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