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1 <tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="0.2.0">
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2 <requirements><requirement type="package">picard</requirement></requirements>
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3 <command interpreter="python">
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4 picard_wrapper.py
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5 --input "$inputFile"
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6 -o $outFile
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7 --header-file $headerFile
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8 --output-format $outputFormat
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9 -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/ReplaceSamHeader.jar"
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10 --tmpdir "${__new_file_path__}"
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11 </command>
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12 <inputs>
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13 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to replace header in (TARGET)"
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14 help="If empty, upload or import a SAM/BAM dataset." />
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15 <param format="bam,sam" name="headerFile" type="data" label="SAM/BAM to reader header from (SOURCE)"
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16 help="If empty, upload or import a SAM/BAM dataset." />
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17 <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
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18 </inputs>
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19 <outputs>
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20 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat} with replaced header">
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21 <change_format>
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22 <when input="outputFormat" value="sam" format="sam" />
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23 </change_format>
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24 </data>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <!-- Command:
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29 java -jar ReplaceSamHeader.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_input_tiny_coord.bam HEADER=test-data/picard_RSH_input1.bam O=picard_RSH_output1.sam
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30 picard_RSH_input1.bam can be made from picard_RSH_input1.sam
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31 -->
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32 <param name="inputFile" value="picard_input_tiny_coord.bam" ftype="bam" />
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33 <param name="headerFile" value="picard_RSH_input1.bam" ftype="bam" />
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34 <param name="outputFormat" value="False" />
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35 <output name="outFile" file="picard_RSH_output1.sam" ftype="sam" />
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36 </test>
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37 <test>
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38 <!-- Command:
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39 java -jar ReplaceSamHeader.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_input_tiny_coord.sam HEADER=test-data/picard_RSH_input1.bam O=picard_RSH_output2.sam
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40 picard_RSH_input1.bam can be made from picard_RSH_input1.sam
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41 -->
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42 <param name="inputFile" value="picard_input_tiny_coord.sam" ftype="sam" />
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43 <param name="headerFile" value="picard_RSH_input1.bam" ftype="bam" />
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44 <param name="outputFormat" value="False" />
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45 <output name="outFile" file="picard_RSH_output2.sam" ftype="sam" />
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46 </test>
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47 <test>
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48 <!-- Command:
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49 java -jar ReplaceSamHeader.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_input_tiny_coord.sam HEADER=test-data/picard_RSH_input1.sam O=picard_RSH_output2.bam
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50 -->
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51 <param name="inputFile" value="picard_input_tiny_coord.sam" ftype="sam" />
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52 <param name="headerFile" value="picard_RSH_input1.sam" ftype="sam" />
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53 <param name="outputFormat" value="True" />
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54 <output name="outFile" file="picard_RSH_output2.bam" ftype="bam" />
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55 </test>
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56 </tests>
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57 <help>
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58
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59
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60 .. class:: infomark
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61
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62 **Purpose**
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63
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64 Replace Sam Header with the header from another sam file. The tool does not do any
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65 significant validation, so it's up to the user to make sure that the elements in
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66 the header are relevant and that the new header has all the required things.
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67
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68 Replace the SAMFileHeader in a SAM file with the given header. Validation is
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69 minimal. It is up to the user to ensure that all the elements referred to in the
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70 SAMRecords are present in the new header. Sort order of the two input files must
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71 be the same.
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72
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73 **Picard documentation**
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74
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75 This is a Galaxy wrapper for ReplaceSamHeader, a part of the external package Picard-tools_.
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76
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77 .. _Picard-tools: http://www.google.com/search?q=picard+samtools
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78
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79 ------
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80
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81 .. class:: infomark
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82
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83 **Inputs and outputs**
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84
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85 Either a sam file or a bam file is required as the file whose header will be replaced.
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86 The header file is also required and can also be either sam or bam (it does not have
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87 to be the same type as the other file). In both cases, if a bam file is used, it must
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88 be coordinate-sorted. Galaxy currently coordinate-sorts all bam files.
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89
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90 The tool will output either bam (the default) or sam. Bam is recommended since it is smaller.
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91
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92 .. class:: warningmark
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93
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94 **Warning on SAM/BAM quality**
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95
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96 Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
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97 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
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98 to be the only way to deal with SAM/BAM that cannot be parsed.
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99
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100
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101
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102 </help>
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103 </tool>
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104
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