mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-25 10:24:38 +08:00
61 lines
2.1 KiB
XML
61 lines
2.1 KiB
XML
<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.3">
|
|
<requirements>
|
|
<requirement type="package">samtools</requirement>
|
|
</requirements>
|
|
<description>converts BAM format to SAM format</description>
|
|
<command interpreter="python">
|
|
bam_to_sam.py
|
|
--input1=$input1
|
|
--output1=$output1
|
|
$header
|
|
</command>
|
|
<inputs>
|
|
<param name="input1" type="data" format="bam" label="BAM File to Convert" />
|
|
<param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" />
|
|
</inputs>
|
|
<outputs>
|
|
<data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" />
|
|
</outputs>
|
|
<tests>
|
|
<test>
|
|
<!--
|
|
Bam-to-Sam command:
|
|
samtools view -o bam_to_sam_out1.sam test-data/bam_to_sam_in1.bam
|
|
bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
|
|
-->
|
|
<param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
|
|
<param name="header" value="" />
|
|
<output name="output1" file="bam_to_sam_out1.sam" sorted="True" />
|
|
</test>
|
|
<test>
|
|
<!--
|
|
Bam-to-Sam command:
|
|
samtools view -o bam_to_sam_out2.sam test-data/bam_to_sam_in2.bam
|
|
bam_to_sam_in2.bam can be created from bam_to_sam_in2.sam
|
|
-->
|
|
<param name="input1" value="bam_to_sam_in2.bam" ftype="bam" />
|
|
<param name="header" value="" />
|
|
<output name="output1" file="bam_to_sam_out2.sam" sorted="True" />
|
|
</test>
|
|
<test>
|
|
<!--
|
|
Bam-to-Sam command:
|
|
samtools view -h -o bam_to_sam_out3.sam test-data/bam_to_sam_in1.bam
|
|
bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
|
|
-->
|
|
<param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
|
|
<param name="header" value="--header" />
|
|
<output name="output1" file="bam_to_sam_out3.sam" sorted="True" lines_diff="6" /><!-- header param not working in func tests so won't produce correct 6-line header (fine in browser) -->
|
|
</test>
|
|
</tests>
|
|
<help>
|
|
|
|
**What it does**
|
|
|
|
This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file.
|
|
|
|
.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
|
|
|
|
</help>
|
|
</tool>
|