |
| 30 | |
| 31 #if str( $library_name ): | |
| 32 LIBRARY_NAME="${library_name}" | |
| 33 #end if | |
| 34 | |
| 35 #if str( $platform_unit ): | |
| 36 PLATFORM_UNIT="${platform_unit}" | |
| 37 #end if | |
| 38 | |
| 39 #if str( $platform ): | |
| 40 PLATFORM="${platform}" | |
| 41 #end if | |
| 42 | |
| 43 #if str( $sequencing_center ): | |
| 44 SEQUENCING_CENTER="${sequencing_center}" | |
| 45 #end if | |
| 46 | |
| 47 #if str( $predicted_insert_size ): | |
| 48 PREDICTED_INSERT_SIZE="${predicted_insert_size}" | |
| 0 | 49 #end if |
| 5 | 50 |
| 51 #if str( $comment ): | |
| 52 COMMENT="${comment}" | |
| 53 #end if | |
| 54 | |
| 55 #if str( $description ): | |
| 56 DESCRIPTION="${description}" | |
| 57 #end if | |
| 58 | |
| 59 #if str( $run_date ): | |
| 60 RUN_DATE="${run_date}" | |
| 61 #end if | |
| 62 | |
| 63 MIN_Q="${min_q}" | |
| 64 MAX_Q="${max_q}" | |
| 65 STRIP_UNPAIRED_MATE_NUMBER="${strip_unpairied_mate_number}" | |
| 66 ALLOW_AND_IGNORE_EMPTY_LINES="${allow_and_ignore_empty_lines}" | |
| 67 | |
| 68 SORT_ORDER=coordinate | |
| 69 VALIDATION_STRINGENCY="${validation_stringency}" | |
| 70 QUIET=true | |
| 71 VERBOSITY=ERROR | |
| 72 | |
| 0 | 73 </command> |
| 74 <inputs> | |
| 5 | 75 <conditional name="input_type"> |
| 76 <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types"> | |
| 77 <option value="se">Single end (single dataset)</option> | |
| 78 <option value="pe">Paired end (two datasets)</option> | |
| 79 <option value="pc">Paired collection</option> | |
| 0 | 80 </param> |
| 5 | 81 <when value="se"> |
| 82 <param name="fastq" type="data" format="fastq" label="Input fastq file for single end data" help="FASTQ"/> | |
| 0 | 83 </when> |
| 5 | 84 <when value="pe"> |
| 85 <param name="fastq" type="data" format="fastq" label="Input fastq file for the first read in paired end data" help="FASTQ"/> | |
| 86 <param name="fastq2" type="data" format="fastq" label="Input fastq file for the second read of paired end data" help="FASTQ2"/> | |
| 87 </when> | |
| 88 <when value="pc"> | |
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9
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
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diff
changeset
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89 <param name="fastq" type="data_collection" collection_type="paired" format="fastq" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/> |
| 0 | 90 </when> |
| 91 </conditional> | |
| 5 | 92 |
| 93 <param name="quality_format" type="select" label="Select quality encoding scheme" help="QUALITY_FORMAT"> | |
| 94 <option value="Standard" selected="True">Sanger (+33)</option> | |
| 95 <option value="Illumina">Illumina (+64)</option> | |
| 96 <option value="Solexa">Solexa (+66)</option> | |
| 97 </param> | |
| 98 | |
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9
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
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99 <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/> |
|
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
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parents:
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changeset
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100 <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/> |
|
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
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101 <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/> |
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5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
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diff
changeset
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102 <param name="platform_unit" type="text" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/> |
|
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
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diff
changeset
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103 <param name="platform" type="text" optional="True" label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/> |
|
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
8
diff
changeset
|
104 <param name="sequencing_center" type="text" optional="True" label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/> |
| 5 | 105 |
| 106 <param name="predicted_insert_size" type="integer" min="0" max="100000" optional="True" label="Predicted median insert size, to insert into the read group header" help="PREDICTED_INSERT_SIZE; Optional"/> | |
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9
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
8
diff
changeset
|
107 <param name="comment" type="text" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/> |
|
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
8
diff
changeset
|
108 <param name="description" type="text" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/> |
| 5 | 109 <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/> |
| 110 <param name="min_q" type="integer" value="0" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MIN_Q; An exception will be thrown if a quality is less than this value; default=0"/> | |
| 111 <param name="max_q" type="integer" value="93" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MAX_Q; An exception will be thrown if a quality is greater than this value; default=93"/> | |
