Mercurial > repos > jjohnson > ensembl_variant_report

annotate ensembl_variant_report.xml @ 0:9f4ea174ce3d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
1 <tool id="ensembl_variant_report" name="Ensembl Variant Report" version="0.1.0">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
2 <requirements>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
3 <requirement type="package" version="1.40">gtf_to_genes</requirement>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
4 <requirement type="package" version="3.1.4">twobitreader</requirement>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
5 <requirement type="package" version="1.62">biopython</requirement>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
6 </requirements>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
7 <stdio>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
8 <exit_code range="1:" />
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
9 </stdio>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
10 <command><![CDATA[
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
11 python '$__tool_directory__/ensembl_variant_report.py'
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
12 #if $ref.ref_source == 'cached':
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
13 --twobit="$ref.ref_loc.fields.path"
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
14 #else
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
15 --twobit="$ref.ref_file"
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
16 #end if
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
17 --gene_model="$gtf_file"
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
18 #if $variant.fmt == 'vcf':
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
19 --input="$variant.input_vcf"
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
20 --format=snpeff
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
21 #else
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
22 --input="$variant.input_tsv"
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
23 --pos_column=$variant.pos_column
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
24 --ref_column=$variant.ref_column
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
25 --alt_column=$variant.alt_column
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
26 --transcript_column=$variant.transcript_column
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
27 --dp_column=$variant.dp_column
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
28 --dpr_column=$variant.dpr_column
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
29 #end if
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
30 #if str($filter.min_depth) != '':
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
31 --min_depth=$filter.min_depth
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
32 #end if
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
33 #if str($filter.min_freq) != '':
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
34 --min_freq=$filter.min_freq
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
35 #end if
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
36 #if str($report.readthrough) != '':
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
37 --readthrough=$report.readthrough
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
38 #end if
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
39 #if str($report.leading_aa) != '':
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
40 --leading_aa=$report.leading_aa
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
41 #end if
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
42 #if str($report.trailing_aa) != '':
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
43 --trailing_aa=$report.trailing_aa
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
44 #end if
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
45 --output="$output"
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
46 ]]></command>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
47 <inputs>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
48 <conditional name="variant">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
49 <param name="fmt" type="select" label="Input format for variants">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
50 <option value="vcf">snpEff vcf</option>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
51 <option value="tsv">tabular from snpsift extract</option>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
52 </param>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
53 <when value="vcf">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
54 <param name="input_vcf" type="data" format="vcf" label="snpEff VCF file"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
55 </when>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
56 <when value="tsv">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
57 <param name="input_tsv" type="data" format="tabular" label="tabular file"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
58 <param name="pos_column" type="data_column" data_ref="input_tsv" label="POS column"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
59 <param name="ref_column" type="data_column" data_ref="input_tsv" label="REF column"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
60 <param name="alt_column" type="data_column" data_ref="input_tsv" label="ALT column"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
61 <param name="transcript_column" type="data_column" data_ref="input_tsv" label="Transcript ID column"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
62 <param name="dp_column" type="data_column" data_ref="input_tsv" label="Read Depth (DP) column"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
63 <param name="dpr_column" type="data_column" data_ref="input_tsv" label="Allele Count (DPR ro AN) column"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
64 </when>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
65 </conditional>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
66 <conditional name="ref">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
67 <param name="ref_source" type="select" label="Source for Genomic Data">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
68 <option value="cached">Locally cached</option>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
69 <option value="history">History</option>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
70 </param>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
71 <when value="cached">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
72 <param name="ref_loc" type="select" label="Select reference 2bit file">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
73 <options from_data_table="twobit" />
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
74 </param>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
75 </when>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
76 <when value="history">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
77 <param name="ref_file" type="data" format="twobit" label="reference 2bit file" />
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
78 </when>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
79 </conditional>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
80 <param name="gtf_file" type="data" format="gtf" label="Ensembl GTF file"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
81 <section name="filter" expanded="false" title="Filter Options">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
82 <param name="min_depth" type="integer" value="" optional="true" min="0" label="Minimum Read Depth to report"
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
83 help="If a value is entered, ignore variants with DP INFO field less than this value"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
84 <param name="min_freq" type="float" value="" optional="true" min="0.0" max="1.0" label="Minimum Alt frequency to report"
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
85 help="If a value is entered, ignore variant alleles where its DPR count divided the sum of DPR is less than this value"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
86 </section>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
87 <section name="report" expanded="false" title="Report Options">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
88 <param name="readthrough" type="integer" value="0" optional="true" min="0" max="4" label="Number of readthrough stop codons to display"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
