Mercurial > repos > devteam > picard
annotate picard_BedToIntervalList.xml @ 14:465cbb0cf2eb draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
| author | devteam |
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| date | Wed, 07 Dec 2016 14:56:30 -0500 |
| parents | 7e6fd3d0f16e |
| children | 5053a18d9bc8 |
| 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="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> | |
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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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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
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7 <command detect_errors="exit_code"><![CDATA[ |
| 5 | 8 @java_options@ |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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9 @symlink_element_identifier@ |
| 5 | 10 #set $picard_dict = "localref.dict" |
| 11 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
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12 |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
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13 ln -s "${reference_source.ref_file}" "${ref_fasta}" && |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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14 |
| 5 | 15 #if str( $reference_source.reference_source_selector ) == "history": |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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16 |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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17 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" |
| 5 | 18 QUIET=true |
| 19 VERBOSITY=ERROR | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
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20 |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
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21 && |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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22 |
| 5 | 23 #else: |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
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diff
changeset
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24 |
| 5 | 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 | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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27 |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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28 #end if |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
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changeset
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29 |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
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30 picard |
| 5 | 31 BedToIntervalList |
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465cbb0cf2eb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
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32 INPUT='$escaped_element_identifier' |
| 5 | 33 OUTPUT="${outFile}" |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
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changeset
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34 |
| 5 | 35 SEQUENCE_DICTIONARY="${picard_dict}" |
| 36 QUIET=true | |
| 37 VERBOSITY=ERROR | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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38 |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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39 ]]></command> |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
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diff
changeset
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40 |
| 5 | 41 <inputs> |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
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42 |
| 5 | 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> | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
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57 <when value="history"> |
| 5 | 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> | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
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61 |
| 5 | 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"/> | |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
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74 <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="8" /> |
| 5 | 75 </test> |
| 76 </tests> | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
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77 |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
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changeset
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78 |
| 5 | 79 <help> |
| 80 | |
| 81 .. class:: infomark | |
| 82 | |
| 83 **Purpose** | |
| 84 | |
| 85 Convert coordinate data (such as BED or Galaxy Interval) into Picard Interval Format. | |
| 86 | |
| 87 @dataset_collections@ | |
| 88 | |
| 89 @description@ | |
| 90 | |
| 91 SEQUENCE_DICTIONARY=File | |
| 92 SD=File The sequence dictionary. You can either use dictionary pre-cached | |
| 93 on this instance of Galaxy, or create one on teh fly from a FASTA | |
| 94 file uploaded to history (right pane of the interface). | |
| 95 | |
| 96 | |
| 97 @more_info@ | |
| 98 </help> | |
| 99 </tool> | |
| 100 | |
| 101 | |
| 102 | |
| 103 | |
| 104 | |
| 105 | |
| 106 | |
| 107 | |
| 108 | |
| 109 | |
| 110 | |
| 111 | |
| 112 |