Mercurial > repos > iuc > snpeff

annotate snpeff_get_chr_names.xml @ 19:36dc3690a82c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
author iuc
date Wed, 12 Sep 2018 14:36:04 -0400
parents dd3622f501f3
children 8f92c2b26e6d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
36dc3690a82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
iuc
parents: 18
diff changeset
1 <tool id="snpEff_get_chr_names" name="SnpEff chromosome-info:" version="@WRAPPER_VERSION@.galaxy1">
18
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
2 <description>list chromosome names/lengths</description>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
3 <macros>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
4 <import>snpEff_macros.xml</import>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
5 </macros>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
6 <requirements>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
7 <expand macro="requirement" />
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
8 </requirements>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
9 <expand macro="stdio" />
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
10 <expand macro="version_command" />
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
11 <command><![CDATA[
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
12 snpEff dump
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
13 #if $snpDb.genomeSrc == 'cached':
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
14 -dataDir ${snpDb.genomeVersion.fields.path}
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
15 $snpDb.genomeVersion
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
16 #elif $snpDb.genomeSrc == 'history':
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
17 -dataDir '${snpDb.snpeff_db.extra_files_path}'
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
18 '${snpDb.snpeff_db.metadata.genome_version}'
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
19 #elif $snpDb.genomeSrc == 'custom':
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
20 -dataDir '${snpDb.snpeff_db.extra_files_path}'
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
21 -configOption '${snpDb.snpeff_db.metadata.genome_version}'.genome='${snpDb.snpeff_db.metadata.genome_version}'
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
22 '${snpDb.snpeff_db.metadata.genome_version}'
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
23 #else
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
24 -download
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
25 '$snpDb.genome_version'
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
26 #end if
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
27 | awk '/# Chromosomes/{y=1;next}y' | grep "#" | grep -E "[0-9]" | awk 'BEGIN {err=1;} {c=$0;sub(/^[^a-zA-Z0-9_]+/, "", c) && err=0; sub(/[^a-zA-Z0-9_]+/, "\t", c) && err=0; sub(/[^0-9]*$/, "", c) && err=0; print c } END {exit err}' > '$chr_names'
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
28 ]]></command>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
29 <inputs>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
30 <conditional name="snpDb">
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
31 <param name="genomeSrc" type="select" label="Genome source">
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
32 <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well -->
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
33 <option value="cached">Locally installed snpEff database</option>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
34 <option value="history">Downloaded snpEff database in your history</option>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
35 <option value="named">Download on demand</option>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
36 <option value="custom">Custom snpEff database in your history</option>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
37 </param>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
38 <when value="cached">
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
39 <param name="genomeVersion" type="select" label="Genome">
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
40 <help>This can only be used on built-in databases manually configured by your galaxy admin.</help>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
41 <options from_data_table="snpeffv_genomedb">
19
36dc3690a82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
iuc
parents: 18
diff changeset
42 <filter type="static_value" name="SNPEFF_VERSION" value="@SNPEFF_VERSION@" column="1"/>
18
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
43 <filter type="unique_value" column="2" />
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
44 </options>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
45 </param>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
46 </when>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
47 <when value="history">
19
36dc3690a82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
iuc
parents: 18
diff changeset
48 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
18
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
49 <help>This can only be used on databases in your history that were downloaded using the snpEff download tool.</help>
19
36dc3690a82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
iuc
parents: 18
diff changeset
50 <options options_filter_attribute="metadata.SNPEFF_VERSION" >
36dc3690a82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
iuc
parents: 18
diff changeset
51 <filter type="add_value" value="@SNPEFF_VERSION@" />
18
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
52 </options>
19
36dc3690a82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
iuc
parents: 18
diff changeset
53 <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.SNPEFF_VERSION == "@SNPEFF_VERSION@"</validator>
18
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
54 </param>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
55 </when>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
56 <when value="named">
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
57 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
58 <help>The list of available databases can be obtained with 'SnpEff databases' tool. If the database name is not found, locate a database here and download it in your history.</help>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
59 <validator type="regex" message="A genome version name is required">\S+</validator>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
60 </param>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
61 </when>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
62 <when value="custom">
19
36dc3690a82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
iuc
parents: 18
diff changeset
63 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
18
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
64 <help>This can only be used on databases in your history that were created using the snpEff build tool.</help>
19
36dc3690a82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
iuc
parents: 18
diff changeset
65 <options options_filter_attribute="metadata.SNPEFF_VERSION" >
36dc3690a82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
iuc
parents: 18
diff changeset
66 <filter type="add_value" value="@SNPEFF_VERSION@" />
18
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
67 </options>
19
36dc3690a82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
iuc
parents: 18
diff changeset
68 <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.SNPEFF_VERSION == "@SNPEFF_VERSION@"</validator>
18
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
69 </param>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
70 </when>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
71 </conditional>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
72 </inputs>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
73 <outputs>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
74 <data format="tabular" name="chr_names" label="Chromosome names and sizes"/>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
75 </outputs>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
76 <tests>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
77 <test>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
78 <param name="genomeSrc" value="named"/>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
79 <param name="genome_version" value="Bacillus_subtilis_subsp_subtilis_str_168"/>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
80 <output name="chr_names">
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
81 <assert_contents>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
82 <has_text text="Chromosome" />
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
83 <has_text text="4215606" />
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
84 </assert_contents>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
85 </output>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
86 </test>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
87 <test expect_failure="True">
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
88 <param name="genomeSrc" value="named"/>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
89 <param name="genome_version" value="should_not_match"/>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
90 </test>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
91 </tests>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
92 <help><![CDATA[
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
93
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
94 **What it does**
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
95
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
96 This tool outputs a tab-delimited file of chromosome names and their lengths, as they are in the selected genome/SnpEff database. The output can be used to validate and rename chromosomes in VCF files in order to annotate its records.
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
97
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
98 Note, make sure that the genome you select from the snpEff database precisely matches the one used in your analysis. As a cursory check, you can use the chromosome lengths in this output to match those in your reference, however the lengths can match, but the version may still differ.
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
99
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
100 Known issue: this strategy will not work if more than 1 chromosome in the same genome has the same length.
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
101
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
102 -------
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
103
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
104 .. class:: infomark
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
105
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
106 **The usage scenario**
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
107
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
108 Suppose you want to use snpEff to annotate a VCF file that was generated using an mouse reference with a different chromosome naming convention than in the snpEff database. To do this you can:
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
109
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
110 #. Use `SnpEff databases` to find the precise genome name for mouse data (e.g. "mm10") as it appears in the snpEff database.
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
111 #. List the chromosome names using this tool. Either select a built-in genome, one in your history, or select "Download on demand" and enter the genome version obtained in the previous step (which only actually downloads if snpEff doesn't already have it).
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
112 #. Check that the chromosomes in the SnpEff database are the same as the reference you used (e.g. as a cursory check, ensure the chromosome lengths reported from the SnpEff database match those of your reference).
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
113 #. Edit your vcf file to replace the chromosome names with the ones the SnpEff database uses.
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
114 #. Use **SnpEff eff** and supply the edited VCF file.
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
115
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
116 ]]></help>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
117 <expand macro="citations" />
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
118 </tool>