Mercurial > repos > iuc > snpeff
annotate snpeff_get_chr_names.xml @ 24:cfcf33df7fc0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4366b6a23223f84039a0590cf0d7079b83d8f84"
author | iuc |
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date | Wed, 13 Oct 2021 23:30:29 +0000 |
parents | 74aebe30fb52 |
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rev | line source |
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74aebe30fb52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 67da1a478db26ad45f36a673218d526f8962d72f"
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1 <tool id="snpEff_get_chr_names" name="SnpEff chromosome-info:" version="@WRAPPER_VERSION@.galaxy2"> |
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dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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2 <description>list chromosome names/lengths</description> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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3 <macros> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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4 <import>snpEff_macros.xml</import> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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5 </macros> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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6 <requirements> |
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74aebe30fb52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 67da1a478db26ad45f36a673218d526f8962d72f"
iuc
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7 <expand macro="requirement"> |
74aebe30fb52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 67da1a478db26ad45f36a673218d526f8962d72f"
iuc
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8 <requirement type="package" version="5.0.1">gawk</requirement> |
74aebe30fb52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 67da1a478db26ad45f36a673218d526f8962d72f"
iuc
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9 </expand> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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10 </requirements> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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11 <expand macro="stdio" /> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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12 <expand macro="version_command" /> |
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74aebe30fb52
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 67da1a478db26ad45f36a673218d526f8962d72f"
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13 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
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14 snpEff @JAVA_OPTIONS@ dump |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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15 #if $snpDb.genomeSrc == 'cached': |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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16 -dataDir ${snpDb.genomeVersion.fields.path} |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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17 $snpDb.genomeVersion |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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18 #elif $snpDb.genomeSrc == 'history': |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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19 -dataDir '${snpDb.snpeff_db.extra_files_path}' |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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20 '${snpDb.snpeff_db.metadata.genome_version}' |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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21 #elif $snpDb.genomeSrc == 'custom': |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
parents:
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22 -dataDir '${snpDb.snpeff_db.extra_files_path}' |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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23 -configOption '${snpDb.snpeff_db.metadata.genome_version}'.genome='${snpDb.snpeff_db.metadata.genome_version}' |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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24 '${snpDb.snpeff_db.metadata.genome_version}' |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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25 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
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26 -dataDir "\$PWD/temp" |
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dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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27 -download |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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28 '$snpDb.genome_version' |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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29 #end if |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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30 | awk '/# Chromosomes/{y=1;next}y' | grep "#" | grep -E "[0-9]" | awk 'BEGIN {err=1;} {c=$0;sub(/^[^a-zA-Z0-9_]+/, "", c) && err=0; sub(/[^a-zA-Z0-9_]+/, "\t", c) && err=0; sub(/[^0-9]*$/, "", c) && err=0; print c } END {exit err}' > '$chr_names' |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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31 ]]></command> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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32 <inputs> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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33 <conditional name="snpDb"> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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34 <param name="genomeSrc" type="select" label="Genome source"> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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35 <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well --> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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36 <option value="cached">Locally installed snpEff database</option> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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37 <option value="history">Downloaded snpEff database in your history</option> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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38 <option value="named">Download on demand</option> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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39 <option value="custom">Custom snpEff database in your history</option> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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40 </param> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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41 <when value="cached"> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
iuc
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42 <param name="genomeVersion" type="select" label="Genome"> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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43 <help>This can only be used on built-in databases manually configured by your galaxy admin.</help> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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44 <options from_data_table="snpeffv_genomedb"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
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45 <filter type="static_value" name="SNPEFF_VERSION" value="@SNPEFF_VERSION@" column="1"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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46 <filter type="unique_value" column="2" /> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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47 </options> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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48 </param> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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49 </when> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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50 <when value="history"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
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51 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data"> |
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dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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52 <help>This can only be used on databases in your history that were downloaded using the snpEff download tool.</help> |
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8f92c2b26e6d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
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53 <options options_filter_attribute="metadata.snpeff_version" > |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
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54 <filter type="add_value" value="@SNPEFF_VERSION@" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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55 </options> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
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56 <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator> |
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dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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57 </param> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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58 </when> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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59 <when value="named"> |
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8f92c2b26e6d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
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60 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)"> |
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61 <help>The list of available databases can be obtained with 'SnpEff databases' tool. If the database name is not found, locate a database here and download it in your history.</help> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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62 <validator type="regex" message="A genome version name is required">\S+</validator> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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63 </param> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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64 </when> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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65 <when value="custom"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
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66 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data"> |
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67 <help>This can only be used on databases in your history that were created using the snpEff build tool.</help> |
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68 <options options_filter_attribute="metadata.snpeff_version" > |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05
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69 <filter type="add_value" value="@SNPEFF_VERSION@" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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70 </options> |
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71 <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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72 </param> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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73 </when> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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74 </conditional> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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75 </inputs> |
dd3622f501f3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 680a6111d751031f02233715a529a336ad4b2bf4
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76 <outputs> |
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77 <data format="tabular" name="chr_names" label="Chromosome names and sizes"/> |
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78 </outputs> |
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79 <tests> |
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80 <test> |
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81 <param name="genomeSrc" value="named"/> |
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82 <param name="genome_version" value="Bacillus_subtilis_subsp_subtilis_str_168"/> |
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83 <output name="chr_names"> |
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84 <assert_contents> |
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85 <has_text text="Chromosome" /> |
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86 <has_text text="4215606" /> |
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87 </assert_contents> |
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88 </output> |
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89 </test> |
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90 <test expect_failure="True"> |
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91 <param name="genomeSrc" value="named"/> |
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92 <param name="genome_version" value="should_not_match"/> |
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93 </test> |
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94 </tests> |
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95 <help><![CDATA[ |
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96 |
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97 **What it does** |
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98 |
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99 This tool outputs a tab-delimited file of chromosome names and their lengths, as they are in the selected genome/SnpEff database. The output can be used to validate and rename chromosomes in VCF files in order to annotate its records. |
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100 |
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101 Note, make sure that the genome you select from the snpEff database precisely matches the one used in your analysis. As a cursory check, you can use the chromosome lengths in this output to match those in your reference, however the lengths can match, but the version may still differ. |
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102 |
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103 Known issue: this strategy will not work if more than 1 chromosome in the same genome has the same length. |
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104 |
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105 ------- |
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106 |
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107 .. class:: infomark |
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108 |
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109 **The usage scenario** |
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110 |
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111 Suppose you want to use snpEff to annotate a VCF file that was generated using an mouse reference with a different chromosome naming convention than in the snpEff database. To do this you can: |
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112 |
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113 #. Use `SnpEff databases` to find the precise genome name for mouse data (e.g. "mm10") as it appears in the snpEff database. |
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114 #. List the chromosome names using this tool. Either select a built-in genome, one in your history, or select "Download on demand" and enter the genome version obtained in the previous step (which only actually downloads if snpEff doesn't already have it). |
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115 #. Check that the chromosomes in the SnpEff database are the same as the reference you used (e.g. as a cursory check, ensure the chromosome lengths reported from the SnpEff database match those of your reference). |
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116 #. Edit your vcf file to replace the chromosome names with the ones the SnpEff database uses. |
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117 #. Use **SnpEff eff** and supply the edited VCF file. |
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118 |
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119 ]]></help> |
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120 <expand macro="citations" /> |
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121 </tool> |