comparison samtools_reheader.xml @ 2:77a6694ebf7a draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

1:8546afbbd7f1

<tool id="samtools_reheader" name="Replace header" version="1.0.0">
    <description>on a BAM or SAM file</description>
    <requirements>
        <requirement type="package" version="1.1">samtools</requirement>
    </requirements>
    <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
    <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error" />
    </stdio>
    <inputs>
        <param name="input_header" type="data" format="sam" label="SAM file or header" />
        <param name="input_file" type="data" format="sam,bam" label="File to reheader" />
    </inputs>
    <outputs>
        <data format="bam" name="output" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
    </tests>
    <help>
**What it does**

This tool runs the ``samtools reheader`` command in the SAMtools toolkit.

Replace the header for a SAM or BAM file with a different header.

**Citation**

For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_


If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
    </help>
</tool>

2:77a6694ebf7a

<tool id="samtools_reheader" name="Reheader" version="2.0">
    <description>copy SAM/BAM header between datasets</description>
    <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="stdio"></expand>
  <expand macro="version_command"></expand>
    <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command>
    <inputs>
        <param name="input_header" type="data" format="sam,bam" label="Select source dataset" help="Header from this dataset will be used to replace header in the target dataset. May be either SAM or BAM dataset."/>
        <param name="input_file" type="data" format="bam" label="Select target dataset" help="Header from the source dataset will be inserted here. Should be a BAM dataset."/>
    </inputs>
    <outputs>
        <data format="bam" name="output" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_header" ftype="bam" value="reheader_input_header.bam"/>
            <param name="input_file" ftype="bam" value="reheader_input_file.bam"/>
            <output name="output" ftype="bam" file="reheader_out.bam"/>
        </test>
    </tests>
    <help>
**What it does**

Copies header from *source* dataset into *target* dataset using ``samtools reheader`` command.

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