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45 lines
1.2 KiB
XML
45 lines
1.2 KiB
XML
<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.1">
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<requirements>
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<requirement type="package">samtools</requirement>
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</requirements>
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<description>converts BAM format to SAM format</description>
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<command interpreter="python">
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bam_to_sam.py
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--input1=$input1
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--output1=$output1
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</command>
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<inputs>
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<param name="input1" type="data" format="bam" label="BAM File to Convert" />
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</inputs>
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<outputs>
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<data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" />
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</outputs>
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<tests>
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<test>
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<!--
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Bam-to-Sam command:
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samtools view -o bam_to_sam_out1.sam test-data/3.bam
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-->
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<param name="input1" value="1.bam" ftype="bam" />
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<output name="output1" file="bam_to_sam_out1.sam" sorted="True" />
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</test>
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<test>
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<!--
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Bam-to-Sam command:
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samtools view -o bam_to_sam_out2.sam test-data/1.bam
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-->
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<param name="input1" value="3.bam" ftype="bam" />
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<output name="output1" file="bam_to_sam_out2.sam" sorted="True" />
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</test>
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</tests>
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<help>
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**What it does**
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This tool uses the SAMTools_ toolkit to produce a SAM file from a 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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