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1 <tool id="ctat_mutations" name="ctat_mutations" version="1.0.0" profile="17.05">
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2 <description>Mutation Pipeline for calling SNPs and variants</description>
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3 <requirements>
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4 <requirement type="package" version="2.0.1">ctat-mutations</requirement>
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5 </requirements>
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6 <command detect_errors="default">
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7 <![CDATA[
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8 python ctat-mutations/ctat_mutations \
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9 --plot \
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10 --out_dir varcalling.outdir \
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11 --threads 8 \
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12 --variant_filtering_mode GATK \
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13 --left "$left" \
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14 --right "$right" \
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15 --genome_lib_dir "${genome_resource_lib.fields.path}" \
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16 --variant_call_mode GATK \
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17 --tissue_type "$tissue_type" \
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18 --email "$cravat_email"
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param format="fastq" name="left" type="data" label="Left/Forward strand reads" help="Left read"/>
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23 <param format="fastq" name="right" type="data" label="Right/Reverse strand reads" help="Right read"/>
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24 <param name="tissue_type" type="select" label="Select a pathology" help="If you don't know, just choose 'General Purpose'">
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25 <options from_data_table="ctat_cravat_tissues">
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26 <filter type="sort_by" column="1"/>
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27 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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28 </options>
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29 </param>
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30 <param name="genome_resource_lib" type="select" label="Select a reference genome">
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31 <options from_data_table="ctat_genome_resource_libs">
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32 <filter type="sort_by" column="2" />
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33 <validator type="no_options" message="No indexes are available" />
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34 </options>
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35 </param>
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36 <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">
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37 </section>
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38 </inputs>
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39 <outputs>
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40 <data format="tabular" name="cancertab" label="${tool.name} on ${on_string}: Cancer Tab" from_work_dir="varcalling.outdir/cancer.tab"/>
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41 <data format="vcf" name="cancerVariants" label="${tool.name} on ${on_string}: Cancer VCF" from_work_dir="varcalling.outdir/cancer.vcf"/>
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42 <data format="vcf" name="allVariants" label="${tool.name} on ${on_string}: All Variants VCF" from_work_dir="varcalling.outdir/variants.vcf"/>
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43 <data format="bam" name="bamfile" label="Bam used in haplotype calling" from_work_dir="varcalling.outdir/misc/recalibrated.bam"/>
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44 <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"/>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="left" value="reads_1.fastq.gz"/>
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49 <param name="right" value="reads_2.fastq.gz"/>
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50 <param name="tissue_type" value="Other"/>
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51 <output name="cancertab" file="varcalling.outdir/cancer.tab" />
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52 <output name="cancerVariants" file="varcalling.outdir/cancer.vcf" />
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53 <output name="allVariants" file="varcalling.outdir/variants.vcf" />
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54 <output name="bamfile" file="varcalling.outdir/misc/recalibrated.bam" />
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55 <output name="cravat" file="varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz"/>
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56 </test>
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57 </tests>
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58 <help>
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59
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60 .. class:: warningmark
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61
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62 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.
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63
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64 </help>
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65 <citations>
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66 </citations>
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67 </tool>
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