Mercurial > repos > devteam > picard
annotate picard_BedToIntervalList.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="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>convert coordinate data into picard interval list format</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 #set $picard_dict = "localref.dict" | |
| 11 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension | |
| 12 | |
| 13 ln -s "${reference_source.ref_file}" "${ref_fasta}" && | |
| 14 | |
| 15 #if str( $reference_source.reference_source_selector ) == "history": | |
| 16 | |
| 17 java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" | |
| 18 QUIET=true | |
| 19 VERBOSITY=ERROR | |
| 20 | |
| 21 && | |
| 22 | |
| 23 #else: | |
| 24 | |
| 25 #set $ref_fasta = str( $reference_source.ref_file.fields.path ) ## getting path of reference fasta file (must end with .fa) | |
| 26 #set $picard_dict=$ref_fasta[:-2]+"dict" ## replacing .fa with .dict | |
| 27 | |
| 28 #end if | |
| 29 | |
| 30 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 31 BedToIntervalList | |
| 32 INPUT="${inputFile}" | |
| 33 OUTPUT="${outFile}" | |
| 34 | |
| 35 SEQUENCE_DICTIONARY="${picard_dict}" | |
| 36 QUIET=true | |
| 37 VERBOSITY=ERROR | |
| 38 | |
| 39 </command> | |
| 40 | |
| 41 <inputs> | |
| 42 | |
| 43 <conditional name="reference_source"> | |
| 44 <param name="reference_source_selector" type="select" label="Load picard dictionary file from"> | |
| 45 <option value="cached">Local cache</option> | |
| 46 <option value="history">History</option> | |
| 47 </param> | |
| 48 <when value="cached"> | |
| 49 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> | |
| 50 <options from_data_table="picard_indexes"> | |
| 51 <filter type="sort_by" column="2" /> | |
| 52 <validator type="no_options" message="No indexes are available" /> | |
| 53 </options> | |
| 54 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> | |
| 55 </param> | |
| 56 </when> | |
| 57 <when value="history"> | |
| 58 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" /> | |
| 59 </when> | |
| 60 </conditional> | |
| 61 | |
| 62 <param format="bed" name="inputFile" type="data" label="Select coordinate dataset or dataset collection" help="This can be a bed or interval dataset" /> | |
| 63 | |
| 64 </inputs> | |
| 65 <outputs> | |
| 66 <data name="outFile" format="picard_interval_list" label="${tool.name} on ${on_string}: Picard interval list"> | |
| 67 </data> | |
| 68 </outputs> | |
| 69 <tests> | |
| 70 <test> | |
| 71 <param name="reference_source_selector" value="history" /> | |
| 72 <param name="ref_file" value="picard_BedToIntervalList_ref.fa" ftype="fasta" /> | |
| 73 <param name="inputFile" value="picard_BedToIntervalList.bed" ftype="bed"/> | |
| 74 <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="2" /> | |
| 75 </test> | |
| 76 </tests> | |
| 77 | |
| 78 <stdio> | |
| 79 <exit_code range="1:" level="fatal"/> | |
| 80 </stdio> | |
| 81 | |
| 82 <help> | |
| 83 | |
| 84 .. class:: infomark | |
| 85 | |
| 86 **Purpose** | |
| 87 | |
| 88 Convert coordinate data (such as BED or Galaxy Interval) into Picard Interval Format. | |
| 89 | |
| 90 @dataset_collections@ | |
| 91 | |
| 92 @description@ | |
| 93 | |
| 94 SEQUENCE_DICTIONARY=File | |
| 95 SD=File The sequence dictionary. You can either use dictionary pre-cached | |
| 96 on this instance of Galaxy, or create one on teh fly from a FASTA | |
| 97 file uploaded to history (right pane of the interface). | |
| 98 | |
| 99 | |
| 100 @more_info@ | |
| 101 </help> | |
| 102 </tool> | |
| 103 | |
| 104 | |
| 105 | |
| 106 | |
| 107 | |
| 108 | |
| 109 | |
| 110 | |
| 111 | |
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| 115 |