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1 <tool name="MergeSamFiles" id="picard_MergeSamFiles" version="1.126.0">
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2 <description>merges multiple SAM/BAM datasets into one</description>
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3 <requirements>
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4 <requirement type="package" version="1.126.0">picard</requirement>
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5 </requirements>
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6
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7 <macros>
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8 <import>picard_macros.xml</import>
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9 </macros>
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10
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11 <command>
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12 @java_options@
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13
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14 java -jar \$JAVA_JAR_PATH/picard.jar
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15 MergeSamFiles
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16
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17 #for $element in $inputFile:
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18 INPUT="${element}"
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19 #end for
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20
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21 OUTPUT="${outFile}"
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22 MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}"
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23
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24 ASSUME_SORTED="${assume_sorted}"
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25 #for $element in $comments:
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26 COMMENT="${element.comment}"
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27 #end for
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28
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29 USE_THREADING=true
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30 SORT_ORDER=coordinate
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31 VALIDATION_STRINGENCY="${validation_stringency}"
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32 QUIET=true
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33 VERBOSITY=ERROR
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34
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35 </command>
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36 <inputs>
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37 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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38 <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/>
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39 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/>
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40
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41 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
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42 <param name="comment" type="text" size="50" label="Add this comment to BAM dataset" help="COMMENT"/>
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43 </repeat>
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44
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45 <expand macro="VS" />
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46
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47 </inputs>
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48
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49 <outputs>
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50 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Merged BAM dataset"/>
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51 </outputs>
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52
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53 <tests>
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54 <test>
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55 <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/>
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56 <param name="assume_sorted" value="False"/>
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57 <param name="merge_sequence_dictionaries" value="False"/>
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58 <param name="validation_stringency" value="LENIENT"/>
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59 <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="2"/>
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60 </test>
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61 </tests>
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62
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63 <stdio>
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64 <exit_code range="1:" level="fatal"/>
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65 </stdio>
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66
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67 <help>
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68
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69 **Purpose**
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70
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71 Merges multiple SAM/BAM datasets into one.
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72
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73 @dataset_collections@
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74
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75 @description@
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76
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77 ASSUME_SORTED=Boolean
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78 AS=Boolean If true, assume that the input files are in the same sort order as the requested output
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79 sort order, even if their headers say otherwise. Default value: false. This option can
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80 be set to 'null' to clear the default value. Possible values: {true, false}
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81
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82 MERGE_SEQUENCE_DICTIONARIES=Boolean
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83 MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null'
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84 to clear the default value. Possible values: {true, false}
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85
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86 COMMENT=String
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87 CO=String Comment(s) to include in the merged output file's header. This option may be specified 0
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88 or more times.
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89
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90
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91 @more_info@
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92
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93 </help>
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94 </tool>
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95
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96
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