annotate annotate_variants.xml @ 1:99dfde12ee53 draft

planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864
author wolma
date Mon, 18 Dec 2017 03:41:24 -0500
parents 01e09a4cacf7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
1 <tool id="mimodd_annotate" name="MiModD Variant Annotation"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
2 version="@MIMODD_WRAPPER_VERSION@">
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
3 <description>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
4 with functional effects on genes and transcripts
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
5 </description>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
6 <macros>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
7 <import>macros.xml</import>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
8 </macros>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
9 <expand macro="requirements" />
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
10 <expand macro="stdio" />
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
11 <expand macro="version_command" />
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
12 <command><![CDATA[
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
13 mimodd annotate
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
14 '$inputfile' '$genome.annotation_source'
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
15 #if $snpeff_settings.stats:
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
16 --stats '$summary_file'
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
17 #end if
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
18 #if $codon_tables.genome_codon_table.strip() or len($codon_tables.table_specs) > 0:
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
19 --codon-tables
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
20 #if $codon_tables.genome_codon_table.strip():
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
21 '$codon_tables.genome_codon_table'
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
22 #end if
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
23 #for $table_spec in $codon_tables.table_specs:
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
24 '$table_spec.contig:$table_spec.table'
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
25 #end for
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
26 #end if
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
27 #if $snpeff_settings.ud:
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
28 --ud ${snpeff_settings.ud}
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
29 #end if
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
30 #if $snpeff_settings.filter:
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
31 #echo ' '.join(str($snpeff_settings.filter).split(','))
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
32 #end if
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
33 --ofile '$ofile'
1
99dfde12ee53 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864
wolma
parents: 0
diff changeset
34 --verbose --quiet
0
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
35 ]]></command>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
36
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
37 <inputs>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
38 <param name="inputfile" type="data" format="vcf"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
39 label="VCF input file to be annotated" />
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
40 <conditional name="genome">
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
41 <param name="selection_method" type="select"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
42 label="Select SnpEff Genome Database">
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
43 <option value="select_from_list">from a list of installed databases</option>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
44 <option value="select_by_name">by name</option>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
45 </param>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
46 <when value="select_from_list">
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
47 <param name="genome_list" type="data" format="tabular" optional="true"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
48 label="List of available SnpEff Genomes"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
49 help="Select a dataset generated with the MiModD List Installed SnpEff Genomes tool to be able to choose from the genome databases listed in it." />
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
50 <param name="annotation_source" type="select"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
51 label="SnpEff Genome to use"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
52 help="Select a genome annotation database for your organism from the ones in the list.">
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
53 <options from_dataset="genome_list">
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
54 <column name="name" index="0"/>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
55 <column name="value" index="1"/>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
56 <filter type="unique_value" name="unique_names" column="0"/>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
57 </options>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
58 </param>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
59 </when>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
60 <when value="select_by_name">
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
61 <param name="annotation_source" type="text"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
62 label="Name of an installed SnpEff genome"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
63 help="Your input needs to exactly match the name of an installed SnpEff database.">
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
64 <validator type="expression" message="A SnpEff genome is required to run this tool.">value.strip()</validator>
1
99dfde12ee53 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864
wolma
parents: 0
diff changeset
65 <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in SnpEff genome names." />
0
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
66 </param>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
67 </when>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
68 </conditional>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
69 <section name="codon_tables" title="Codon Table Configuration" expanded="false">
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
70 <param name="genome_codon_table" type="text"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
71 label="Genome codon table"
1
99dfde12ee53 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864
wolma
parents: 0
diff changeset
72 help="If this genome uses a non-standard codon table and this fact is not declared in the SnpEff config file, specify the table here. The name you provide must match exactly the name of a codon table known to SnpEff.">
99dfde12ee53 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864
wolma
parents: 0
diff changeset
73 <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in codon table names." />
99dfde12ee53 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864
wolma
parents: 0
diff changeset
74 </param>
0
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
75 <repeat name="table_specs" default="0" min="0"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
76 title="Codon tables to use for specific contigs"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
77 help="Use if certain contigs in the reference genome use a distinct codon table. A typical example is a mitochondrial genome contained as a contig in the reference genome. Contig/codon table assignments declared here will take precedence over a genome codon table set above.">
