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annotate picard_MergeSamFiles.xml @ 13:7e6fd3d0f16e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:41 -0500
parents 05087b27692a
children 5053a18d9bc8
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1 <tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.0">
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2 <description>merges multiple SAM/BAM datasets into one</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 detect_errors="exit_code"><![CDATA[
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8 @java_options@
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9 picard
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10 MergeSamFiles
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12 #for $element in $inputFile:
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13 INPUT="${element}"
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14 #end for
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16 OUTPUT="${outFile}"
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17 MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}"
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18
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19 ASSUME_SORTED="${assume_sorted}"
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20 #for $element in $comments:
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21 COMMENT="${element.comment}"
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22 #end for
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23
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24 USE_THREADING=true
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25 SORT_ORDER=coordinate
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26 VALIDATION_STRINGENCY="${validation_stringency}"
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27 QUIET=true
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28 VERBOSITY=ERROR
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30 ]]></command>
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31 <inputs>
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32 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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33 <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/>
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34 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/>
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35
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36 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
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37 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
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38 </repeat>
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40 <expand macro="VS" />
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42 </inputs>
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43
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44 <outputs>
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45 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Merged BAM dataset"/>
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46 </outputs>
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48 <tests>
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49 <test>
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50 <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/>
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51 <param name="assume_sorted" value="False"/>
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52 <param name="merge_sequence_dictionaries" value="False"/>
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53 <param name="validation_stringency" value="LENIENT"/>
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54 <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="4"/>
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55 </test>
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56 </tests>
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58
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59 <help>
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60
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61 **Purpose**
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62
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63 Merges multiple SAM/BAM datasets into one.
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64
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65 @dataset_collections@
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67 @description@
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69 ASSUME_SORTED=Boolean
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70 AS=Boolean If true, assume that the input files are in the same sort order as the requested output
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71 sort order, even if their headers say otherwise. Default value: false. This option can
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72 be set to 'null' to clear the default value. Possible values: {true, false}
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74 MERGE_SEQUENCE_DICTIONARIES=Boolean
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75 MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null'
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76 to clear the default value. Possible values: {true, false}
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78 COMMENT=String
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79 CO=String Comment(s) to include in the merged output file's header. This option may be specified 0
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80 or more times.
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83 @more_info@
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85 </help>
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86 </tool>
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