Mercurial > repos > iuc > snpeff
annotate snpEff_create_db.xml @ 17:32705945a08e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 0310c734a944901fffb975937b20f55bfc1d9f46
| author | iuc |
|---|---|
| date | Sat, 07 Apr 2018 15:45:45 -0400 |
| parents | 7c4ede6d88a2 |
| children | 718842784732 |
| rev | line source |
|---|---|
|
17
32705945a08e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 0310c734a944901fffb975937b20f55bfc1d9f46
iuc
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1 <tool id="snpEff_build_gb" name="SnpEff build:" version="@wrapper_version@.galaxy2"> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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2 <description> database from Genbank record</description> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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3 <macros> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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4 <import>snpEff_macros.xml</import> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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5 </macros> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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6 <requirements> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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7 <expand macro="requirement" /> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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8 <requirement type="package" version="3.6">python</requirement> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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9 <requirement type="package" version="1.70">biopython</requirement> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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10 <requirement type="package" version="0.4.15">python-magic</requirement> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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11 <requirement type="package" version="5.32">libmagic</requirement> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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12 </requirements> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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13 <expand macro="stdio" /> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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14 <expand macro="version_command" /> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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15 <command><![CDATA[ |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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16 |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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17 #if str( $fasta.fasta_selector ) == "yes": |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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18 python3 '$__tool_directory__/gbk2fa.py' '${input_gbk}' '${output_fasta}' |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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19 #if $fasta.remove_version: |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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20 '${fasta.remove_version}' |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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21 #end if |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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22 && |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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23 #end if |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
diff
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24 |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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25 mkdir -p '${snpeff_output.files_path}'/'${genome_version}' && |
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16
7c4ede6d88a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents:
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26 |
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14
a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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27 ln -s '${input_gbk}' '${snpeff_output.files_path}'/'${genome_version}'/genes.gbk && |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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28 |
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16
7c4ede6d88a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents:
15
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29 snpEff @java_options@ build -v |
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7c4ede6d88a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
iuc
parents:
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30 -configOption '${genome_version}'.genome='${genome_version}' |
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14
a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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31 -configOption '${genome_version}'.codonTable='${codon_table}' |
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17
32705945a08e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 0310c734a944901fffb975937b20f55bfc1d9f46
iuc
parents:
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32 -genbank -dataDir '${snpeff_output.files_path}' '${genome_version}' && |
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32705945a08e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 0310c734a944901fffb975937b20f55bfc1d9f46
iuc
parents:
16
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33 echo "${genome_version}.genome : ${genome_version}" >> '${snpeff_output.files_path}'/snpEff.config && |
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32705945a08e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 0310c734a944901fffb975937b20f55bfc1d9f46
iuc
parents:
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34 echo "${genome_version}.codonTable : ${codon_table}" >> '${snpeff_output.files_path}'/snpEff.config |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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35 |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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36 ]]></command> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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37 <inputs> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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38 <param name="genome_version" type="text" value="" label="Name for the database" help="for E. coli K12 you may want to use 'EcK12' etc."> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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39 <validator type="regex" message="A genome version name is required">\S+</validator> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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40 </param> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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41 <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"/> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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42 <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"> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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43 <option selected="true" value="Standard">Standard</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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44 <option value="Vertebrate_Mitochondrial">Vertebrate_Mitochondrial</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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45 <option value="Yeast_Mitochondrial">Yeast_Mitochondrial</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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46 <option value="Mold_Mitochondrial">Mold_Mitochondrial</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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47 <option value="Protozoan_Mitochondrial">Protozoan_Mitochondrial</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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48 <option value="Coelenterate">Coelenterate</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
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49 <option value="Mitochondrial">Mitochondrial</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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50 <option value="Mycoplasma">Mycoplasma</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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51 <option value="Spiroplasma">Spiroplasma</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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52 <option value="Invertebrate_Mitochondrial">Invertebrate_Mitochondrial</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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53 <option value="Ciliate_Nuclear">Ciliate_Nuclear</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
