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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
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1 <tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
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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 <token name="@WRAPPER_VERSION@">0</token>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 @java_options@
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10 picard 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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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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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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29
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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"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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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"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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34 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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35 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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36 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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37 </repeat>
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38 <expand macro="VS"/>
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39 </inputs>
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40 <outputs>
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41 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Merged BAM dataset"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/>
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46 <param name="assume_sorted" value="False"/>
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47 <param name="merge_sequence_dictionaries" value="False"/>
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48 <param name="validation_stringency" value="LENIENT"/>
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49 <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="4"/>
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50 </test>
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51 </tests>
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52 <help>
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53
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54 **Purpose**
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55
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56 Merges multiple SAM/BAM datasets into one.
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57
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58 @dataset_collections@
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59
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60 @description@
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62 ASSUME_SORTED=Boolean
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63 AS=Boolean If true, assume that the input files are in the same sort order as the requested output
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64 sort order, even if their headers say otherwise. Default value: false. This option can
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65 be set to 'null' to clear the default value. Possible values: {true, false}
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66
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67 MERGE_SEQUENCE_DICTIONARIES=Boolean
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68 MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null'
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69 to clear the default value. Possible values: {true, false}
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71 COMMENT=String
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72 CO=String Comment(s) to include in the merged output file's header. This option may be specified 0
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73 or more times.
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76 @more_info@
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78 </help>
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79 <expand macro="citations"/>
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80 </tool>