Mercurial > repos > iuc > snpeff
comparison snpeff_get_chr_names.xml @ 20:8f92c2b26e6d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
author | iuc |
---|---|
date | Fri, 25 Jan 2019 12:29:48 -0500 |
parents | 36dc3690a82c |
children | 74aebe30fb52 |
comparison
equal
deleted
inserted
replaced
19:36dc3690a82c | 20:8f92c2b26e6d |
---|---|
7 <expand macro="requirement" /> | 7 <expand macro="requirement" /> |
8 </requirements> | 8 </requirements> |
9 <expand macro="stdio" /> | 9 <expand macro="stdio" /> |
10 <expand macro="version_command" /> | 10 <expand macro="version_command" /> |
11 <command><![CDATA[ | 11 <command><![CDATA[ |
12 snpEff dump | 12 snpEff @JAVA_OPTIONS@ dump |
13 #if $snpDb.genomeSrc == 'cached': | 13 #if $snpDb.genomeSrc == 'cached': |
14 -dataDir ${snpDb.genomeVersion.fields.path} | 14 -dataDir ${snpDb.genomeVersion.fields.path} |
15 $snpDb.genomeVersion | 15 $snpDb.genomeVersion |
16 #elif $snpDb.genomeSrc == 'history': | 16 #elif $snpDb.genomeSrc == 'history': |
17 -dataDir '${snpDb.snpeff_db.extra_files_path}' | 17 -dataDir '${snpDb.snpeff_db.extra_files_path}' |
19 #elif $snpDb.genomeSrc == 'custom': | 19 #elif $snpDb.genomeSrc == 'custom': |
20 -dataDir '${snpDb.snpeff_db.extra_files_path}' | 20 -dataDir '${snpDb.snpeff_db.extra_files_path}' |
21 -configOption '${snpDb.snpeff_db.metadata.genome_version}'.genome='${snpDb.snpeff_db.metadata.genome_version}' | 21 -configOption '${snpDb.snpeff_db.metadata.genome_version}'.genome='${snpDb.snpeff_db.metadata.genome_version}' |
22 '${snpDb.snpeff_db.metadata.genome_version}' | 22 '${snpDb.snpeff_db.metadata.genome_version}' |
23 #else | 23 #else |
24 -dataDir "\$PWD/temp" | |
24 -download | 25 -download |
25 '$snpDb.genome_version' | 26 '$snpDb.genome_version' |
26 #end if | 27 #end if |
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' | 28 | 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' |
28 ]]></command> | 29 ]]></command> |
45 </param> | 46 </param> |
46 </when> | 47 </when> |
47 <when value="history"> | 48 <when value="history"> |
48 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data"> | 49 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data"> |
49 <help>This can only be used on databases in your history that were downloaded using the snpEff download tool.</help> | 50 <help>This can only be used on databases in your history that were downloaded using the snpEff download tool.</help> |
50 <options options_filter_attribute="metadata.SNPEFF_VERSION" > | 51 <options options_filter_attribute="metadata.snpeff_version" > |
51 <filter type="add_value" value="@SNPEFF_VERSION@" /> | 52 <filter type="add_value" value="@SNPEFF_VERSION@" /> |
52 </options> | 53 </options> |
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> | 54 <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> |
54 </param> | 55 </param> |
55 </when> | 56 </when> |
56 <when value="named"> | 57 <when value="named"> |
57 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> | 58 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)"> |
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> | 59 <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> |
59 <validator type="regex" message="A genome version name is required">\S+</validator> | 60 <validator type="regex" message="A genome version name is required">\S+</validator> |
60 </param> | 61 </param> |
61 </when> | 62 </when> |
62 <when value="custom"> | 63 <when value="custom"> |
63 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data"> | 64 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data"> |
64 <help>This can only be used on databases in your history that were created using the snpEff build tool.</help> | 65 <help>This can only be used on databases in your history that were created using the snpEff build tool.</help> |
65 <options options_filter_attribute="metadata.SNPEFF_VERSION" > | 66 <options options_filter_attribute="metadata.snpeff_version" > |
66 <filter type="add_value" value="@SNPEFF_VERSION@" /> | 67 <filter type="add_value" value="@SNPEFF_VERSION@" /> |
67 </options> | 68 </options> |
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> | 69 <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> |
69 </param> | 70 </param> |
70 </when> | 71 </when> |
71 </conditional> | 72 </conditional> |
72 </inputs> | 73 </inputs> |
73 <outputs> | 74 <outputs> |