89 <param name="leading_aa" type="integer" value="10" optional="true" min="0" label="Number of Amino Acids prior to variant to display"
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
90 help="Ignored for frame shifts"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
91 <param name="trailing_aa" type="integer" value="10" optional="true" min="0" label="Number of Amino Acids following the variant to display"
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
92 help="Ignored for frame shifts"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
93 </section>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
94
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
95 </inputs>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
96 <outputs>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
97 <data name="output" format="tabular" />
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
98 </outputs>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
99 <tests>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
100 <test>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
101 <param name="fmt" value="vcf"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
102 <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
103 <param name="ref_source" value="history"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
104 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
105 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
106 <output name="output">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
107 <assert_contents>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
108 <has_text text="MGGQ_A_SASNSFSRLH" />
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
109 <not_has_text text="*REDHAAGPEA" />
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
110 </assert_contents>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
111 </output>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
112 </test>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
113 <test>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
114 <param name="fmt" value="vcf"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
115 <param name="input_vcf" value="GRCh38_X400k_EFF.vcf" ftype="vcf"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
116 <param name="ref_source" value="history"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
117 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
118 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
119 <output name="output">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
120 <assert_contents>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
121 <has_text text="MGGQ_A_SASNSFSRLH" />
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
122 <not_has_text text="*REDHAAGPEA" />
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
123 </assert_contents>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
124 </output>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
125 </test>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
126 <test>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
127 <param name="fmt" value="vcf"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
128 <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
129 <param name="ref_source" value="history"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
130 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
131 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
132 <param name="readthrough" value="1"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
133 <output name="output">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
134 <assert_contents>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
135 <has_text text="MGGQ_A_SASNSFSRLH" />
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
136 <has_text text="*REDHAAGPEA" />
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
137 </assert_contents>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
138 </output>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
139 </test>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
140 <test>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
141 <param name="fmt" value="vcf"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
142 <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
143 <param name="ref_source" value="history"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
144 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
145 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
146 <param name="min_depth" value="100"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
147 <param name="min_freq" value=".80"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
148 <output name="output">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
149 <assert_contents>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
150 <has_text text="EQLDAGVRYL_E_LRIAHMLEGS" />
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
151 <not_has_text text="EYDILVAEET_V_GEPWEDGFEA" />
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
152 </assert_contents>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
153 </output>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
154 </test>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
155 <test>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
156 <param name="fmt" value="tsv"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
157 <param name="input_tsv" value="GRCh38_X400k.tsv" ftype="tabular"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
158 <param name="ref_source" value="history"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
159 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
160 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
161 <param name="pos_column" value="2"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
162 <param name="ref_column" value="3"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
163 <param name="alt_column" value="4"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
164 <param name="transcript_column" value="7"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
165 <param name="dp_column" value="8"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
166 <param name="dpr_column" value="9"/>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
167 <output name="output">
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
168 <assert_contents>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
169 <has_text text="MGGQ_A_SASNSFSRLH" />
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
170 <not_has_text text="*REDHAAGPEA" />
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
171 </assert_contents>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
172 </output>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
173 </test>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
174 </tests>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
175 <help><![CDATA[
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
176 Uses an Essembl GTF and a genome 2bit reference to report variant peptides from snpEff reported missense and frameshift variants.
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
177 Allows readthrough of stop codons, and reports the stop codons.
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
178
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
179 Input can be a snpEff vcf file using either ANN or EFF annotations.
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
180 Alternatively, the input can be a tabular file that has columns:
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
181
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
182 - pos
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
183 - ref
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
184 - alt
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
185 - Ensembl Transcript ID
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
186 - Read Depth (DP)
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
187 - AlleleDepth (DPR)
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
188
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
189 ]]></help>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
190 <citations>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
191 <citation type="doi">10.1093/bioinformatics/btt385</citation>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
192 </citations>
9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
parents:
diff changeset
193 </tool>