Mercurial > repos > iuc > snpeff

annotate snpeff_get_chr_names.xml @ 25:5c7b70713fb5 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 a4c17efb8ec4b3a315766f5b5602effa275fade3
author iuc
date Wed, 03 Aug 2022 16:33:45 +0000
parents 74aebe30fb52
children 6322be79bd8e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
23
74aebe30fb52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 67da1a478db26ad45f36a673218d526f8962d72f"
iuc
parents: 20
diff changeset
1 <tool id="snpEff_get_chr_names" name="SnpEff chromosome-info:" version="@WRAPPER_VERSION@.galaxy2">
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>
23
74aebe30fb52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 67da1a478db26ad45f36a673218d526f8962d72f"
iuc
parents: 20
diff changeset
7 <expand macro="requirement">
74aebe30fb52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 67da1a478db26ad45f36a673218d526f8962d72f"
iuc
parents: 20
diff changeset
8 <requirement type="package" version="5.0.1">gawk</requirement>
74aebe30fb52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 67da1a478db26ad45f36a673218d526f8962d72f"
iuc
parents: 20
diff changeset
9 </expand>
18
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
10 </requirements>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
11 <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
12 <expand macro="version_command" />
23
74aebe30fb52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 67da1a478db26ad45f36a673218d526f8962d72f"
iuc
parents: 20
diff changeset
13 <command detect_errors="exit_code"><![CDATA[
20
8f92c2b26e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
iuc
parents: 19
diff changeset
14 snpEff @JAVA_OPTIONS@ dump
18
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
15 #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
16 -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
17 $snpDb.genomeVersion
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
18 #elif $snpDb.genomeSrc == 'history':
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
19 -dataDir '${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
20 '${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
21 #elif $snpDb.genomeSrc == 'custom':
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
22 -dataDir '${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
23 -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
24 '${snpDb.snpeff_db.metadata.genome_version}'
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
25 #else
20
8f92c2b26e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
iuc
parents: 19
diff changeset
26 -dataDir "\$PWD/temp"
18
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
27 -download
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
28 '$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
29 #end if
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
30 | 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
31 ]]></command>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
32 <inputs>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
33 <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
34 <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
35 <!-- 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
36 <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
37 <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
38 <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
39 <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
40 </param>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
41 <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
42 <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
43 <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
44 <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
45 <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
46 <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
47 </options>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
48 </param>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
49 </when>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
50 <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
51 <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
52 <help>This can only be used on databases in your history that were downloaded using the snpEff download tool.</help>
20
8f92c2b26e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
iuc
parents: 19
diff changeset
53 <options options_filter_attribute="metadata.snpeff_version" >
19
36dc3690a82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
iuc
parents: 18
diff changeset
54 <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
55 </options>
20
8f92c2b26e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
iuc
parents: 19
diff changeset
56 <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
57 </param>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
58 </when>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
59 <when value="named">
20
8f92c2b26e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
iuc
parents: 19
diff changeset
60 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)">
18
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
61 <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
62 <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
63 </param>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
64 </when>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
65 <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
66 <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
67 <help>This can only be used on databases in your history that were created using the snpEff build tool.</help>
20
8f92c2b26e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
iuc
parents: 19
diff changeset
68 <options options_filter_attribute="metadata.snpeff_version" >
19
36dc3690a82c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
iuc
parents: 18
diff changeset
69 <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
70 </options>
20
8f92c2b26e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
iuc
parents: 19
diff changeset
71 <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
72 </param>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
73 </when>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
74 </conditional>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
75 </inputs>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
76 <outputs>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
77 <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
78 </outputs>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
79 <tests>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
80 <test>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
81 <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
82 <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
83 <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
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 <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
86 <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
87 </assert_contents>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
88 </output>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
89 </test>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
90 <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
91 <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
92 <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
93 </test>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
94 </tests>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
95 <help><![CDATA[
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
96
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
97 **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
98
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
99 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
100
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
101 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
102
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
103 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
104
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
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
107 .. class:: infomark
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
108
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
109 **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
110
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
111 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
112
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
113 #. 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
114 #. 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
115 #. 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
116 #. 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
117 #. 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
118
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
119 ]]></help>
dd3622f501f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
diff changeset
120 <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
121 </tool>