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
78 <param name="contig" type="text" label="contig or chromosome name">
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
79 <validator type="expression" message="This is a required field for a contig/codon table assignment.">value.strip()</validator>
1
99dfde12ee53 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864
wolma
parents: 0
diff changeset
80 <expand macro="lex_sam_header" message="Non-ASCII characters are not allowed in contig/chromosome names" />
0
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
81 </param>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
82 <param name="table" type="text" label="uses codon table">
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
83 <validator type="expression" message="This is a required field for a contig/codon table assignment.">value.strip()</validator>
1
99dfde12ee53 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864
wolma
parents: 0
diff changeset
84 <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in codon table names." />
0
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
85 </param>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
86 </repeat>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
87 </section>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
88 <section name="snpeff_settings" title="More SnpEff options" expanded="false">
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
89 <param name="stats" type="boolean" checked="false"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
90 label="Have SnpEff produce a summary file of results" />
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
91 <param name="ud" type="integer" optional="true"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
92 label="upstream downstream interval length (default = 5000 bases)"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
93 help="specify the upstream/downstream interval length. Variants more than INTERVAL nts from the next annotated gene will be considered intergenic"/>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
94 <param name="filter" type="select" display="checkboxes" multiple="true"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
95 label="Disable select types of annotations"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
96 help="The corresponding variants will still be retained (without annotations) in the output">
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
97 <option value="--no-downstream">Do not annotate DOWNSTREAM changes</option>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
98 <option value="--no-upstream">Do not annotate UPSTREAM changes</option>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
99 <option value="--no-intergenic">Do not annotate INTERGENIC changes</option>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
100 <option value="--no-intron">Do not annotate INTRON changes</option>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
101 <option value="--no-utr">Do not annotate 5_PRIME_UTR or 3_PRIME_UTR changes</option>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
102 </param>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
103 </section>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
104 </inputs>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
105
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
106 <outputs>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
107 <data name="ofile" format="vcf"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
108 label="Variants annotated with MiModd from ${on_string}" />
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
109 <data name="summary_file" format="html"
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
110 label="Summary of MiModD variant annotation of ${on_string}">
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
111 <filter>snpeff_settings['stats']</filter>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
112 </data>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
113 </outputs>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
114
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
115 <help><![CDATA[
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
116 .. class:: warningmark
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
117
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
118 This tool requires the variant annotation software SnpEff, which is not part of
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
119 the MiModD package! It also needs the correct SnpEff genome database for your
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
120 organism and reference sequence version installed with SnpEff.
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
121
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
122 .. class:: infomark
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
123
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
124 **What it does**
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
125
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
126 This tool uses SnpEff to annotate the variants in the VCF input dataset with
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
127 the effects that these variants have on known genomic features, i.e. on genes
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
128 and transcripts.
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
129
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
130 To do its job, SnpEff requires a database of known genome annotations for your
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
131 organism of interest. If you know the exact name of the genome database that
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
132 you want to use, you can enter it directly. Otherwise, you should use the
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
133 MiModD *List Installed SnpEff Genomes* tool first to generate a new dataset in
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
134 your history that lists all SnpEff genome databases currently available to
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
135 SnpEff on the system, then when you select this dataset as the *List of
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
136 available SnpEff Genomes* above, you will be able to choose the SnpEff Genome
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
137 from a dropdown list.
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
138
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
139 The tool will create a new dataset in VCF format with the annotations added to
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
140 the corresponding variant records. Do not expect this format to be very
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
141 readable, but use the *MiModD Variant Reports* tool to turn it into a human
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
142 friendly form.
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
143
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
144 In addition, you can instruct the tool to produce an additional dataset with a
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
145 summary of the variants and their effects in html format.
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
146
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
147 @HELP_FOOTER@
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
148 ]]></help>
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
149 <expand macro="citations" />
01e09a4cacf7 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
150 </tool>