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comparison ctat_mutations.xml @ 0:de4e183593ac draft

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author trinity_ctat
date Wed, 14 Nov 2018 12:15:15 -0500
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1 <tool id="ctat_mutations" name="ctat_mutations" version="1.0.0" profile="17.05">
2 <description>Mutation Pipeline for calling SNPs and variants</description>
3 <requirements>
4 <requirement type="package" version="2.0.1">ctat-mutations</requirement>
5 </requirements>
6 <command detect_errors="default">
7 <![CDATA[
8 ctat_mutations \
9 --plot \
10 --out_dir varcalling.outdir \
11 --threads 8 \
12 --variant_filtering_mode GATK \
13 --left "$left" \
14 --right "$right" \
15 --genome_lib_dir "${genome_resource_lib.fields.path}" \
16 --variant_call_mode GATK \
17 --tissue_type "$tissue_type" \
18 --email "$cravat_email"
19 ]]>
20 </command>
21 <inputs>
22 <param format="fastq" name="left" type="data" label="Left/Forward strand reads" help="Left read"/>
23 <param format="fastq" name="right" type="data" label="Right/Reverse strand reads" help="Right read"/>
24 <param name="tissue_type" type="select" label="Select a pathology" help="If you don't know, just choose 'General Purpose'">
25 <options from_data_table="ctat_cravat_tissues">
26 <filter type="sort_by" column="1"/>
27 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
28 </options>
29 </param>
30 <param name="genome_resource_lib" type="select" label="Select a reference genome">
31 <options from_data_table="ctat_genome_resource_libs">
32 <filter type="sort_by" column="2" />
33 <validator type="no_options" message="No indexes are available" />
34 </options>
35 </param>
36 <param name="cravat_email" type="text" label="CRAVAT email" help="CRAVAT registered email id"/>
37 <section name="adv" title="This service uses the GATK4. GATK4 is licensed by the Broad Institute and is made available to academic users of this service for non-commercial use only. The full text of the license is available here: https://www.broadinstitute.org/gatk/about/license.html. For more information about GATK and full documentation, please visit the GATK website: https://www.broadinstitute.org." expanded="False">
38 </section>
39 </inputs>
40 <outputs>
41 <data format="tabular" name="cancertab" label="${tool.name} on ${on_string}: Cancer Tab" from_work_dir="varcalling.outdir/cancer.tab"/>
42 <data format="vcf" name="cancerVariants" label="${tool.name} on ${on_string}: Cancer VCF" from_work_dir="varcalling.outdir/cancer.vcf"/>
43 <data format="vcf" name="allVariants" label="${tool.name} on ${on_string}: All Variants VCF" from_work_dir="varcalling.outdir/variants.vcf"/>
44 <data format="bam" name="bamfile" label="Bam used in haplotype calling" from_work_dir="varcalling.outdir/misc/recalibrated.bam"/>
45 <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"/>
46 </outputs>
47 <tests>
48 <test>
49 <param name="left" value="reads_1.fastq.gz"/>
50 <param name="right" value="reads_2.fastq.gz"/>
51 <param name="tissue_type" value="Other"/>
52 <output name="cancertab" file="varcalling.outdir/cancer.tab" />
53 <output name="cancerVariants" file="varcalling.outdir/cancer.vcf" />
54 <output name="allVariants" file="varcalling.outdir/variants.vcf" />
55 <output name="bamfile" file="varcalling.outdir/misc/recalibrated.bam" />
56 <output name="cravat" file="varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz"/>
57 </test>
58 </tests>
59 <help>
60
61 .. class:: warningmark
62
63 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.
64
65 </help>
66 <citations>
67 </citations>
68 </tool>