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54 <option value="Dasycladacean_Nuclear">Dasycladacean_Nuclear</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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55 <option value="Hexamita_Nuclear">Hexamita_Nuclear</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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56 <option value="Echinoderm_Mitochondrial">Echinoderm_Mitochondrial</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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57 <option value="Flatworm_Mitochondrial">Flatworm_Mitochondrial</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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58 <option value="Euplotid_Nuclear">Euplotid_Nuclear</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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59 <option value="Bacterial_and_Plant_Plastid">Bacterial_and_Plant_Plastid</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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60 <option value="Alternative_Yeast_Nuclear">Alternative_Yeast_Nuclear</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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61 <option value="Ascidian_Mitochondrial">Ascidian_Mitochondrial</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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62 <option value="Alternative_Flatworm_Mitochondrial">Alternative_Flatworm_Mitochondrial</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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63 <option value="Blepharisma_Macronuclear">Blepharisma_Macronuclear</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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64 <option value="Chlorophycean_Mitochondrial">Chlorophycean_Mitochondrial</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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65 <option value="Trematode_Mitochondrial">Trematode_Mitochondrial</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
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parents:
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66 <option value="Scenedesmus_obliquus_Mitochondrial">Scenedesmus_obliquus_Mitochondrial</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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67 <option value="Thraustochytrium_Mitochondrial">Thraustochytrium_Mitochondrial</option> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
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68 </param> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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69 <conditional name="fasta"> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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70 <param name="fasta_selector" 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"> |
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a7c106b938dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
iuc
parents:
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71 <option value="yes" selected="true">Yes</option> |
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72 <option value="no">No</option> |
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73 </param> |
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74 <when value="yes"> |
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75 <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"/> |
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76 </when> |
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77 <when value="no"/> |
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78 </conditional> |
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79 </inputs> |
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80 <outputs> |
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81 <data name="snpeff_output" format="snpeffdb" label="@snpeff_version@ database for ${genome_version}"/> |
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15
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82 <data name="output_fasta" format="fasta" label="Fasta sequences for ${genome_version}"> |
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14
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83 <filter>fasta['fasta_selector'] == 'yes'</filter> |
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84 </data> |
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85 </outputs> |
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86 <tests> |
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87 <test> |
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88 <param name="genome_version" value="pBR322"/> |
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89 <param name="input_gbk" value="pBR322.gbk" /> |
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90 <output name="snpeff_output"> |
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91 <assert_contents> |
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92 <has_text text="pBR322" /> |
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93 </assert_contents> |
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94 </output> |
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95 <output name="output_fasta" value="pBR322.fna"/> |
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96 </test> |
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97 </tests> |
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98 <help><![CDATA[ |
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99 **What it does** |
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100 |
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101 This tool uses `"snpEff build -genbank"` command to create a snpEff database from a Genbank dataset. If **Parse Genbank into Fasta** is selected (the default behavior) the tool will also convert Genbank dataset into a single FASTA dataset. |
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102 |
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103 |
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104 Using Genbank data for creating databases has several advantages: |
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105 |
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106 #. Genbank files contains annotations (such as locations of genes) together with sequences. This was one ensures that these two are in sync with each other |
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107 #. When you are analyzing small genomes it is much more convenient to create a database on the fly and use it. |
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108 |
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109 ------- |
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110 |
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111 .. class:: infomark |
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112 |
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113 **The usage scenario** |
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114 |
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115 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: |
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116 |
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117 #. Download genome from `NCBI <https://www.ncbi.nlm.nih.gov>`_ into Galaxy. |
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118 #. Use this tool to generate a snpEff database and FASTA sequences from the file you downloaded at step 1. |
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119 #. Use your Illumina reads to map against FASTA dataset generated in the previous step using BWA-MEM. |
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120 #. Call variants using **Freebayes**. |
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121 #. Annotate vcf output of Freebayes with **SnpEff eff** using database generated at step 2 (using *Custom* option for **Genome source** parameter). |
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122 |
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123 In this scenario Genbank dataset is used twice. First, it is used to produce FASTA sequences that are using by BWA to map against. Second, it is used to create snpEff database. This guarantees that you will not have any issues related to reference sequence naming. |
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124 |
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125 @snpeff_in_galaxy_info@ |
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126 @external_documentation@ |
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127 ]]> |
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128 </help> |
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129 <expand macro="citations" /> |
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130 </tool> |