[2] | 1 | <tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.0"> |
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| 2 | <requirements> |
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| 3 | <requirement type="package">samtools</requirement> |
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| 4 | </requirements> |
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| 5 | <description>converts BAM format to SAM format</description> |
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| 6 | <command interpreter="python">bam_to_sam.py --input1=$input1 --output1=$output1</command> |
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| 7 | <inputs> |
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| 8 | <param name="input1" type="data" format="bam" label="BAM File to Convert" /> |
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| 9 | </inputs> |
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| 10 | <outputs> |
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| 11 | <data name="output1" format="sam" /> |
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| 12 | </outputs> |
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| 13 | <tests> |
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| 14 | <test> |
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| 15 | <!-- |
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| 16 | Bam-to-Sam command: |
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| 17 | samtools view -o test-data/3.bam bam_to_sam_out1.sam |
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| 18 | --> |
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| 19 | <param name="input1" value="1.bam" ftype="bam" /> |
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| 20 | <output name="output1" file="bam_to_sam_out1.sam" /> |
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| 21 | </test> |
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| 22 | <test> |
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| 23 | <!-- |
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| 24 | Bam-to-Sam command: |
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| 25 | samtools view -o test-data/1.sam bam_to_sam_out2.sam |
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| 26 | --> |
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| 27 | <param name="input1" value="3.bam" ftype="bam" /> |
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| 28 | <param name="output1" file="bam_to_sam_out2.sam" /> |
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| 29 | </test> |
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| 30 | </tests> |
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| 31 | <help> |
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| 32 | |
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| 33 | **What it does** |
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| 34 | |
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| 35 | This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file. |
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| 36 | |
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| 37 | .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml |
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| 38 | |
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| 39 | </help> |
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| 40 | </tool> |
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