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1 <tool name="BedToIntervalList" id="picard_BedToIntervalList" version="1.135">
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2 <description>convert coordinate data into picard interval list format</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command>
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8 @java_options@
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9
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10 #set $picard_dict = "localref.dict"
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11 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
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12
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13 ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
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14
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15 #if str( $reference_source.reference_source_selector ) == "history":
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16
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17 java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
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18 QUIET=true
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19 VERBOSITY=ERROR
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20
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21 &&
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22
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23 #else:
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24
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25 #set $ref_fasta = str( $reference_source.ref_file.fields.path ) ## getting path of reference fasta file (must end with .fa)
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26 #set $picard_dict=$ref_fasta[:-2]+"dict" ## replacing .fa with .dict
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27
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28 #end if
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29
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30 java -jar \$JAVA_JAR_PATH/picard.jar
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31 BedToIntervalList
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32 INPUT="${inputFile}"
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33 OUTPUT="${outFile}"
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34
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35 SEQUENCE_DICTIONARY="${picard_dict}"
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36 QUIET=true
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37 VERBOSITY=ERROR
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38
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39 </command>
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40
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41 <inputs>
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42
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43 <conditional name="reference_source">
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44 <param name="reference_source_selector" type="select" label="Load picard dictionary file from">
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45 <option value="cached">Local cache</option>
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46 <option value="history">History</option>
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47 </param>
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48 <when value="cached">
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49 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
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50 <options from_data_table="picard_indexes">
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51 <filter type="sort_by" column="2" />
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52 <validator type="no_options" message="No indexes are available" />
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53 </options>
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54 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
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55 </param>
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56 </when>
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57 <when value="history">
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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" />
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59 </when>
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60 </conditional>
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61
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62 <param format="bed" name="inputFile" type="data" label="Select coordinate dataset or dataset collection" help="This can be a bed or interval dataset" />
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63
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64 </inputs>
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65 <outputs>
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66 <data name="outFile" format="picard_interval_list" label="${tool.name} on ${on_string}: Picard interval list">
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67 </data>
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param name="reference_source_selector" value="history" />
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72 <param name="ref_file" value="picard_BedToIntervalList_ref.fa" ftype="fasta" />
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73 <param name="inputFile" value="picard_BedToIntervalList.bed" ftype="bed"/>
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74 <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="2" />
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75 </test>
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76 </tests>
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77
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78 <stdio>
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79 <exit_code range="1:" level="fatal"/>
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80 </stdio>
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81
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82 <help>
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83
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84 .. class:: infomark
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85
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86 **Purpose**
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87
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88 Convert coordinate data (such as BED or Galaxy Interval) into Picard Interval Format.
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89
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90 @dataset_collections@
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91
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92 @description@
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93
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94 SEQUENCE_DICTIONARY=File
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95 SD=File The sequence dictionary. You can either use dictionary pre-cached
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96 on this instance of Galaxy, or create one on teh fly from a FASTA
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97 file uploaded to history (right pane of the interface).
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98
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99
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100 @more_info@
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101 </help>
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102 </tool>
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103
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