Mercurial > repos > devteam > picard
annotate picard_DownsampleSam.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
devteam
parents:
5
diff
changeset
|
1 <tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>Downsample a file to retain a subset of the reads</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 java -jar | |
| 10 \$JAVA_JAR_PATH/picard.jar | |
| 11 DownsampleSam | |
| 12 INPUT="${inputFile}" | |
| 13 OUTPUT="${outFile}" | |
| 14 PROBABILITY=${probability} | |
| 15 RANDOM_SEED=${seed} | |
| 16 QUIET=true | |
| 17 VERBOSITY=ERROR | |
| 18 VALIDATION_STRINGENCY=${validation_stringency} | |
| 19 </command> | |
| 20 <inputs> | |
| 21 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset" /> | |
|
9
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
8
diff
changeset
|
22 <param name="probability" type="float" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" /> |
|
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
8
diff
changeset
|
23 <param name="seed" type="integer" label="Random seed value" help="RANDOM_SEED; default=1" value="1" /> |
| 5 | 24 |
| 25 <expand macro="VS" /> | |
| 26 | |
| 27 </inputs> | |
| 28 | |
| 29 <stdio> | |
| 30 <exit_code range="1:" level="fatal"/> | |
| 31 </stdio> | |
| 32 | |
| 33 <outputs> | |
| 34 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/> | |
| 35 </outputs> | |
| 36 | |
| 37 <tests> | |
| 38 <test> | |
| 39 <param name="inputFile" value="picard_DownsampleSam.bam" ftype="bam" /> | |
| 40 <param name="probability" value="0.1" /> | |
| 41 <param name="seed" value="1024" /> | |
| 42 <param name="validation_stringency" value="LENIENT" /> | |
| 43 <output name="outFile" file="picard_DownsampleSam_test1.bam" ftype="bam"/> | |
| 44 </test> | |
| 45 </tests> | |
| 46 <help> | |
| 47 | |
| 48 .. class:: infomark | |
| 49 | |
| 50 **Purpose** | |
| 51 | |
| 52 Randomly down-sample a SAM or BAM file to retain a random subset of the reads. Mate-pairs are either both kept or both discarded. Reads marked as not primary alignments are all discarded. Each read is given a probability P of being retained - results with the exact same input in the same order and with the same value for RANDOM_SEED will produce the same results. | |
| 53 | |
| 54 @dataset_collections@ | |
| 55 | |
| 56 @description@ | |
| 57 | |
| 58 INPUT=File | |
| 59 I=File The input SAM or BAM file to downsample. Required. | |
| 60 | |
| 61 OUTPUT=File | |
| 62 O=File The output, downsampled, SAM or BAM file to write. Required. | |
| 63 | |
| 64 RANDOM_SEED=Long | |
| 65 R=Long Random seed to use if reproducibilty is desired. Setting to null will cause multiple | |
| 66 invocations to produce different results. | |
| 67 | |
| 68 PROBABILITY=Double | |
| 69 P=Double The probability of keeping any individual read, between 0 and 1. | |
| 70 | |
| 71 | |
| 72 | |
| 73 @more_info@ | |
| 74 </help> | |
| 75 </tool> |