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comparison snpEff_create_db.xml @ 25:166c2e25a3b6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit aeb660e92b9eb60dc5f90a2078f552018cca96e0"
author iuc
date Tue, 15 Oct 2019 14:12:30 -0400
parents 9939612ba3cf
children b1b327f475ac
comparison
equal deleted inserted replaced
24:4c790901c495 25:166c2e25a3b6
1 <tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy3"> 1 <tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy4">
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>
30 ln -s '${input_type.input_gbk}' '${snpeff_output.files_path}'/'${genome_version}'/genes.gbk && 30 ln -s '${input_type.input_gbk}' '${snpeff_output.files_path}'/'${genome_version}'/genes.gbk &&
31 #elif $input_type.input_gbk.is_of_type("genbank.gz"): 31 #elif $input_type.input_gbk.is_of_type("genbank.gz"):
32 ln -s '${input_type.input_gbk}' '${snpeff_output.files_path}'/'${genome_version}'/genes.gbk.gz && 32 ln -s '${input_type.input_gbk}' '${snpeff_output.files_path}'/'${genome_version}'/genes.gbk.gz &&
33 #end if 33 #end if
34 #elif str( $input_type.input_type_selector ) == "gff": 34 #elif str( $input_type.input_type_selector ) == "gff":
35 #if $input_type.input_fasta.is_of_type("fasta"): 35 #if $input_type.reference_source.reference_source_selector == "history":
36 ln -s '${input_type.input_fasta}' '${snpeff_output.files_path}'/'${genome_version}'/sequences.fa && 36 #if $input_type.reference_source.input_fasta.is_of_type("fasta"):
37 #elif $input_type.input_fasta.is_of_type("fasta.gz"): 37 ln -s '${input_type.reference_source.input_fasta}' '${snpeff_output.files_path}'/'${genome_version}'/sequences.fa &&
38 ln -s '${input_type.input_fasta}' '${snpeff_output.files_path}'/'${genome_version}'/sequences.fa.gz && 38 #elif $input_type.reference_source.input_fasta.is_of_type("fasta.gz"):
39 #end if 39 ln -s '${input_type.reference_source.input_fasta}' '${snpeff_output.files_path}'/'${genome_version}'/sequences.fa.gz &&
40 #end if
41 #elif $input_type.reference_source.reference_source_selector == "cached":
42 ln -s '${input_type.reference_source.ref_file.fields.path}' '${snpeff_output.files_path}'/'${genome_version}'/sequences.fa &&
43 #end if
40 ln -s '${input_type.input_gff}' '${snpeff_output.files_path}'/'${genome_version}'/genes.gff && 44 ln -s '${input_type.input_gff}' '${snpeff_output.files_path}'/'${genome_version}'/genes.gff &&
45 #elif str( $input_type.input_type_selector ) == "gtf":
46 #if $input_type.reference_source.reference_source_selector == "history":
47 #if $input_type.reference_source.input_fasta.is_of_type("fasta"):
48 ln -s '${input_type.reference_source.input_fasta}' '${snpeff_output.files_path}'/'${genome_version}'/sequences.fa &&
49 #elif $input_type.reference_source.input_fasta.is_of_type("fasta.gz"):
50 ln -s '${input_type.reference_source.input_fasta}' '${snpeff_output.files_path}'/'${genome_version}'/sequences.fa.gz &&
51 #end if
52 #elif $input_type.reference_source.reference_source_selector == "cached":
53 ln -s '${input_type.reference_source.ref_file.fields.path}' '${snpeff_output.files_path}'/'${genome_version}'/sequences.fa &&
54 #end if
55 ln -s '${input_type.input_gtf}' '${snpeff_output.files_path}'/'${genome_version}'/genes.gtf &&
41 #end if 56 #end if
42 57
43 snpEff @JAVA_OPTIONS@ build -v 58 snpEff @JAVA_OPTIONS@ build -v
44 -configOption '${genome_version}'.genome='${genome_version}' 59 -configOption '${genome_version}'.genome='${genome_version}'
45 -configOption '${genome_version}'.codonTable='${codon_table}' 60 -configOption '${genome_version}'.codonTable='${codon_table}'
46 #if str( $input_type.input_type_selector ) == "gb": 61 #if str( $input_type.input_type_selector ) == "gb":
47 -genbank 62 -genbank
48 #elif str( $input_type.input_type_selector ) == "gff": 63 #elif str( $input_type.input_type_selector ) == "gff":
49 -gff3 64 -gff3
65 #elif str( $input_type.input_type_selector ) == "gtf":
66 -gtf22
50 #end if 67 #end if
51 -dataDir '${snpeff_output.files_path}' '${genome_version}' && 68 -dataDir '${snpeff_output.files_path}' '${genome_version}' &&
52 echo "${genome_version}.genome : ${genome_version}" >> '${snpeff_output.files_path}'/snpEff.config && 69 echo "${genome_version}.genome : ${genome_version}" >> '${snpeff_output.files_path}'/snpEff.config &&
53 echo "${genome_version}.codonTable : ${codon_table}" >> '${snpeff_output.files_path}'/snpEff.config 70 echo "${genome_version}.codonTable : ${codon_table}" >> '${snpeff_output.files_path}'/snpEff.config
54 71
59 </param> 76 </param>
60 <conditional name="input_type"> 77 <conditional name="input_type">
61 <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"> 78 <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">
62 <option value="gb" selected="true">GenBank</option> 79 <option value="gb" selected="true">GenBank</option>
63 <option value="gff">GFF</option> 80 <option value="gff">GFF</option>
81 <option value="gtf">GTF</option>
64 </param> 82 </param>
65 <when value="gb"> 83 <when value="gb">
