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annotate picard_ReorderSam.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 | 05087b27692a |
| rev | line source |
|---|---|
|
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="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>reorder reads to match ordering in reference sequences</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( $reference_source.ref_file.fields.path ) | |
| 25 | |
| 26 #end if | |
| 27 | |
| 28 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 29 ReorderSam | |
| 30 INPUT="${inputFile}" | |
| 31 OUTPUT="${outFile}" | |
| 32 REFERENCE="${ref_fasta}" | |
| 33 ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}" | |
| 34 ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}" | |
| 35 | |
| 36 VALIDATION_STRINGENCY="${validation_stringency}" | |
| 37 QUIET=true | |
| 38 VERBOSITY=ERROR | |
| 39 | |
| 0 | 40 </command> |
| 5 | 41 |
| 0 | 42 <inputs> |
| 5 | 43 |
| 44 <conditional name="reference_source"> | |
| 45 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
| 46 <option value="cached">Local cache</option> | |
| 0 | 47 <option value="history">History</option> |
| 48 </param> | |
| 5 | 49 <when value="cached"> |
| 50 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> | |
| 51 <options from_data_table="picard_indexes"> | |
| 52 <filter type="sort_by" column="2" /> | |
| 53 <validator type="no_options" message="No indexes are available" /> | |
| 54 </options> | |
| 55 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> | |
| 0 | 56 </param> |
| 57 </when> | |
| 5 | 58 <when value="history"> |
| 59 <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" /> | |
| 0 | 60 </when> |
| 61 </conditional> | |
| 5 | 62 |
| 63 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> | |
| 64 <param name="allow_incomplete_dict_concordance" type="boolean" label="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs" help="ALLOW_INCOMPLETE_DICT_CONCORDANCE; By default, this tool requires a corresponding contig in the new reference for each read contig; default=False"/> | |
| 65 <param name="allow_contig_length_discordance" type="boolean" label="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length" help="ALLOW_CONTIG_LENGTH_DISCORDANCE; HIGHLY DANGEROUS! Only use if you know what you are doing; default=False"/> | |
| 66 <expand macro="VS" /> | |
| 67 | |
| 0 | 68 </inputs> |
| 69 <outputs> | |
| 5 | 70 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/> |
| 0 | 71 </outputs> |
| 72 <tests> | |
| 73 <test> | |
| 5 | 74 <param name="reference_source_selector" value="history" /> |
| 75 <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" /> | |
| 76 <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/> | |
| 77 <param name="allow_incomplete_dict_concordance" value="false"/> | |
| 78 <param name="allow_contig_length_discordance" value="false"/> | |
| 79 <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="2"/> | |
| 0 | 80 </test> |
| 81 </tests> | |
| 5 | 82 |
| 83 <stdio> | |
| 84 <exit_code range="1:" level="fatal"/> | |
| 85 </stdio> | |
| 86 | |
| 0 | 87 <help> |
| 88 | |
| 89 .. class:: infomark | |
| 90 | |
| 91 **Purpose** | |
| 92 | |
| 5 | 93 ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are dropped. |
| 0 | 94 |
| 5 | 95 @dataset_collections@ |
| 0 | 96 |
| 5 | 97 ---- |
| 0 | 98 |
| 99 .. class:: warningmark | |
| 100 | |
| 5 | 101 Not to be confused with **SortSam**. |
| 102 | |
| 103 @description@ | |
| 0 | 104 |
| 5 | 105 ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean |
| 106 S=Boolean If true, then allows only a partial overlap of the BAM contigs with the new reference | |
| 107 sequence contigs. By default, this tool requires a corresponding contig in the new | |
| 108 reference for each read contig Default value: false. Possible values: {true, false} | |
| 109 | |
| 110 ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean | |
| 111 U=Boolean If true, then permits mapping from a read contig to a new reference contig with the same | |
| 112 name but a different length. Highly dangerous, only use if you know what you are doing. | |
| 113 Default value: false. Possible values: {true, false} | |
| 0 | 114 |
| 5 | 115 @more_info@ |
| 0 | 116 </help> |
| 117 </tool> | |
| 118 | |
| 119 | |
| 120 | |
| 121 | |
| 122 | |
| 123 | |
| 124 | |
| 125 | |
| 126 | |
| 127 | |
| 128 | |
| 129 | |
| 5 | 130 |