Mercurial > repos > jjohnson > ensembl_variant_report
diff ensembl_variant_report.xml @ 0:9f4ea174ce3d draft
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
| author | jjohnson |
|---|---|
| date | Thu, 14 Jun 2018 17:51:39 -0400 |
| parents | |
| children | f87fe6bc48f4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ensembl_variant_report.xml Thu Jun 14 17:51:39 2018 -0400 @@ -0,0 +1,193 @@ +<tool id="ensembl_variant_report" name="Ensembl Variant Report" version="0.1.0"> + <requirements> + <requirement type="package" version="1.40">gtf_to_genes</requirement> + <requirement type="package" version="3.1.4">twobitreader</requirement> + <requirement type="package" version="1.62">biopython</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + python '$__tool_directory__/ensembl_variant_report.py' + #if $ref.ref_source == 'cached': + --twobit="$ref.ref_loc.fields.path" + #else + --twobit="$ref.ref_file" + #end if + --gene_model="$gtf_file" + #if $variant.fmt == 'vcf': + --input="$variant.input_vcf" + --format=snpeff + #else + --input="$variant.input_tsv" + --pos_column=$variant.pos_column + --ref_column=$variant.ref_column + --alt_column=$variant.alt_column + --transcript_column=$variant.transcript_column + --dp_column=$variant.dp_column + --dpr_column=$variant.dpr_column + #end if + #if str($filter.min_depth) != '': + --min_depth=$filter.min_depth + #end if + #if str($filter.min_freq) != '': + --min_freq=$filter.min_freq + #end if + #if str($report.readthrough) != '': + --readthrough=$report.readthrough + #end if + #if str($report.leading_aa) != '': + --leading_aa=$report.leading_aa + #end if + #if str($report.trailing_aa) != '': + --trailing_aa=$report.trailing_aa + #end if + --output="$output" + ]]></command> + <inputs> + <conditional name="variant"> + <param name="fmt" type="select" label="Input format for variants"> + <option value="vcf">snpEff vcf</option> + <option value="tsv">tabular from snpsift extract</option> + </param> + <when value="vcf"> + <param name="input_vcf" type="data" format="vcf" label="snpEff VCF file"/> + </when> + <when value="tsv"> + <param name="input_tsv" type="data" format="tabular" label="tabular file"/> + <param name="pos_column" type="data_column" data_ref="input_tsv" label="POS column"/> + <param name="ref_column" type="data_column" data_ref="input_tsv" label="REF column"/> + <param name="alt_column" type="data_column" data_ref="input_tsv" label="ALT column"/> + <param name="transcript_column" type="data_column" data_ref="input_tsv" label="Transcript ID column"/> + <param name="dp_column" type="data_column" data_ref="input_tsv" label="Read Depth (DP) column"/> + <param name="dpr_column" type="data_column" data_ref="input_tsv" label="Allele Count (DPR ro AN) column"/> + </when> + </conditional> + <conditional name="ref"> + <param name="ref_source" type="select" label="Source for Genomic Data"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_loc" type="select" label="Select reference 2bit file"> + <options from_data_table="twobit" /> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="twobit" label="reference 2bit file" /> + </when> + </conditional> + <param name="gtf_file" type="data" format="gtf" label="Ensembl GTF file"/> + <section name="filter" expanded="false" title="Filter Options"> + <param name="min_depth" type="integer" value="" optional="true" min="0" label="Minimum Read Depth to report" + help="If a value is entered, ignore variants with DP INFO field less than this value"/> + <param name="min_freq" type="float" value="" optional="true" min="0.0" max="1.0" label="Minimum Alt frequency to report" + help="If a value is entered, ignore variant alleles where its DPR count divided the sum of DPR is less than this value"/> + </section> + <section name="report" expanded="false" title="Report Options"> + <param name="readthrough" type="integer" value="0" optional="true" min="0" max="4" label="Number of readthrough stop codons to display"/> + <param name="leading_aa" type="integer" value="10" optional="true" min="0" label="Number of Amino Acids prior to variant to display" + help="Ignored for frame shifts"/> + <param name="trailing_aa" type="integer" value="10" optional="true" min="0" label="Number of Amino Acids following the variant to display" + help="Ignored for frame shifts"/> + </section> + + </inputs> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <tests> + <test> + <param name="fmt" value="vcf"/> + <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/> + <param name="ref_source" value="history"/> + <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> + <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> + <output name="output"> + <assert_contents> + <has_text text="MGGQ_A_SASNSFSRLH" /> + <not_has_text text="*REDHAAGPEA" /> + </assert_contents> + </output> + </test> + <test> + <param name="fmt" value="vcf"/> + <param name="input_vcf" value="GRCh38_X400k_EFF.vcf" ftype="vcf"/> + <param name="ref_source" value="history"/> + <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> + <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> + <output name="output"> + <assert_contents> + <has_text text="MGGQ_A_SASNSFSRLH" /> + <not_has_text text="*REDHAAGPEA" /> + </assert_contents> + </output> + </test> + <test> + <param name="fmt" value="vcf"/> + <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/> + <param name="ref_source" value="history"/> + <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> + <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> + <param name="readthrough" value="1"/> + <output name="output"> + <assert_contents> + <has_text text="MGGQ_A_SASNSFSRLH" /> + <has_text text="*REDHAAGPEA" /> + </assert_contents> + </output> + </test> + <test> + <param name="fmt" value="vcf"/> + <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/> + <param name="ref_source" value="history"/> + <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> + <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> + <param name="min_depth" value="100"/> + <param name="min_freq" value=".80"/> + <output name="output"> + <assert_contents> + <has_text text="EQLDAGVRYL_E_LRIAHMLEGS" /> + <not_has_text text="EYDILVAEET_V_GEPWEDGFEA" /> + </assert_contents> + </output> + </test> + <test> + <param name="fmt" value="tsv"/> + <param name="input_tsv" value="GRCh38_X400k.tsv" ftype="tabular"/> + <param name="ref_source" value="history"/> + <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> + <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> + <param name="pos_column" value="2"/> + <param name="ref_column" value="3"/> + <param name="alt_column" value="4"/> + <param name="transcript_column" value="7"/> + <param name="dp_column" value="8"/> + <param name="dpr_column" value="9"/> + <output name="output"> + <assert_contents> + <has_text text="MGGQ_A_SASNSFSRLH" /> + <not_has_text text="*REDHAAGPEA" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +Uses an Essembl GTF and a genome 2bit reference to report variant peptides from snpEff reported missense and frameshift variants. +Allows readthrough of stop codons, and reports the stop codons. + +Input can be a snpEff vcf file using either ANN or EFF annotations. +Alternatively, the input can be a tabular file that has columns: + + - pos + - ref + - alt + - Ensembl Transcript ID + - Read Depth (DP) + - AlleleDepth (DPR) + + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btt385</citation> + </citations> +</tool>