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

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

8:9def47f3c1e4

<tool id="callcodonvar" name="Codon Variants" version="0.7.0">
    <description>Identifies codon variants and non-synonymous/synonymous mutations</description>
    <requirements>
          <requirement type="package" version="0.7.0">quasitools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        cat $input_genes &&

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

		#if $var_file:
			$var_file 
		#end if

Call codon variants for a given BAM. A report is generated that details nucleotide variants within a
codon and the resulting AA variants. The report indicates whether the nucleotide variants correspond to
a synonymous or non-synonymous mutation.

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

9:18aad692772a

<tool id="callcodonvar" name="Codon Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>Identifies codon variants and non-synonymous/synonymous mutations</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[

        cat $input_genes &&

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

        quasitools call codonvar '${input_bam.name}' $ref_file $offset $input_genes

		#if $var_file:
			$var_file 
		#end if

Call codon variants for a given BAM. A report is generated that details nucleotide variants within a
codon and the resulting AA variants. The report indicates whether the nucleotide variants correspond to
a synonymous or non-synonymous mutation.

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