comparison affy2vcf.xml @ 2:02025c366fca draft

Uploaded

1:a2f0931898be

<tool id="affr2vcf" name="Convert Affymetrix" version="1.9">
    <description>genotype calls and intensities to VCF</description>
    <requirements>
        <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#set text_outputs_dir = 'text_outputs'
export BCFTOOLS_PLUGINS=\$(dirname `which bcftools`)/../libexec/bcftools &&
mkdir $text_outputs_dir &&
bcftools +\$BCFTOOLS_PLUGINS/affy2vcf.so
#if str($reference_genome_source_cond.reference_genome_source) == "history":
    --fasta-ref '$reference_genome_source_cond.history_item'
#else:

#if str($append_version) == "no":
    --no-version
#end if
--output '$output'
--output-type $output_type
--threads \${GALAXY_SLOTS:-4}
    ]]></command>
    <inputs>
        <param name="annot" type="data" format="csv" label="Probeset annotation file" />
        <param name="summary" type="data" format="txt" label="Apt-probeset genotype summary file" />
        <param name="snp_posteriors" type="data" format="txt" label="Apt-probeset genotype snp-posteriors file" />

            <option value="u" selected="true">Uncompressed BCF</option>
            <option value="b">Compressed BCF</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="vcf" />
        <data name="output_gender_estimate" format="txt" label="${tool.name} (gender estimate) on ${on_string}">
            <filter>output_gender_estimate_cond['output_gender_estimate'] == "yes"</filter>
        </data>
    </outputs>
    <tests>

 * **Output apt-probeset-genotype gender estimate** - output apt-probeset-genotype gender estimate into an additional dataset.
 * **Append version and command line to the header** - append version and command line to the header of the output VCF dataset.
 * **Select format for output** - select one of uncompressed/compressed VCF/BCF.
    </help>
    <citations>
        <citation type="bibtex">
            @misc{None,
            journal = {None},
            author = {Genovese, Giulio},
            title = {None},

2:02025c366fca

<tool id="affr2vcf" name="Convert Affymetrix" version="@WRAPPER_VERSION@">
    <description>genotype calls and intensities to VCF</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
@PREPARE_ENV@
#set text_outputs_dir = 'text_outputs'
mkdir $text_outputs_dir &&
bcftools +\$BCFTOOLS_PLUGINS/affy2vcf.so
#if str($reference_genome_source_cond.reference_genome_source) == "history":
    --fasta-ref '$reference_genome_source_cond.history_item'
#else:

#if str($append_version) == "no":
    --no-version
#end if
--output '$output'
--output-type $output_type
@THREADS@
    ]]></command>
    <inputs>
        <param name="annot" type="data" format="csv" label="Probeset annotation file" />
        <param name="summary" type="data" format="txt" label="Apt-probeset genotype summary file" />
        <param name="snp_posteriors" type="data" format="txt" label="Apt-probeset genotype snp-posteriors file" />

            <option value="u" selected="true">Uncompressed BCF</option>
            <option value="b">Compressed BCF</option>
        </param>
    </inputs>
    <outputs>
        <expand macro="vcf_output"/>
        <data name="output_gender_estimate" format="txt" label="${tool.name} (gender estimate) on ${on_string}">
            <filter>output_gender_estimate_cond['output_gender_estimate'] == "yes"</filter>
        </data>
    </outputs>
    <tests>

 * **Output apt-probeset-genotype gender estimate** - output apt-probeset-genotype gender estimate into an additional dataset.
 * **Append version and command line to the header** - append version and command line to the header of the output VCF dataset.
 * **Select format for output** - select one of uncompressed/compressed VCF/BCF.
    </help>
    <citations>
        <expand macro="citation1"/>
        <citation type="bibtex">
            @misc{None,
            journal = {None},
            author = {Genovese, Giulio},
            title = {None},