comparison callntvar.xml @ 9:18aad692772a draft default tip

planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e

8:9def47f3c1e4

<tool id="callntvar" name="Nucleotide Variants" version="0.7.0">
    <description>Identifies nucleotide variants</description>
    <requirements>
          <requirement type="package" version="0.7.0">quasitools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
        quasitools call ntvar $input_bam $ref_file

        #if $error_rate:
            -e $error_rate
        #end if

===================

Call nucleotide variants for a given BAM file and a supplied reference file.

    ]]></help>
    <citations>
		<citation type="bibtex">
			@misc{GitHubquasitoolscallntvar,
			title = {quasitools callntvar},
			publisher = {phac-nml},
			journal = {GitHub repository},
			url = {https://github.com/phac-nml/quasitools},
			}
		</citation>
    </citations>
</tool>

9:18aad692772a

<tool id="callntvar" name="Nucleotide Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>Identifies nucleotide variants</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[

        ln -s $input_bam '${input_bam.name}' &&
        ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&

        quasitools call ntvar '${input_bam.name}' $ref_file

        #if $error_rate:
            -e $error_rate
        #end if

===================

Call nucleotide variants for a given BAM file and a supplied reference file.

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