<tool id="ctat_mutations" name="ctat_mutations" version="1.0.0" profile="17.05">
    <description>Mutation Pipeline for calling SNPs and variants</description>
    <requirements>
        <requirement type="package" version="2.0.1">ctat-mutations</requirement>
    </requirements>
    <command detect_errors="default">
      <![CDATA[
            ctat_mutations \
                   --plot \
                   --out_dir varcalling.outdir \
                   --threads 8 \
                   --variant_filtering_mode GATK \
                   --left "$left" \
                   --right "$right" \
                   --genome_lib_dir "${genome_resource_lib.fields.path}" \
                   --variant_call_mode GATK \
                   --tissue_type "$tissue_type" \
                   --email "$cravat_email"
      ]]>
    </command>
    <inputs>
      <param format="fastq" name="left" type="data" label="Left/Forward strand reads" help="Left read"/>
      <param format="fastq" name="right" type="data" label="Right/Reverse strand reads" help="Right read"/>
      <param name="tissue_type" type="select" label="Select a pathology" help="If you don't know, just choose 'General Purpose'">
        <options from_data_table="ctat_cravat_tissues">
  <filter type="sort_by" column="1"/>
  <validator type="no_options" message="No indexes are available for the selected input dataset"/>
        </options>
      </param>
      <param name="genome_resource_lib" type="select" label="Select a reference genome">
        <options from_data_table="ctat_genome_resource_libs">
          <filter type="sort_by" column="2" />
          <validator type="no_options" message="No indexes are available" />
        </options>
      </param>
      <param name="cravat_email" type="text" label="CRAVAT email" help="CRAVAT registered email id"/>      
      <section name="adv" title="This service uses the GATK4. GATK4 is licensed by the Broad Institute and is made available to academic users of this service for non-commercial use only. The full text of the license is available here: https://www.broadinstitute.org/gatk/about/license.html. For more information about GATK and full documentation, please visit the GATK website: https://www.broadinstitute.org." expanded="False">
      </section>
    </inputs>
    <outputs>
      <data format="tabular" name="cancertab" label="${tool.name} on ${on_string}: Cancer Tab" from_work_dir="varcalling.outdir/cancer.tab"/> 
      <data format="vcf" name="cancerVariants" label="${tool.name} on ${on_string}: Cancer VCF" from_work_dir="varcalling.outdir/cancer.vcf"/> 
      <data format="vcf" name="allVariants" label="${tool.name} on ${on_string}: All Variants VCF" from_work_dir="varcalling.outdir/variants.vcf"/> 
      <data format="bam" name="bamfile" label="Bam used in haplotype calling" from_work_dir="varcalling.outdir/misc/recalibrated.bam"/>
      <data format="txt" name="cravat" label="Annotated (lightly filtered) VCF file" from_work_dir="varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz"/>
    </outputs>
    <tests>
        <test>
           <param name="left" value="reads_1.fastq.gz"/>
           <param name="right" value="reads_2.fastq.gz"/>
           <param name="tissue_type" value="Other"/>
           <output name="cancertab" file="varcalling.outdir/cancer.tab" />
           <output name="cancerVariants" file="varcalling.outdir/cancer.vcf" />
           <output name="allVariants" file="varcalling.outdir/variants.vcf" />
           <output name="bamfile" file="varcalling.outdir/misc/recalibrated.bam" />
           <output name="cravat" file="varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz"/>
        </test>
    </tests>
    <help>

.. class:: warningmark

Mutation detection in RNA-Seq highlights the GATK Best Practices in RNA-Seq variant calling, several sources of variant annotation, and filtering based on CRAVAT.

    </help>
    <citations>
    </citations>
</tool>