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comparison ensembl_variant_report.xml @ 3:652d35c42bca draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit d3b7ff1c2f0a1eed7a65af7208e987a35627402c-dirty
author jjohnson
date Wed, 20 Mar 2019 15:27:02 -0400
parents f87fe6bc48f4
children 7fc91849ab21
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2:f87fe6bc48f4 3:652d35c42bca
1 <tool id="ensembl_variant_report" name="Ensembl Variant Report" version="0.2.0"> 1 <tool id="ensembl_variant_report" name="Ensembl Variant Report" version="0.3.0">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="1.40">gtf_to_genes</requirement> 3 <requirement type="package" version="1.40">gtf_to_genes</requirement>
4 <requirement type="package" version="3.1.4">twobitreader</requirement> 4 <requirement type="package" version="3.1.4">twobitreader</requirement>
5 <requirement type="package" version="1.62">biopython</requirement> 5 <requirement type="package" version="1.62">biopython</requirement>
6 </requirements> 6 </requirements>
95 </inputs> 95 </inputs>
96 <outputs> 96 <outputs>
97 <data name="output" format="tabular" > 97 <data name="output" format="tabular" >
98 <actions> 98 <actions>
99 <action name="column_names" type="metadata" 99 <action name="column_names" type="metadata"
100 default="Gene,Ref_location,Ref_seq,Var_seq,Frequency,DP,Ensemble_Gene_transcript,AA_pos,AA_var,Protein_len,Stop_Codon,Variant_Peptide,Transcipt_type"/> 100 default="Gene,Ref_location,Ref_seq,Var_seq,Frequency,DP,Ensemble_Gene_transcript,AA_pos,AA_var,Protein_len,Stop_Codon,Variant_Peptide,Transcript_type"/>
101 </actions> 101 </actions>
102 </data> 102 </data>
103 </outputs> 103 </outputs>
104 <tests> 104 <tests>
105 <test> 105 <test>
177 </output> 177 </output>
178 </test> 178 </test>
179 </tests> 179 </tests>
180 <help><![CDATA[ 180 <help><![CDATA[
181 Uses an Essembl GTF and a genome 2bit reference to report variant peptides from snpEff reported missense and frameshift variants. 181 Uses an Essembl GTF and a genome 2bit reference to report variant peptides from snpEff reported missense and frameshift variants.
182 Allows readthrough of stop codons, and reports the stop codons. 182 Allows readthrough of stop codons, and reports the stop codons. Translation readthrough is known to occur with some antibiotics.
183
184 The variant peptides can be converted to a fasta file with text and fasta tools, then used as input to epitope binding prediction
185 applications such as netMHC or IEDB.
186
187 **Input**
183 188
184 Input can be a snpEff vcf file using either ANN or EFF annotations. 189 Input can be a snpEff vcf file using either ANN or EFF annotations.
190
185 Alternatively, the input can be a tabular file that has columns: 191 Alternatively, the input can be a tabular file that has columns:
186 192
187 - pos 193 - genomic_location
188 - ref 194 - reference_bases
189 - alt 195 - variant_bases
190 - Ensembl Transcript ID 196 - Ensembl Transcript ID
191 - Read Depth (DP) 197 - Read Depth (DP)
192 - AlleleDepth (DPR) 198 - AlleleDepth (DPR)
199
200 **Output**
201
202 Sample Output ::
203
204 ====== ============= ======= ======= ========= === =============================== ====== ====== =========== =============== ======================= =======================
205 Gene Ref_location Ref_seq Var_seq Frequency DP Ensemble_Gene_transcript AA_pos AA_var Protein_len Stop_Codon Variant_Peptide Transcript_type
206 ====== ============= ======= ======= ========= === =============================== ====== ====== =========== =============== ======================= =======================
207 ACTL8 1:18149510 + G T 1.00 12 ENSG00000117148|ENST00000375406 3 A3S 367 G-TGA MA_S_RTVIIDHGSG protein_coding
208 BDH2 4:104013796 - A G 0.47 159 ENSG00000164039|ENST00000511354 70 N70S 91 c-tag TKKKQIDQFA_S_EVERLDVLFN nonsense_mediated_decay
209 CENPE 4:104061993 - G C 0.83 6 ENSG00000138778|ENST00000265148 1911 S1911T 2702 G-TAG LKLERDQLKE_T_LQETKARDLE protein_coding
210 CCHCR1 6:31110391 - C G 0.40 65 ENSG00000204536|ENST00000396268 865 S865C 872 C-TAA QGDNLDRCSS_C_NPQMSS* protein_coding
211 NPRL3 16:138772 - CT CCT 0.58 123 ENSG00000103148|ENST00000399953 489 S489L 569 A-TGA-C,C-TGA-G LGA*TRSHPQCTRSPEP* protein_coding
212 ====== ============= ======= ======= ========= === =============================== ====== ====== =========== =============== ======================= =======================
213
214 The Variant_Peptide column:
215 - misense: prior amino acids _ variant amino acid _ following amino acids
216 - frameshift: variant amino acids with stop codons indicated by *
217
193 218
194 ]]></help> 219 ]]></help>
195 <citations> 220 <citations>
196 <citation type="doi">10.1093/bioinformatics/btt385</citation> 221 <citation type="doi">10.1093/bioinformatics/btt385</citation>
197 </citations> 222 </citations>