comparison bam_to_sam.xml @ 4:af7c50162f0b draft

Uploaded

3:c1419fa820c6

<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.6">
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="version_command"></expand>
  <expand macro="stdio"></expand>
  <description>converts BAM format to SAM format</description>  
    <command>
<![CDATA[
  samtools sort -O bam -@ \${GALAXY_SLOTS:-1} "$input1" -o sorted_input.bam -T temp && 
  samtools view sorted_input.bam $header -o $output1 -@ \${GALAXY_SLOTS:-1}
]]>
    </command>
    <inputs>
        <param format="bam" label="BAM File to Convert" name="input1" type="data" />
        <param checked="False" falsevalue="" label="Include header in output" name="header" truevalue="-h" type="boolean" />
    </inputs>
    <outputs>
        <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" />
    </outputs>
    <tests>
        <test>
            <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" />
        </test>
        <test>
            <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" />
        </test>
        <test>
            <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" />
        </test>
    </tests>
    <help>
<![CDATA[

**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>
  <expand macro="citations"></expand>
</tool>

4:af7c50162f0b

<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0">
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="version_command"></expand>
  <expand macro="stdio"></expand>
  <description>convert BAM to SAM</description>  
    <command>
<![CDATA[
  samtools view -o "${output1}" ${header} "${input1}"
]]>
    </command>
    <inputs>
        <param format="bam" label="BAM File to Convert" name="input1" type="data" />
        <param name="header" label="Header options" type="select" help="Allows to choose between seeing the entire dataset with the header, header only, or data only.">
          <option value="-h">Include header in SAM output (-h)</option>
          <option value="-H">Print header only (-H)</option>
          <option value="">Exclude header</option>
        </param>
    </inputs>
    <outputs>
        <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" />
    </outputs>
    <tests>
        <test>
            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
            <param name="header" value="-h" />
            <output file="bam_to_sam_out1.sam" name="output1" sorted="True" />
        </test>
        <test>
            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
            <param name="header" value="-H" />
            <output file="bam_to_sam_out2.sam" name="output1" sorted="True" />
        </test>
        <test>
            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
            <param name="header" value="" />
            <output file="bam_to_sam_out3.sam" name="output1" sorted="True" />
        </test>
    </tests>
    <help>
<![CDATA[

**What it does**

Converts BAM dataset to SAM using ``samtools view`` command::

 samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM] 

]]>
  </help>
  <expand macro="citations"></expand>
</tool>