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comparison snpEff_create_db.xml @ 30:0c8a8cd9dd5b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd
author iuc
date Sat, 28 Sep 2024 16:27:42 +0000
parents 030fe29d4c47
children b7029a54f73e
comparison
equal deleted inserted replaced
29:030fe29d4c47 30:0c8a8cd9dd5b
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.">
120 <filter>input_type['input_type_selector'] == 'gb'</filter> 122 <filter>input_type['input_type_selector'] == 'gb'</filter>
121 <filter>input_type['fasta'] == 'yes'</filter> 123 <filter>input_type['fasta'] == 'yes'</filter>
122 </data> 124 </data>
123 </outputs> 125 </outputs>
124 <tests> 126 <tests>
125 <test> 127 <test expect_num_outputs="2">
126 <param name="genome_version" value="pBR322"/> 128 <param name="genome_version" value="pBR322"/>
127 <param name="input_type_selector" value="gb"/> 129 <param name="input_type_selector" value="gb"/>
128 <param name="input" value="pBR322.gbk" /> 130 <param name="input" value="pBR322.gbk" />
129 <output name="snpeff_output"> 131 <output name="snpeff_output">
130 <assert_contents> 132 <assert_contents>
131 <has_text text="pBR322" /> 133 <has_text text="pBR322" />
132 </assert_contents> 134 </assert_contents>
133 </output> 135 </output>
134 <output name="output_fasta" value="pBR322_test1.fna"/> 136 <output name="output_fasta" value="pBR322_test1.fna"/>
135 </test> 137 </test>
136 <test> 138 <test expect_num_outputs="2">
137 <param name="genome_version" value="pBR322"/> 139 <param name="genome_version" value="pBR322"/>
138 <param name="input_type_selector" value="gb"/> 140 <param name="input_type_selector" value="gb"/>
139 <param name="input" value="pBR322.gbk.gz" /> 141 <param name="input" value="pBR322.gbk.gz" />
140 <output name="snpeff_output"> 142 <output name="snpeff_output">
141 <assert_contents> 143 <assert_contents>
142 <has_text text="pBR322" /> 144 <has_text text="pBR322" />
143 </assert_contents> 145 </assert_contents>
144 </output> 146 </output>
145 <output name="output_fasta" value="pBR322_test1.fna"/> 147 <output name="output_fasta" value="pBR322_test1.fna"/>
146 </test> 148 </test>
147 <test> 149 <test expect_num_outputs="1">
148 <param name="genome_version" value="pBR322"/> 150 <param name="genome_version" value="pBR322"/>
149 <param name="input_type_selector" value="gff"/> 151 <param name="input_type_selector" value="gff"/>
150 <param name="reference_source_selector" value="history"/> 152 <param name="reference_source_selector" value="history"/>
151 <param name="input_fasta" value="pBR322_test2.fna" /> 153 <param name="input_fasta" value="pBR322_test2.fna" />
152 <param name="input" value="pBR322.gff3"/> 154 <param name="input" value="pBR322.gff3"/>
154 <assert_contents> 156 <assert_contents>
155 <has_text text="pBR322" /> 157 <has_text text="pBR322" />
156 </assert_contents> 158 </assert_contents>
157 </output> 159 </output>
158 </test> 160 </test>
159 <test> 161 <test expect_num_outputs="1">
160 <param name="genome_version" value="pBR322"/> 162 <param name="genome_version" value="pBR322"/>
161 <param name="input_type_selector" value="gff"/> 163 <param name="input_type_selector" value="gff"/>
162 <param name="reference_source_selector" value="history"/> 164 <param name="reference_source_selector" value="history"/>
163 <param name="input_fasta" value="pBR322_test2.fna.gz" /> 165 <param name="input_fasta" value="pBR322_test2.fna.gz" />
164 <param name="input" value="pBR322.gff3"/> 166 <param name="input" value="pBR322.gff3"/>
166 <assert_contents> 168 <assert_contents>
167 <has_text text="pBR322" /> 169 <has_text text="pBR322" />
168 </assert_contents> 170 </assert_contents>
169 </output> 171 </output>
170 </test> 172 </test>
171 <test> 173 <test expect_num_outputs="1">
172 <param name="genome_version" value="Saccharomyces_mito"/> 174 <param name="genome_version" value="Saccharomyces_mito"/>
173 <param name="input_type_selector" value="gtf"/> 175 <param name="input_type_selector" value="gtf"/>
174 <param name="reference_source_selector" value="history"/> 176 <param name="reference_source_selector" value="history"/>
175 <param name="input_fasta" value="Saccharomyces_mito.fa.gz" /> 177 <param name="input_fasta" value="Saccharomyces_mito.fa.gz" />
176 <param name="input" value="Saccharomyces_mito.gtf" /> 178 <param name="input" value="Saccharomyces_mito.gtf" />