| 112 <param name="strip_unpairied_mate_number" type="boolean" truevalue="true" falsevalue="false" label="If true and this is an unpaired fastq any occurance of '/1' will be removed from the end of a read name" help="STRIP_UNPAIRED_MATE_NUMBER; default=false"/> | |
| 113 <param name="allow_and_ignore_empty_lines" type="boolean" truevalue="true" falsevalue="false" label="Allow (and ignore) empty lines" help="ALLOW_AND_IGNORE_EMPTY_LINES; default=false"/> | |
| 114 | |
| 115 <expand macro="VS" /> | |
| 116 | |
| 117 </inputs> | |
| 118 | |
| 0 | 119 <outputs> |
| 5 | 120 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/> |
| 0 | 121 </outputs> |
| 5 | 122 |
| 0 | 123 <tests> |
| 5 | 124 <test> |
| 125 <param name="input_type_selector" value="pe" /> | |
| 126 <param name="quality_format" value="Standard" /> | |
| 127 <param name="read_group_name" value="A" /> | |
| 128 <param name="sample_name" value="sample-a" /> | |
| 129 <param name="library_name" value="A"/> | |
| 130 <param name="platform_unit" value="A"/> | |
| 131 <param name="platform" value="Illumina"/> | |
| 132 <param name="sequencing_center" value="A"/> | |
| 133 <param name="predicted_insert_size" value="300"/> | |
| 134 <param name="comment" value="A"/> | |
| 135 <param name="description" value="A"/> | |
| 136 <param name="run_date" value="2014-10-10"/> | |
| 137 <param name="min_q" value="0" /> | |
| 138 <param name="max_q" value="93" /> | |
| 139 <param name="strip_unpairied_mate_number" value="False" /> | |
| 140 <param name="allow_and_ignore_empty_lines" value="False" /> | |
| 141 <param name="validation_stringency" value="LENIENT"/> | |
| 142 <param name="fastq" value="picard_FastqToSam_read1.fq" ftype="fastq" /> | |
| 143 <param name="fastq2" value="picard_FastqToSam_read2.fq" ftype="fastq" /> | |
| 144 <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="bam" lines_diff="4"/> | |
| 145 </test> | |
| 0 | 146 </tests> |
| 5 | 147 |
| 0 | 148 <help> |
| 5 | 149 |
| 150 .. class:: infomark | |
| 151 | |
| 152 **Purpose** | |
| 153 | |
| 154 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. | |
| 155 | |
| 156 @dataset_collections@ | |
| 157 | |
| 158 @RG@ | |
| 159 | |
| 160 @description@ | |
| 0 | 161 |
| 5 | 162 FASTQ=File |
| 163 F1=File Input fastq file for single end data, or first read in paired end | |
| 164 data. Required. | |
| 165 | |
| 166 FASTQ2=File | |
| 167 F2=File Input fastq file for the second read of paired end data (if used). | |
| 168 | |
| 169 QUALITY_FORMAT=FastqQualityFormat | |
| 170 V=FastqQualityFormat A value describing how the quality values are encoded in the fastq. Either Solexa for | |
| 171 pre-pipeline 1.3 style scores (solexa scaling + 66), Illumina for pipeline 1.3 and above | |
| 172 (phred scaling + 64) or Standard for phred scaled scores with a character shift of 33. | |
| 173 If this value is not specified, the quality format will be detected automatically. | |
| 174 Default value: null. Possible values: {Solexa, Illumina, Standard} | |
| 0 | 175 |
| 5 | 176 READ_GROUP_NAME=String |
| 177 RG=String Read group name Default value: A. | |
| 178 | |
| 179 SAMPLE_NAME=String | |
| 180 SM=String Sample name to insert into the read group header Required. | |
| 181 | |
| 182 LIBRARY_NAME=String | |
| 183 LB=String The library name to place into the LB attribute in the read group header. | |
| 184 | |
| 185 PLATFORM_UNIT=String | |
| 186 PU=String The platform unit (often run_barcode.lane) to insert into the read group header. | |
| 187 | |
| 188 PLATFORM=String | |
| 189 PL=String The platform type (e.g. illumina, solid) to insert into the read group header. | |
| 190 | |
| 191 SEQUENCING_CENTER=String | |
| 192 CN=String The sequencing center from which the data originated. | |
| 193 | |
| 194 PREDICTED_INSERT_SIZE=Integer | |
| 195 PI=Integer Predicted median insert size, to insert into the read group header. | |
| 196 | |
| 197 COMMENT=String | |
| 198 CO=String Comment to include in the merged output file's header. | |
| 199 | |
| 200 DESCRIPTION=String | |
| 201 DS=String Inserted into the read group header. | |
| 202 | |
| 203 RUN_DATE=Iso8601Date | |
| 204 DT=Iso8601Date Date the run was produced, to insert into the read group header. | |
| 205 | |
| 206 MIN_Q=Integer Minimum quality allowed in the input fastq. An exception will be thrown if a quality is | |
| 207 less than this value. Default value: 0. | |
| 208 | |
| 209 MAX_Q=Integer Maximum quality allowed in the input fastq. An exception will be thrown if a quality is | |
| 210 greater than this value. Default value: 93. | |
| 211 | |
| 212 STRIP_UNPAIRED_MATE_NUMBER=Boolean | |
| 213 If true and this is an unpaired fastq any occurance of '/1' will be removed from the end | |
| 214 of a read name. Default value: false. Possible values: {true, false} | |
| 215 | |
| 216 ALLOW_AND_IGNORE_EMPTY_LINES=Boolean | |
| 217 Allow (and ignore) empty lines Default value: false. Possible values: {true, false} | |
| 218 | |
| 0 | 219 |
| 5 | 220 @more_info@ |
| 0 | 221 |
| 5 | 222 </help> |
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5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
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223 <citations> |
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5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
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224 </citations> |
| 5 | 225 </tool> |