[2] | 1 | <tool id="sam_merge" name="Merge BAM Files" version="1.1.0"> |
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| 2 | <description>merges BAM files together</description> |
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| 3 | <requirements> |
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| 4 | <requirement type="package">samtools</requirement> |
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| 5 | </requirements> |
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| 6 | <command interpreter="python"> |
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| 7 | sam_merge.py |
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| 8 | $input1 |
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| 9 | $output1 |
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| 10 | $input2 |
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| 11 | #for $i in $inputs |
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| 12 | ${i.input} |
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| 13 | #end for |
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| 14 | </command> |
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| 15 | <inputs> |
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| 16 | <param name="input1" label="First file" type="data" format="bam" /> |
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| 17 | <param name="input2" label="with file" type="data" format="bam" help="Need to add more files? Use controls below." /> |
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| 18 | <repeat name="inputs" title="Input Files"> |
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| 19 | <param name="input" label="Add file" type="data" format="bam" /> |
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| 20 | </repeat> |
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| 21 | </inputs> |
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| 22 | <outputs> |
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| 23 | <data name="output1" format="bam" /> |
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| 24 | </outputs> |
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| 25 | <tests> |
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| 26 | <!-- TODO: add ability to test framework to test without at least |
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| 27 | one repeat element value |
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| 28 | <test> |
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| 29 | --> |
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| 30 | <!-- |
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| 31 | Bam merge command: |
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| 32 | samtools merge test-data/sam_merge_out1.bam test-data/sam_merge_in1.bam test-data/sam_merge_in2.bam |
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| 33 | --> |
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| 34 | <!-- |
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| 35 | <param name="input1" value="sam_merge_in1.bam" ftype="bam" /> |
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| 36 | <param name="input2" value="sam_merge_in2.bam" ftype="bam" /> |
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| 37 | <output name="output1" file="sam_merge_out1.bam" ftype="bam" /> |
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| 38 | </test> |
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| 39 | --> |
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| 40 | <test> |
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| 41 | <!-- |
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| 42 | Bam merge command: |
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| 43 | samtools merge test-data/sam_merge_out2.bam test-data/sam_merge_in1.bam test-data/sam_merge_in2.bam test-data/sam_merge_in3.bam |
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| 44 | --> |
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| 45 | <param name="input1" value="sam_merge_in1.bam" ftype="bam" /> |
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| 46 | <param name="input2" value="sam_merge_in2.bam" ftype="bam" /> |
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| 47 | <param name="input" value="sam_merge_in3.bam" ftype="bam" /> |
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| 48 | <output name="output1" file="sam_merge_out2.bam" ftype="bam" /> |
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| 49 | </test> |
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| 50 | <!-- TODO: add ability to test code to be able to test with multiple |
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| 51 | inputs (parameters with same value) |
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| 52 | <test> |
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| 53 | --> |
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| 54 | <!-- |
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| 55 | Bam merge command: |
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| 56 | samtools merge test-data/sam_merge_out3.bam test-data/sam_merge_in1.bam test-data/sam_merge_in2.bam test-data/sam_merge_in3.bam test-data/sam_merge_in4.bam |
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| 57 | --> |
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| 58 | <!-- |
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| 59 | <param name="input1" value="sam_merge_in1.bam" ftype="bam" /> |
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| 60 | <param name="input2" value="sam_merge_in2.bam" ftype="bam" /> |
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| 61 | <param name="input" value="sam_merge_in3.bam" ftype="bam" /> |
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| 62 | <param name="input" value="sam_merge_in4.bam" ftype="bam" /> |
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| 63 | <output name="output1" file="sam_merge_out3.bam" ftype="bam" /> |
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| 64 | </test> |
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| 65 | --> |
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| 66 | </tests> |
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| 67 | <help> |
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| 68 | |
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| 69 | **What it does** |
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| 70 | |
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| 71 | This tool uses SAMTools_' merge command to merge any number of BAM files together into one BAM file. |
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| 72 | |
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| 73 | .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml |
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| 74 | |
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| 75 | </help> |
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| 76 | </tool> |
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