66 <param name="input_gbk" type="data" format="genbank,genbank.gz" label="Genbank dataset to build database from" help="This Genbank file will be used to generate snpEff database"/> 84 <param name="input_gbk" type="data" format="genbank,genbank.gz" label="Genbank dataset to build database from" help="This Genbank file will be used to generate snpEff database"/>
67 <param name="fasta" type="select" display="radio" label="Parse Genbank into Fasta" help="This will generate an additional dataset containing all sequences from Genbank file in FASTA format"> 85 <param name="fasta" type="select" display="radio" label="Parse Genbank into Fasta" help="This will generate an additional dataset containing all sequences from Genbank file in FASTA format">
68 <option value="yes" selected="true">Yes</option> 86 <option value="yes" selected="true">Yes</option>
70 </param> 88 </param>
71 <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" /> 89 <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" />
72 </when> 90 </when>
73 <when value="gff"> 91 <when value="gff">
74 <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"/> 92 <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"/>
75 <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."/> 93 <conditional name="reference_source">
94 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
95 <option value="cached">Locally cached</option>
96 <option value="history">History</option>
97 </param>
98 <when value="cached">
99 <param name="ref_file" type="select" label="Select reference genome">
100 <options from_data_table="fasta_indexes"/>
101 </param>
102 </when>
103 <when value="history">
104 <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."/>
105 </when>
106 </conditional>
107 </when>
108 <when value="gtf">
109 <param name="input_gtf" type="data" format="gtf" label="GTF dataset to build database from" help="This GTF file will be used to generate snpEff database"/>
110 <conditional name="reference_source">
111 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
112 <option value="cached">Locally cached</option>
113 <option value="history">History</option>
114 </param>
115 <when value="cached">
116 <param name="ref_file" type="select" label="Select reference genome">
117 <options from_data_table="fasta_indexes"/>
118 </param>
119 </when>
120 <when value="history">
121 <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."/>
122 </when>
123 </conditional>
76 </when> 124 </when>
77 </conditional> 125 </conditional>
78 <param name="codon_table" type="select" label="Select genetic code for this sequence" help="If this sequence uses non-standard genetic code, select one from these options"> 126 <param name="codon_table" type="select" label="Select genetic code for this sequence" help="If this sequence uses non-standard genetic code, select one from these options">
79 <option selected="true" value="Standard">Standard</option> 127 <option selected="true" value="Standard">Standard</option>
80 <option value="Vertebrate_Mitochondrial">Vertebrate_Mitochondrial</option> 128 <option value="Vertebrate_Mitochondrial">Vertebrate_Mitochondrial</option>
134 <output name="output_fasta" value="pBR322_test1.fna"/> 182 <output name="output_fasta" value="pBR322_test1.fna"/>
135 </test> 183 </test>
136 <test> 184 <test>
137 <param name="genome_version" value="pBR322"/> 185 <param name="genome_version" value="pBR322"/>
138 <param name="input_type_selector" value="gff"/> 186 <param name="input_type_selector" value="gff"/>
187 <param name="reference_source_selector" value="history"/>
139 <param name="input_fasta" value="pBR322_test2.fna" /> 188 <param name="input_fasta" value="pBR322_test2.fna" />
140 <param name="input_gff" value="pBR322.gff3" /> 189 <param name="input_gff" value="pBR322.gff3" />
141 <output name="snpeff_output"> 190 <output name="snpeff_output">
142 <assert_contents> 191 <assert_contents>
143 <has_text text="pBR322" /> 192 <has_text text="pBR322" />
145 </output> 194 </output>
146 </test> 195 </test>
147 <test> 196 <test>
148 <param name="genome_version" value="pBR322"/> 197 <param name="genome_version" value="pBR322"/>
149 <param name="input_type_selector" value="gff"/> 198 <param name="input_type_selector" value="gff"/>
199 <param name="reference_source_selector" value="history"/>
150 <param name="input_fasta" value="pBR322_test2.fna.gz" /> 200 <param name="input_fasta" value="pBR322_test2.fna.gz" />
151 <param name="input_gff" value="pBR322.gff3" /> 201 <param name="input_gff" value="pBR322.gff3" />
152 <output name="snpeff_output"> 202 <output name="snpeff_output">
153 <assert_contents> 203 <assert_contents>
154 <has_text text="pBR322" /> 204 <has_text text="pBR322" />
205 </assert_contents>
206 </output>
207 </test>
208 <test>
209 <param name="genome_version" value="Saccharomyces_mito"/>
210 <param name="input_type_selector" value="gtf"/>
211 <param name="reference_source_selector" value="history"/>
212 <param name="input_fasta" value="Saccharomyces_mito.fa.gz" />
213 <param name="input_gtf" value="Saccharomyces_mito.gtf" />
214 <output name="snpeff_output">
215 <assert_contents>
216 <has_text text="Saccharomyces_mito" />
155 </assert_contents> 217 </assert_contents>
156 </output> 218 </output>
157 </test> 219 </test>
158 </tests> 220 </tests>
159 <help><![CDATA[ 221 <help><![CDATA[