Mercurial > repos > iuc > snpeff
diff snpEff_create_db.xml @ 17:65ae79bddc69 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102
| author | iuc |
|---|---|
| date | Thu, 06 Sep 2018 13:23:57 -0400 |
| parents | 479c4f2f4826 |
| children | de67e5082c48 |
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--- a/snpEff_create_db.xml Tue Aug 28 03:03:45 2018 -0400 +++ b/snpEff_create_db.xml Thu Sep 06 13:23:57 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="snpEff_build_gb" name="SnpEff build:" version="@wrapper_version@.galaxy3"> +<tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy3"> <description> database from Genbank or GFF record</description> <macros> <import>snpEff_macros.xml</import> @@ -13,7 +13,6 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ - #if str( $input_type.input_type_selector ) == "gb": #if str( $input_type.fasta ) == "yes": python3 '$__tool_directory__/gbk2fa.py' '${input_type.input_gbk}' '${output_fasta}' @@ -41,7 +40,7 @@ ln -s '${input_type.input_gff}' '${snpeff_output.files_path}'/'${genome_version}'/genes.gff && #end if - snpEff @java_options@ build -v + snpEff @JAVA_OPTIONS@ build -v -configOption '${genome_version}'.genome='${genome_version}' -configOption '${genome_version}'.codonTable='${codon_table}' #if str( $input_type.input_type_selector ) == "gb": @@ -55,8 +54,8 @@ ]]></command> <inputs> - <param name="genome_version" type="text" value="" label="Name for the database" help="for E. coli K12 you may want to use 'EcK12' etc."> - <validator type="regex" message="A genome version name is required">\S+</validator> + <param name="genome_version" type="text" value="" label="Name for the database" help="For E. coli K12 you may want to use 'EcK12' etc."> + <validator type="empty_field" message="A genome version name is required" /> </param> <conditional name="input_type"> <param name="input_type_selector" type="select" display="radio" label="Input annotations are in" help="Specify format for annotations you are using to create SnpEff database"> @@ -69,9 +68,9 @@ <option value="yes" selected="true">Yes</option> <option value="no">No</option> </param> - <param type="boolean" name="remove_version" truevalue="--remove_version" falsevalue="" checked="true" label="Remove sequence version label?" help="Genbank sequences have vesion numbers such as B000564.2. This option removes them leaving only B000564" argument="--remove_version"/> + <param argument="--remove_version" type="boolean" truevalue="--remove_version" falsevalue="" checked="true" label="Remove sequence version label?" help="Genbank sequences have vesion numbers such as B000564.2. This option removes them leaving only B000564" /> </when> - <when value="gff"> + <when value="gff"> <param name="input_gff" type="data" format="gff3" label="GFF dataset to build database from" help="This GFF file will be used to generate snpEff database"/> <param name="input_fasta" type="data" format="fasta,fasta.gz" label="Genome in FASTA format" help="This dataset is required for generating SnpEff database. See help section below."/> </when> @@ -105,7 +104,7 @@ </param> </inputs> <outputs> - <data name="snpeff_output" format="snpeffdb" label="@snpeff_version@ database for ${genome_version}"/> + <data name="snpeff_output" format="snpeffdb" label="@SNPEFF_VERSION@ database for ${genome_version}"/> <data name="output_fasta" format="fasta" label="Fasta sequences for ${genome_version}"> <filter>input_type['input_type_selector'] == 'gb'</filter> <filter>input_type['fasta'] == 'yes'</filter> @@ -160,7 +159,7 @@ <help><![CDATA[ **What it does** -This tool uses `"snpEff build -genbank"` or `"snpEff build -gff3"` commands to create a snpEff database. +This tool uses `"snpEff build -genbank"` or `"snpEff build -gff3"` commands to create a snpEff database. ------ @@ -170,12 +169,12 @@ Using Genbank data for creating databases has several advantages: - #. Genbank files contain annotations (such as locations of genes) together with sequences. This ensures that these two are in sync with each other. + #. Genbank files contain annotations (such as locations of genes) together with sequences. This ensures that these two are in sync with each other. #. When you are analyzing small genomes (or not so small) it is much more convenient to create a database on the fly and use it. .. class:: warningmark - SnpEff errors out on highly fragmented genomes containing multiple scaffolds. This is because a single gene may be split between multiple scaffolds causing SnpEff to crash. If this is happening use GFF route described below. + SnpEff errors out on highly fragmented genomes containing multiple scaffolds. This is because a single gene may be split between multiple scaffolds causing SnpEff to crash. If this is happening use GFF route described below. ------- @@ -184,7 +183,7 @@ Suppose you have a series of Illumina reads from an experiment involving *E. coli* K-12 MG1655. You want to map these reads to the reference genome of K-12 MG1655, call variants, and annotate them using snpEff. This tool enables you to follow the following analysis steps: #. Go to `NCBI <http://www.ncbi.nlm.nih.gov>`_ page for K-12 MG1655 genome (note that all NCBI genomes have similar list of files associated with them). - #. Copy URL for file with extension `gbff.gz` + #. Copy URL for file with extension `gbff.gz` #. Paste the URL into upload tool and set datatype to `genbank.gz`. #. Use this tool to generate a snpEff database and FASTA sequences from the dataset you've uploaded during the previous step. #. Use your Illumina reads to map against FASTA dataset generated in the previous step using BWA-MEM. @@ -208,7 +207,7 @@ ------ -**GFF usage scenario** +**GFF usage scenario** The following example also uses *E. coli* K-12 MG1655: @@ -219,8 +218,8 @@ #. Map your reads against the FASTA dataset and continue as described in the above example. -@snpeff_in_galaxy_info@ -@external_documentation@ +@SNPEFF_IN_GALAXY_INFO@ +@EXTERNAL_DOCUMENTATION@ ]]> </help> <expand macro="citations" />