comparison bam_to_sam.xml @ 3:c1419fa820c6 draft

Uploaded

2:c09a20532957

<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.4">
  <requirements>
    <requirement type="package" version="0.1.19">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>
  <citations>
      <citation type="doi">10.1093/bioinformatics/btp352</citation>
  </citations>
</tool>

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>