Mercurial > repos > jjohnson > ensembl_variant_report

comparison ensembl_variant_report.xml @ 3:bfc8ceb44c5f 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 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
author jjohnson
date Fri, 06 Jan 2017 17:40:24 -0500
parents bf2687e2511e
children 9e83cc05d384
comparison
equal deleted inserted replaced
2:bf2687e2511e 3:bfc8ceb44c5f
1 <tool id="ensembl_variant_report" name="Ensembl Variant Report" version="0.1.0"> 1 <tool id="ensembl_variant_report" name="Ensembl Variant Report" version="0.1.0">
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 </requirements> 6 </requirements>
6 <stdio> 7 <stdio>
7 <exit_code range="1:" /> 8 <exit_code range="1:" />
8 </stdio> 9 </stdio>
9 <command><![CDATA[ 10 <command><![CDATA[
60 <param name="transcript_column" type="data_column" data_ref="input_tsv" label="Transcript ID column"/> 61 <param name="transcript_column" type="data_column" data_ref="input_tsv" label="Transcript ID column"/>
61 <param name="dp_column" type="data_column" data_ref="input_tsv" label="Read Depth (DP) column"/> 62 <param name="dp_column" type="data_column" data_ref="input_tsv" label="Read Depth (DP) column"/>
62 <param name="dpr_column" type="data_column" data_ref="input_tsv" label="Allele Count (DPR ro AN) column"/> 63 <param name="dpr_column" type="data_column" data_ref="input_tsv" label="Allele Count (DPR ro AN) column"/>
63 </when> 64 </when>
64 </conditional> 65 </conditional>
65 <conditional name="ref_source"> 66 <conditional name="ref">
66 <param name="index_source" type="select" label="Source for Genomic Data"> 67 <param name="ref_source" type="select" label="Source for Genomic Data">
67 <option value="cached">Locally cached</option> 68 <option value="cached">Locally cached</option>
68 <option value="history">History</option> 69 <option value="history">History</option>
69 </param> 70 </param>
70 <when value="cached"> 71 <when value="cached">
71 <param name="ref_loc" type="data" format="twobit" label="Select reference 2bit file"> 72 <param name="ref_loc" type="data" format="twobit" label="Select reference 2bit file">
87 <param name="trailing_aa" type="integer" value="" optional="true" min="0" label="Number of Amino Acids following the variant to display"/> 88 <param name="trailing_aa" type="integer" value="" optional="true" min="0" label="Number of Amino Acids following the variant to display"/>
88 </section> 89 </section>
89 90
90 </inputs> 91 </inputs>
91 <outputs> 92 <outputs>
92 <data name="output" format="tabular" label="${input} report"/> 93 <data name="output" format="tabular" />
93 </outputs> 94 </outputs>
94 <tests> 95 <tests>
95 <test> 96 <test>
96 <param name="fmt" value="vcf"/> 97 <param name="fmt" value="vcf"/>
97 <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/> 98 <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
98 <param name="index_source" value="history"/> 99 <param name="ref_source" value="history"/>
99 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> 100 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
100 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> 101 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
101 <output name="output_file"> 102 <output name="output_file">
102 <assert_contents> 103 <assert_contents>
103 <has_text text="MGGQ_A_SASNSFSRLH" /> 104 <has_text text="MGGQ_A_SASNSFSRLH" />
106 </output> 107 </output>
107 </test> 108 </test>
108 <test> 109 <test>
109 <param name="fmt" value="vcf"/> 110 <param name="fmt" value="vcf"/>
110 <param name="input_vcf" value="GRCh38_X400k_EFF.vcf" ftype="vcf"/> 111 <param name="input_vcf" value="GRCh38_X400k_EFF.vcf" ftype="vcf"/>
111 <param name="index_source" value="history"/> 112 <param name="ref_source" value="history"/>
112 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> 113 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
113 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/> 114 <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
114 <output name="output_file"> 115 <output name="output_file">
115 <assert_contents> 116 <assert_contents>
116 <has_text text="MGGQ_A_SASNSFSRLH" /> 117 <has_text text="MGGQ_A_SASNSFSRLH" />
119 </output> 120 </output>
120 </test> 121 </test>
121 <test> 122 <test>
122 <param name="fmt" value="vcf"/> 123 <param name="fmt" value="vcf"/>
123 <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/> 124 <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
124 <param name="index_source" value="history"/> 125 <param name="ref_source" value="history"/>
125 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> 126 <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="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
127 <param name="readthrough" value="1"/> 128 <param name="readthrough" value="1"/>
128 <output name="output_file"> 129 <output name="output_file">
129 <assert_contents> 130 <assert_contents>
133 </output> 134 </output>
134 </test> 135 </test>
135 <test> 136 <test>
136 <param name="fmt" value="vcf"/> 137 <param name="fmt" value="vcf"/>
137 <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/> 138 <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
138 <param name="index_source" value="history"/> 139 <param name="ref_source" value="history"/>
139 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> 140 <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="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
141 <param name="min_depth" value="100"/> 142 <param name="min_depth" value="100"/>
142 <param name="min_freq" value=".80"/> 143 <param name="min_freq" value=".80"/>
143 <output name="output_file"> 144 <output name="output_file">
148 </output> 149 </output>
149 </test> 150 </test>
150 <test> 151 <test>
151 <param name="fmt" value="tsv"/> 152 <param name="fmt" value="tsv"/>
152 <param name="input_tsv" value="GRCh38_X400k.tsv" ftype="tabular"/> 153 <param name="input_tsv" value="GRCh38_X400k.tsv" ftype="tabular"/>
153 <param name="index_source" value="history"/> 154 <param name="ref_source" value="history"/>
154 <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/> 155 <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="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
156 <param name="pos_column" value="2"/> 157 <param name="pos_column" value="2"/>
157 <param name="ref_column" value="3"/> 158 <param name="ref_column" value="3"/>
158 <param name="alt_column" value="4"/> 159 <param name="alt_column" value="4"/>