Mercurial > repos > devteam > picard
annotate picard_ReplaceSamHeader.xml @ 3:bf1c3f9f8282
Fix for FastqToSam MAX_Q usage detection.
| author | Daniel Blankenberg <dan@bx.psu.edu> |
|---|---|
| date | Fri, 03 May 2013 17:13:01 -0400 |
| parents | 9227b8c3093b |
| children | 3d4f1fa26f0e |
| rev | line source |
|---|---|
| 0 | 1 <tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="1.56.0"> |
| 2 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> | |
| 3 <command interpreter="python"> | |
| 4 picard_wrapper.py | |
|
2
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
5 --input "${inputFile}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
6 -o "${outFile}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
7 --header-file "${headerFile}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
8 --output-format "${outputFormat}" |
| 0 | 9 -j "\$JAVA_JAR_PATH/ReplaceSamHeader.jar" |
| 10 --tmpdir "${__new_file_path__}" | |
| 11 </command> | |
| 12 <inputs> | |
| 13 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to replace header in (TARGET)" | |
| 14 help="If empty, upload or import a SAM/BAM dataset." /> | |
| 15 <param format="bam,sam" name="headerFile" type="data" label="SAM/BAM to reader header from (SOURCE)" | |
| 16 help="If empty, upload or import a SAM/BAM dataset." /> | |
| 17 <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" /> | |
| 18 </inputs> | |
| 19 <outputs> | |
| 20 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat} with replaced header"> | |
| 21 <change_format> | |
| 22 <when input="outputFormat" value="sam" format="sam" /> | |
| 23 </change_format> | |
| 24 </data> | |
| 25 </outputs> | |
| 26 <tests> | |
| 27 <test> | |
| 28 <!-- Command: | |
| 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 | |
| 30 picard_RSH_input1.bam can be made from picard_RSH_input1.sam | |
| 31 --> | |
| 32 <param name="inputFile" value="picard_input_tiny_coord.bam" ftype="bam" /> | |
| 33 <param name="headerFile" value="picard_RSH_input1.bam" ftype="bam" /> | |
| 34 <param name="outputFormat" value="False" /> | |
| 35 <output name="outFile" file="picard_RSH_output1.sam" ftype="sam" /> | |
| 36 </test> | |
| 37 <test> | |
| 38 <!-- Command: | |
| 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 | |
| 40 picard_RSH_input1.bam can be made from picard_RSH_input1.sam | |
| 41 --> | |
| 42 <param name="inputFile" value="picard_input_tiny_coord.sam" ftype="sam" /> | |
| 43 <param name="headerFile" value="picard_RSH_input1.bam" ftype="bam" /> | |
| 44 <param name="outputFormat" value="False" /> | |
| 45 <output name="outFile" file="picard_RSH_output2.sam" ftype="sam" /> | |
| 46 </test> | |
| 47 <test> | |
| 48 <!-- Command: | |
| 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 | |
| 50 --> | |
| 51 <param name="inputFile" value="picard_input_tiny_coord.sam" ftype="sam" /> | |
| 52 <param name="headerFile" value="picard_RSH_input1.sam" ftype="sam" /> | |
| 53 <param name="outputFormat" value="True" /> | |
| 54 <output name="outFile" file="picard_RSH_output2.bam" ftype="bam" /> | |
| 55 </test> | |
| 56 </tests> | |
| 57 <help> | |
| 58 | |
| 59 | |
| 60 .. class:: infomark | |
| 61 | |
| 62 **Purpose** | |
| 63 | |
| 64 Replace Sam Header with the header from another sam file. The tool does not do any | |
| 65 significant validation, so it's up to the user to make sure that the elements in | |
| 66 the header are relevant and that the new header has all the required things. | |
| 67 | |
| 68 Replace the SAMFileHeader in a SAM file with the given header. Validation is | |
| 69 minimal. It is up to the user to ensure that all the elements referred to in the | |
| 70 SAMRecords are present in the new header. Sort order of the two input files must | |
| 71 be the same. | |
| 72 | |
| 73 **Picard documentation** | |
| 74 | |
| 75 This is a Galaxy wrapper for ReplaceSamHeader, a part of the external package Picard-tools_. | |
| 76 | |
| 77 .. _Picard-tools: http://www.google.com/search?q=picard+samtools | |
| 78 | |
| 79 ------ | |
| 80 | |
| 81 .. class:: infomark | |
| 82 | |
| 83 **Inputs and outputs** | |
| 84 | |
| 85 Either a sam file or a bam file is required as the file whose header will be replaced. | |
| 86 The header file is also required and can also be either sam or bam (it does not have | |
| 87 to be the same type as the other file). In both cases, if a bam file is used, it must | |
| 88 be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. | |
| 89 | |
| 90 The tool will output either bam (the default) or sam. Bam is recommended since it is smaller. | |
| 91 | |
| 92 .. class:: warningmark | |
| 93 | |
| 94 **Warning on SAM/BAM quality** | |
| 95 | |
| 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** | |
| 97 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears | |
| 98 to be the only way to deal with SAM/BAM that cannot be parsed. | |
| 99 | |
| 100 | |
| 101 | |
| 102 </help> | |
| 103 </tool> | |
| 104 | |
| 105 | |
| 106 | |
| 107 | |
| 108 | |
| 109 | |
| 110 | |
| 111 | |
| 112 | |
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| 115 |