Mercurial > repos > devteam > picard
annotate picard_FilterSamReads.xml @ 11:efc56ee1ade4 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:23:17 -0500 |
| 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="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>include or exclude aligned and unaligned reads and read lists</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 | |
| 10 ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order | |
| 11 | |
| 12 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 13 SortSam | |
| 14 INPUT="${inputFile}" | |
| 15 OUTPUT=query_sorted_bam.bam | |
| 16 SORT_ORDER=queryname | |
| 17 VALIDATION_STRINGENCY=LENIENT | |
| 18 QUIET=true | |
| 19 VERBOSITY=ERROR | |
| 20 | |
| 21 && | |
| 22 | |
| 23 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 24 FilterSamReads | |
| 25 INPUT=query_sorted_bam.bam | |
| 26 FILTER="${filter_type.filter}" | |
| 27 | |
| 28 #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ): | |
| 29 READ_LIST_FILE="${filter_type.read_list_file}" | |
| 30 #end if | |
| 31 | |
| 32 OUTPUT="${outFile}" | |
| 33 SORT_ORDER=coordinate | |
| 34 VALIDATION_STRINGENCY="${validation_stringency}" | |
| 35 QUIET=true | |
| 36 VERBOSITY=ERROR | |
| 37 | |
| 38 </command> | |
| 39 <inputs> | |
|
8
3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
5
diff
changeset
|
40 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> |
| 5 | 41 <conditional name="filter_type"> |
| 42 <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info"> | |
| 43 <option value="includeAligned">Include aligned</option> | |
| 44 <option value="excludeAligned">Exclude aligned</option> | |
| 45 <option value="includeReadList">Include read list</option> | |
| 46 <option value="excludeReadList">Exclude read list</option> | |
| 47 </param> | |
| 48 <when value="includeAligned"/> <!-- do nothing --> | |
| 49 <when value="excludeAligned"/> <!-- do nothing --> | |
| 50 <when value="includeReadList"> | |
| 51 <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be INCLUDED in the output" help="READ_LIST_FILE"/> | |
| 52 </when> | |
| 53 <when value="excludeReadList"> | |
| 54 <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be EXCLUDED in the output" help="READ_LIST_FILE"/> | |
| 55 </when> | |
| 56 </conditional> | |
| 57 | |
| 58 <expand macro="VS" /> | |
| 59 | |
| 60 </inputs> | |
| 61 | |
| 62 <outputs> | |
| 63 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/> | |
| 64 </outputs> | |
| 65 | |
| 66 <tests> | |
| 67 <test> | |
| 68 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/> | |
| 69 <param name="filter" value="includeReadList"/> | |
| 70 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/> | |
| 71 <param name="validation_stringency" value="LENIENT"/> | |
| 72 <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="2"/> | |
| 73 </test> | |
| 74 <test> | |
| 75 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/> | |
| 76 <param name="filter" value="excludeReadList"/> | |
| 77 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/> | |
| 78 <param name="validation_stringency" value="LENIENT"/> | |
| 79 <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="2"/> | |
| 80 </test> | |
| 81 </tests> | |
| 82 | |
| 83 <stdio> | |
| 84 <exit_code range="1:" level="fatal"/> | |
| 85 </stdio> | |
| 86 | |
| 87 <help> | |
| 88 | |
| 89 **Purpose** | |
| 90 | |
| 91 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. | |
| 92 | |
| 93 ------ | |
| 94 | |
| 95 .. class:: warningmark | |
| 96 | |
| 97 **Warning on using this tool on BWA-MEM output** | |
| 98 | |
| 99 This tool will likely fail on BAM datasets generated by BWA MEM as it generates partial read alignemnts. | |
| 100 | |
| 101 @dataset_collections@ | |
| 102 | |
| 103 @description@ | |
| 104 | |
| 105 FILTER=Filter Filter. Required. Possible values: | |
| 106 includeAligned [OUTPUT SAM/BAM will contain aligned | |
| 107 reads only. (Note that *both* first and | |
| 108 second of paired reads must be aligned to be included | |
| 109 in the OUTPUT SAM or BAM)], | |
| 110 | |
| 111 excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only. | |
| 112 (Note that *both* first and second of pair must be aligned to be | |
| 113 excluded from the OUTPUT SAM or BAM)] | |
| 114 | |
| 115 includeReadList [OUTPUT SAM/BAM will contain reads | |
| 116 that are supplied in the READ_LIST_FILE file] | |
| 117 | |
| 118 excludeReadList [OUTPUT bam will contain | |
| 119 reads that are *not* supplied in the READ_LIST_FILE file]} | |
| 120 | |
| 121 READ_LIST_FILE=File | |
| 122 RLF=File Read List File containing reads that will be included or excluded from the OUTPUT SAM or | |
| 123 BAM file. Default value: null. | |
| 124 | |
| 125 @more_info@ | |
| 126 | |
| 127 </help> | |
| 128 </tool> | |
| 129 | |
| 130 |