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77 lines
2.7 KiB
XML
77 lines
2.7 KiB
XML
<tool id="sam_merge" name="Merge BAM Files" version="1.1.1">
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<description>merges BAM files together</description>
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<requirements>
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<requirement type="package">samtools</requirement>
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</requirements>
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<command interpreter="python">
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sam_merge.py
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$input1
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$output1
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$input2
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#for $i in $inputs
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${i.input}
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#end for
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</command>
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<inputs>
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<param name="input1" label="First file" type="data" format="bam" />
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<param name="input2" label="with file" type="data" format="bam" help="Need to add more files? Use controls below." />
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<repeat name="inputs" title="Input Files">
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<param name="input" label="Add file" type="data" format="bam" />
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</repeat>
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</inputs>
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<outputs>
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<data format="bam" name="output1" label="${tool.name} on ${on_string}: merged BAM" />
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</outputs>
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<tests>
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<!-- TODO: add ability to test framework to test without at least
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one repeat element value
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<test>
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-->
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<!--
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Bam merge command:
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samtools merge test-data/sam_merge_out1.bam test-data/sam_merge_in1.bam test-data/sam_merge_in2.bam
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-->
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<!--
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<param name="input1" value="sam_merge_in1.bam" ftype="bam" />
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<param name="input2" value="sam_merge_in2.bam" ftype="bam" />
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<output name="output1" file="sam_merge_out1.bam" ftype="bam" />
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</test>
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-->
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<test>
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<!--
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Bam merge command:
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samtools merge 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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-->
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<param name="input1" value="sam_merge_in1.bam" ftype="bam" />
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<param name="input2" value="sam_merge_in2.bam" ftype="bam" />
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<param name="input" value="sam_merge_in3.bam" ftype="bam" />
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<output name="output1" file="sam_merge_out2.bam" ftype="bam" />
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</test>
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<!-- TODO: add ability to test code to be able to test with multiple
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inputs (parameters with same value)
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<test>
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-->
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<!--
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Bam merge command:
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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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-->
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<!--
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<param name="input1" value="sam_merge_in1.bam" ftype="bam" />
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<param name="input2" value="sam_merge_in2.bam" ftype="bam" />
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<param name="input" value="sam_merge_in3.bam" ftype="bam" />
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<param name="input" value="sam_merge_in4.bam" ftype="bam" />
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<output name="output1" file="sam_merge_out3.bam" ftype="bam" />
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</test>
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-->
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</tests>
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<help>
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**What it does**
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This tool uses SAMTools_' merge command to merge any number of BAM files together into one BAM file.
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.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
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</help>
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</tool>
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