view bam_to_sam.xml @ 3:c1419fa820c6 draft

author devteam
date Wed, 18 Mar 2015 15:44:51 -0400
parents c09a20532957
children af7c50162f0b
line wrap: on
line source

<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.6">
  <expand macro="requirements"></expand>
  <expand macro="version_command"></expand>
  <expand macro="stdio"></expand>
  <description>converts BAM format to SAM format</description>  
  samtools sort -O bam -@ \${GALAXY_SLOTS:-1} "$input1" -o sorted_input.bam -T temp && 
  samtools view sorted_input.bam $header -o $output1 -@ \${GALAXY_SLOTS:-1}
        <param format="bam" label="BAM File to Convert" name="input1" type="data" />
        <param checked="False" falsevalue="" label="Include header in output" name="header" truevalue="-h" type="boolean" />
        <data format="sam" label="${} on ${on_string}: converted SAM" name="output1" />
            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
            <param name="header" value="" />
            <output file="bam_to_sam_out1.sam" name="output1" sorted="True" />
            <param ftype="bam" name="input1" value="bam_to_sam_in2.bam" />
            <param name="header" value="" />
            <output file="bam_to_sam_out2.sam" name="output1" sorted="True" />
            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
            <param name="header" value="True" />
            <output file="bam_to_sam_out3.sam" name="output1" sorted="True" />

**What it does**

This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file.

.. _SAMTools:
  <expand macro="citations"></expand>