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1 <tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="1.106.0">
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2 <!-- taken from https://github.com/najoshi/ucd-biocore-galaxy/blob/master/tools/picard/picard_ReplaceSamHeader.xml -->
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3 <requirements><requirement type="package">picard</requirement></requirements>
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4 <command interpreter="python">
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5 picard_wrapper.py
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6 --input "$inputFile"
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7 -o $outFile
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8 --header-file $headerFile
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9 --output-format $outputFormat
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10 -j "\$JAVA_JAR_PATH/ReplaceSamHeader.jar"
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11 --tmpdir "${__new_file_path__}"
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12 </command>
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13 <inputs>
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14 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to replace header in (TARGET)"
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15 help="If empty, upload or import a SAM/BAM dataset." />
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16 <param format="bam,sam" name="headerFile" type="data" label="SAM/BAM to reader header from (SOURCE)"
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17 help="If empty, upload or import a SAM/BAM dataset." />
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18 <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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19 </inputs>
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20 <outputs>
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21 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat} with replaced header">
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22 <change_format>
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23 <when input="outputFormat" value="sam" format="sam" />
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24 </change_format>
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25 </data>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <!-- Command:
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30 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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31 picard_RSH_input1.bam can be made from picard_RSH_input1.sam
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32 -->
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33 <param name="inputFile" value="picard_input_tiny_coord.bam" ftype="bam" />
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34 <param name="headerFile" value="picard_RSH_input1.bam" ftype="bam" />
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35 <param name="outputFormat" value="False" />
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36 <output name="outFile" file="picard_RSH_output1.sam" ftype="sam" />
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37 </test>
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38 <test>
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39 <!-- Command:
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40 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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41 picard_RSH_input1.bam can be made from picard_RSH_input1.sam
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42 -->
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43 <param name="inputFile" value="picard_input_tiny_coord.sam" ftype="sam" />
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44 <param name="headerFile" value="picard_RSH_input1.bam" ftype="bam" />
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45 <param name="outputFormat" value="False" />
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46 <output name="outFile" file="picard_RSH_output2.sam" ftype="sam" />
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47 </test>
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48 <test>
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49 <!-- Command:
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50 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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51 -->
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52 <param name="inputFile" value="picard_input_tiny_coord.sam" ftype="sam" />
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53 <param name="headerFile" value="picard_RSH_input1.sam" ftype="sam" />
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54 <param name="outputFormat" value="True" />
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55 <output name="outFile" file="picard_RSH_output2.bam" ftype="bam" />
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56 </test>
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57 </tests>
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58 <help>
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59
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60
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61 .. class:: infomark
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62
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63 **Purpose**
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64
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65 Replace Sam Header with the header from another sam file. The tool does not do any
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66 significant validation, so it's up to the user to make sure that the elements in
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67 the header are relevant and that the new header has all the required things.
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68
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69 Replace the SAMFileHeader in a SAM file with the given header. Validation is
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70 minimal. It is up to the user to ensure that all the elements referred to in the
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71 SAMRecords are present in the new header. Sort order of the two input files must
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72 be the same.
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73
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74 **Picard documentation**
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75
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76 This is a Galaxy wrapper for ReplaceSamHeader, a part of the external package Picard-tools_.
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77
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78 .. _Picard-tools: http://www.google.com/search?q=picard+samtools
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79
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80 ------
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81
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82 .. class:: infomark
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83
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84 **Inputs and outputs**
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85
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86 Either a sam file or a bam file is required as the file whose header will be replaced.
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87 The header file is also required and can also be either sam or bam (it does not have
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88 to be the same type as the other file). In both cases, if a bam file is used, it must
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89 be coordinate-sorted. Galaxy currently coordinate-sorts all bam files.
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90
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91 The tool will output either bam (the default) or sam. Bam is recommended since it is smaller.
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92
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93 .. class:: warningmark
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94
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95 **Warning on SAM/BAM quality**
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96
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97 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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98 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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99 to be the only way to deal with SAM/BAM that cannot be parsed.
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100
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101
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102
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103 </help>
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104 </tool>
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