Mercurial > repos > iuc > snpeff
comparison snpEff_create_db.xml @ 27:9473cd297a76 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit af2e922183065d2a950e07b4027cc6600503d38a
| author | iuc |
|---|---|
| date | Wed, 22 Nov 2023 19:44:16 +0000 |
| parents | 5c7b70713fb5 |
| children |
comparison
equal
deleted
inserted
replaced
| 26:5b80f544c67f | 27:9473cd297a76 |
|---|---|
| 1 <tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy5"> | 1 <tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy6" profile="22.01"> |
| 2 <description> database from Genbank or GFF record</description> | 2 <description> database from Genbank or GFF record</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>snpEff_macros.xml</import> | 4 <import>snpEff_macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <requirements> | 6 <requirements> |
| 12 <command><![CDATA[ | 12 <command><![CDATA[ |
| 13 #if str($input_type.input_type_selector) == "gb" and str($input_type.fasta) == "yes": | 13 #if str($input_type.input_type_selector) == "gb" and str($input_type.fasta) == "yes": |
| 14 python3 '$__tool_directory__/gbk2fa.py' '${input_type.input}' '${output_fasta}' ${input_type.remove_version} && | 14 python3 '$__tool_directory__/gbk2fa.py' '${input_type.input}' '${output_fasta}' ${input_type.remove_version} && |
| 15 #end if | 15 #end if |
| 16 | 16 |
| 17 mkdir -p '${snpeff_output.files_path}'/'${genome_version}' && | 17 mkdir -p '${snpeff_output.files_path}/${genome_version}' && |
| 18 mkdir -p snpeff_output/'${genome_version}' && | |
| 18 | 19 |
| 19 #if str($input_type.input_type_selector) == "gb": | 20 #if str($input_type.input_type_selector) == "gb": |
| 20 #if $input_type.input.is_of_type("genbank"): | 21 #if $input_type.input.is_of_type("genbank"): |
| 21 ln -s '${input_type.input}' '${snpeff_output.files_path}/${genome_version}/genes.gbk' && | 22 ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.gbk' && |
| 22 #elif $input_type.input.is_of_type("genbank.gz"): | 23 #elif $input_type.input.is_of_type("genbank.gz"): |
| 23 ln -s '${input_type.input}' '${snpeff_output.files_path}/${genome_version}/genes.gbk.gz' && | 24 ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.gbk.gz' && |
| 24 #end if | 25 #end if |
| 25 #else: | 26 #else: |
| 26 #if $input_type.reference_source.reference_source_selector == "history": | 27 #if $input_type.reference_source.reference_source_selector == "history": |
| 27 #if $input_type.reference_source.input_fasta.is_of_type("fasta"): | 28 #if $input_type.reference_source.input_fasta.is_of_type("fasta"): |
| 28 ln -s '${input_type.reference_source.input_fasta}' '${snpeff_output.files_path}/${genome_version}/sequences.fa' && | 29 ln -s '${input_type.reference_source.input_fasta}' 'snpeff_output/${genome_version}/sequences.fa' && |
| 29 #elif $input_type.reference_source.input_fasta.is_of_type("fasta.gz"): | 30 #elif $input_type.reference_source.input_fasta.is_of_type("fasta.gz"): |
| 30 ln -s '${input_type.reference_source.input_fasta}' '${snpeff_output.files_path}/${genome_version}/sequences.fa.gz' && | 31 ln -s '${input_type.reference_source.input_fasta}' 'snpeff_output/${genome_version}/sequences.fa.gz' && |
| 31 #end if | 32 #end if |
| 32 #elif $input_type.reference_source.reference_source_selector == "cached": | 33 #elif $input_type.reference_source.reference_source_selector == "cached": |
| 33 ln -s '${input_type.reference_source.ref_file.fields.path}' '${snpeff_output.files_path}/${genome_version}/sequences.fa' && | 34 ln -s '${input_type.reference_source.ref_file.fields.path}' 'snpeff_output/${genome_version}/sequences.fa' && |
| 34 #end if | 35 #end if |
| 35 ln -s '${input_type.input}' '${snpeff_output.files_path}/${genome_version}/genes.${input_type.input_type_selector}' && | 36 ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.${input_type.input_type_selector}' && |
| 36 #end if | 37 #end if |
| 37 | 38 |
| 38 snpEff @JAVA_OPTIONS@ build -v | 39 snpEff @JAVA_OPTIONS@ build -v |
| 39 -configOption '${genome_version}'.genome='${genome_version}' | 40 -configOption '${genome_version}'.genome='${genome_version}' |
| 40 -configOption '${genome_version}'.codonTable='${codon_table}' | 41 -configOption '${genome_version}'.codonTable='${codon_table}' |
| 43 #elif str($input_type.input_type_selector) == "gff": | 44 #elif str($input_type.input_type_selector) == "gff": |
| 44 -gff3 | 45 -gff3 |
| 45 #elif str($input_type.input_type_selector) == "gtf": | 46 #elif str($input_type.input_type_selector) == "gtf": |
| 46 -gtf22 | 47 -gtf22 |
| 47 #end if | 48 #end if |
| 48 -dataDir '${snpeff_output.files_path}' '${genome_version}' && | 49 -dataDir "\$(pwd)/snpeff_output" '${genome_version}' && |
| 50 mv snpeff_output/'${genome_version}'/*.bin '${snpeff_output.files_path}/${genome_version}' && | |
| 49 echo '${genome_version}.genome : ${genome_version}' >> '${snpeff_output.files_path}'/snpEff.config && | 51 echo '${genome_version}.genome : ${genome_version}' >> '${snpeff_output.files_path}'/snpEff.config && |
| 50 echo '${genome_version}.codonTable : ${codon_table}' >> '${snpeff_output.files_path}'/snpEff.config | 52 echo '${genome_version}.codonTable : ${codon_table}' >> '${snpeff_output.files_path}'/snpEff.config |
| 51 ]]></command> | 53 ]]></command> |
| 52 <inputs> | 54 <inputs> |
| 53 <param name="genome_version" type="text" value="" label="Name for the database" help="For E. coli K12, for example, you may want to use 'EcK12'. Note: Spaces are not allowed in the name and will get converted to underscores."> | 55 <param name="genome_version" type="text" value="" label="Name for the database" help="For E. coli K12, for example, you may want to use 'EcK12'. Note: Spaces are not allowed in the name and will get converted to underscores."> |