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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4 |
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added:
snpeff_get_chr_names.xml |
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| diff -r 65ae79bddc69 -r dd3622f501f3 snpeff_get_chr_names.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpeff_get_chr_names.xml Fri Sep 07 10:30:41 2018 -0400 |
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| @@ -0,0 +1,118 @@ +<tool id="snpEff_get_chr_names" name="SnpEff chromosome-info:" version="@wrapper_version@.galaxy1"> + <description>list chromosome names/lengths</description> + <macros> + <import>snpEff_macros.xml</import> + </macros> + <requirements> + <expand macro="requirement" /> + </requirements> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + snpEff dump + #if $snpDb.genomeSrc == 'cached': + -dataDir ${snpDb.genomeVersion.fields.path} + $snpDb.genomeVersion + #elif $snpDb.genomeSrc == 'history': + -dataDir '${snpDb.snpeff_db.extra_files_path}' + '${snpDb.snpeff_db.metadata.genome_version}' + #elif $snpDb.genomeSrc == 'custom': + -dataDir '${snpDb.snpeff_db.extra_files_path}' + -configOption '${snpDb.snpeff_db.metadata.genome_version}'.genome='${snpDb.snpeff_db.metadata.genome_version}' + '${snpDb.snpeff_db.metadata.genome_version}' + #else + -download + '$snpDb.genome_version' + #end if + | 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' + ]]></command> + <inputs> + <conditional name="snpDb"> + <param name="genomeSrc" type="select" label="Genome source"> + <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well --> + <option value="cached">Locally installed snpEff database</option> + <option value="history">Downloaded snpEff database in your history</option> + <option value="named">Download on demand</option> + <option value="custom">Custom snpEff database in your history</option> + </param> + <when value="cached"> + <param name="genomeVersion" type="select" label="Genome"> + <help>This can only be used on built-in databases manually configured by your galaxy admin.</help> + <options from_data_table="snpeffv_genomedb"> + <filter type="static_value" name="snpeff_version" value="@snpeff_version@" column="1"/> + <filter type="unique_value" column="2" /> + </options> + </param> + </when> + <when value="history"> + <param name="snpeff_db" type="data" format="snpeffdb" label="@snpeff_version@ Genome Data"> + <help>This can only be used on databases in your history that were downloaded using the snpEff download tool.</help> + <options options_filter_attribute="metadata.snpeff_version" > + <filter type="add_value" value="@snpeff_version@" /> + </options> + <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> + </param> + </when> + <when value="named"> + <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> + <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> + <validator type="regex" message="A genome version name is required">\S+</validator> + </param> + </when> + <when value="custom"> + <param name="snpeff_db" type="data" format="snpeffdb" label="@snpeff_version@ Genome Data"> + <help>This can only be used on databases in your history that were created using the snpEff build tool.</help> + <options options_filter_attribute="metadata.snpeff_version" > + <filter type="add_value" value="@snpeff_version@" /> + </options> + <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> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data format="tabular" name="chr_names" label="Chromosome names and sizes"/> + </outputs> + <tests> + <test> + <param name="genomeSrc" value="named"/> + <param name="genome_version" value="Bacillus_subtilis_subsp_subtilis_str_168"/> + <output name="chr_names"> + <assert_contents> + <has_text text="Chromosome" /> + <has_text text="4215606" /> + </assert_contents> + </output> + </test> + <test expect_failure="True"> + <param name="genomeSrc" value="named"/> + <param name="genome_version" value="should_not_match"/> + </test> + </tests> + <help><![CDATA[ + +**What it does** + +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. + +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. + +Known issue: this strategy will not work if more than 1 chromosome in the same genome has the same length. + +------- + +.. class:: infomark + +**The usage scenario** + +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: + + #. Use `SnpEff databases` to find the precise genome name for mouse data (e.g. "mm10") as it appears in the snpEff database. + #. 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). + #. 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). + #. Edit your vcf file to replace the chromosome names with the ones the SnpEff database uses. + #. Use **SnpEff eff** and supply the edited VCF file. + + ]]></help> + <expand macro="citations" /> +</tool> |