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comparison snpEff_create_db.xml @ 29:ca2b512e8d7c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
author iuc
date Mon, 21 Oct 2024 13:56:15 +0000
parents 6322be79bd8e
children
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28:6322be79bd8e 29:ca2b512e8d7c
1 <tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy6" profile="22.01"> 1 <tool id="snpEff_build_gb" name="SnpEff build:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
2 <description> database from Genbank or GFF record</description> 2 <description> database from Genbank or GFF record</description>
3 <macros> 3 <macros>
4 <import>snpEff_macros.xml</import> 4 <import>snpEff_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <expand macro="requirement" /> 7 <expand macro="requirement" />
8 <requirement type="package" version="1.79">biopython</requirement> 8 <requirement type="package" version="1.84">biopython</requirement>
9 </requirements> 9 </requirements>
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command><![CDATA[ 12 <command><![CDATA[
13 #if str($input_type.input_type_selector) == "gb" and str($input_type.fasta) == "yes": 13 #if str($input_type.input_type_selector) == "gb" and str($input_type.fasta) == "yes":
34 ln -s '${input_type.reference_source.ref_file.fields.path}' 'snpeff_output/${genome_version}/sequences.fa' && 34 ln -s '${input_type.reference_source.ref_file.fields.path}' 'snpeff_output/${genome_version}/sequences.fa' &&
35 #end if 35 #end if
36 ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.${input_type.input_type_selector}' && 36 ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.${input_type.input_type_selector}' &&
37 #end if 37 #end if
38 38
39 snpEff @JAVA_OPTIONS@ build -v 39 snpEff @JAVA_OPTIONS@ build -noCheckCds -noCheckProtein -v
40 -configOption '${genome_version}'.genome='${genome_version}' 40 -configOption '${genome_version}'.genome='${genome_version}'
41 -configOption '${genome_version}'.codonTable='${codon_table}' 41 -configOption '${genome_version}'.codonTable='${codon_table}'
42 #if str($input_type.input_type_selector) == "gb": 42 #if str($input_type.input_type_selector) == "gb":
43 -genbank 43 -genbank
44 #elif str($input_type.input_type_selector) == "gff": 44 #elif str($input_type.input_type_selector) == "gff":
184 </test> 184 </test>
185 </tests> 185 </tests>
186 <help><![CDATA[ 186 <help><![CDATA[
187 **What it does** 187 **What it does**
188 188
189 This tool uses `"snpEff build -genbank"` or `"snpEff build -gff3"` commands to create a snpEff database. 189 This tool uses `snpEff build` to create a snpEff database.
190 190
191 ------ 191 ------
192 192
193 .. class:: infomark 193 .. class:: infomark
194 194
199 #. Genbank files contain annotations (such as locations of genes) together with sequences. This ensures that these two are in sync with each other. 199 #. Genbank files contain annotations (such as locations of genes) together with sequences. This ensures that these two are in sync with each other.
200 #. When you are analyzing small genomes (or not so small) it is much more convenient to create a database on the fly and use it. 200 #. When you are analyzing small genomes (or not so small) it is much more convenient to create a database on the fly and use it.
201 201
202 .. class:: warningmark 202 .. class:: warningmark
203 203
204 SnpEff errors out on highly fragmented genomes containing multiple scaffolds. This is because a single gene may be split between multiple scaffolds causing SnpEff to crash. If this is happening use GFF route described below. 204 SnpEff errors out on highly fragmented genomes containing multiple scaffolds. This is because a single gene may be split between multiple scaffolds causing SnpEff to crash. If this is happening use the GFF route described below.
205 205
206 ------- 206 -------
207 207
208 **Genbank usage scenario** 208 **Genbank usage scenario**
209 209