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comparison ensembl_variant_report.xml @ 0:c3a9e63e8c51 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
author jjohnson
date Fri, 06 Jan 2017 16:19:40 -0500
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children bf2687e2511e
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-1:000000000000 0:c3a9e63e8c51
1 <tool id="ensembl_variant_report" name="Ensembl Variant Report" version="0.1.0">
2 <requirements>
3 <requirement type="package" version="1.40">gtf_to_genes</requirement>
4 <requirement type="package" version="3.1.4">twobitreader</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command><![CDATA[
10 python '$__tool_directory__/ensembl_variant_report.py'
11 #if $ref.ref_source == 'cached':
12 --twobit="$ref.ref_loc.fields.path"
13 #else
14 --twobit="$ref.ref_file"
15 #end if
16 --gene_model="$gtf_file"
17 #if $variant.fmt == 'vcf':
18 --input="$variant.input_vcf"
19 --format=snpeff
20 #else
21 --input="$variant.input_tsv"
22 --pos_column=$pos_column
23 --ref_column=$ref_column
24 --alt_column=$alt_column
25 --transcript_column=$transcript_column
26 --dp_column=$dp_column
27 --dpr_column=$dpr_column
28 #end if
29 #if str($filter.min_depth) != '':
30 --min_depth=$filter.min_depth
31 #end if
32 #if str($filter.min_freq) != '':
33 --min_freq=$filter.min_freq
34 #end if
35 #if str($report.readthrough) != '':
36 --readthrough=$report.readthrough
37 #end if
38 #if str($report.leading_aa) != '':
39 --leading_aa=$report.leading_aa
40 #end if
41 #if str($report.trailing_aa) != '':
42 --trailing_aa=$report.trailing_aa
43 #end if
44 --output="$output"
45 ]]></command>
46 <inputs>
47 <conditional name="variant">
48 <param name="fmt" type="select" label="">
49 <option value="vcf">snpEff vcf</option>
50 <option value="tsv">tabular from snpsift extract</option>
51 </param>
52 <when value="vcf">
53 <param name="input_vcf" type="data" format="vcf" label="snpEff VCF file"/>
54 </when>
55 <when value="tsv">
56 <param name="input_tsv" type="data" format="vcf" label="tabular file"/>
57 <param name="pos_column" type="data_column" data_ref="input" label="POS column"/>
58 <param name="ref_column" type="data_column" data_ref="input" label="REF column"/>
59 <param name="alt_column" type="data_column" data_ref="input" label="ALT column"/>
60 <param name="transcript_column" type="data_column" data_ref="input" label="Transcript ID column"/>
61 <param name="dp_column" type="data_column" data_ref="input" label="Read Depth (DP) column"/>
62 <param name="dpr_column" type="data_column" data_ref="input" label="Allele Count (DPR ro AN) column"/>
63 </when>
64 </conditional>
65 <conditional name="ref_source">
66 <param name="index_source" type="select" label="Source for Genomic Data">
67 <option value="cached">Locally cached</option>
68 <option value="history">History</option>
69 </param>
70 <when value="cached">
71 <param name="ref_loc" type="data" format="twobit" label="Select reference 2bit file">
72 <options from_data_table="twobit" />
73 </param>
74 </when>
75 <when value="history">
76 <param name="ref_file" type="data" format="twobit" label="reference 2bit file" />
77 </when>
78 </conditional>
79 <param name="gtf_file" type="data" format="gtf" label="Ensembl GTF file"/>
80 <section name="filter" expanded="false" title="Filter Options">
81 <param name="min_depth" type="integer" value="" optional="true" min="0" label="Minimum Read Depth to report"/>
82 <param name="min_freq" type="float" value="" optional="true" min="0.0" max="1.0" label="Minimum Alt frequency to report"/>
83 </section>
84 <section name="report" expanded="false" title="Report Options">
85 <param name="readthrough" type="integer" value="" optional="true" min="0" max="4" label="Number of readthrough stop codons to display"/>
86 <param name="leading_aa" type="integer" value="" optional="true" min="0" label="Number of Amino Acids prior to variant to display"/>
87 <param name="trailing_aa" type="integer" value="" optional="true" min="0" label="Number of Amino Acids following the variant to display"/>
88 </section>
89
90 </inputs>
91 <outputs>
92 <data name="output" format="tabular" label="${input} report"/>
93 </outputs>
94 <tests>
95 <test>
96 <param name="fmt" value="vcf"/>
97 <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
98 <param name="index_source" value="history"/>
99 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
100 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
101 <output name="output_file">
102 <assert_contents>
103 <has_text text="MGGQ_A_SASNSFSRLH" />
104 <not_has_text text="*REDHAAGPEA" />
105 </assert_contents>
106 </output>
107 </test>
108 <test>
109 <param name="fmt" value="vcf"/>
110 <param name="input_vcf" value="GRCh38_X400k_EFF.vcf" ftype="vcf"/>
111 <param name="index_source" value="history"/>
112 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
113 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
114 <output name="output_file">
115 <assert_contents>
116 <has_text text="MGGQ_A_SASNSFSRLH" />
117 <not_has_text text="*REDHAAGPEA" />
118 </assert_contents>
119 </output>
120 </test>
121 <test>
122 <param name="fmt" value="vcf"/>
123 <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
124 <param name="index_source" value="history"/>
125 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
126 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
127 <param name="readthrough" value="1"/>
128 <output name="output_file">
129 <assert_contents>
130 <has_text text="MGGQ_A_SASNSFSRLH" />
131 <has_text text="*REDHAAGPEA" />
132 </assert_contents>
133 </output>
134 </test>
135 <test>
136 <param name="fmt" value="vcf"/>
137 <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
138 <param name="index_source" value="history"/>
139 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
140 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
141 <param name="min_depth" value="100"/>
142 <param name="min_freq" value=".80"/>
143 <output name="output_file">
144 <assert_contents>
145 <has_text text="EQLDAGVRYL_E_LRIAHMLEGS" />
146 <not_has_text text="EYDILVAEET_V_GEPWEDGFEA" />
147 </assert_contents>
148 </output>
149 </test>
150 <test>
151 <param name="fmt" value="tsv"/>
152 <param name="input_tsv" value="GRCh38_X400k.tsv" ftype="tabular"/>
153 <param name="index_source" value="history"/>
154 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
155 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
156 <param name="pos_column" value="2"/>
157 <param name="ref_column" value="3"/>
158 <param name="alt_column" value="4"/>
159 <param name="transcript_column" value="7"/>
160 <param name="dp_column" value="8"/>
161 <param name="dpr_column" value="9"/>
162 <output name="output_file">
163 <assert_contents>
164 <has_text text="MGGQ_A_SASNSFSRLH" />
165 <not_has_text text="*REDHAAGPEA" />
166 </assert_contents>
167 </output>
168 </test>
169 </tests>
170 <help><![CDATA[
171 Uses an Essembl GTF and a genome 2bit reference to report variant peptides from snpEff reported missense and frameshift variants.
172 Allows readthrough of stop codons, and reports the stop codons.
173
174 Input can be a snpEff vcf file using either ANN or EFF annotations.
175 Alternatively, the input can be a tabular file that has columns:
176 - pos
177 - ref
178 - alt
179 - Ensembl Transcript ID
180 - Read Depth (DP)
181 - AlleleDepth (DPR)
182
183 ]]></help>
184 <citations>
185 <citation type="doi">10.1093/bioinformatics/btt385</citation>
186 </citations>
187 </tool>