Mercurial > repos > iuc > data_manager_dram_database_downloader
annotate data_manager/data_manager_dram_download.xml @ 1:40c8fc0a2bb0 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 08664fb0e31a61514b787021d54ee5464be6043d
author | iuc |
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date | Tue, 13 Sep 2022 09:08:55 +0000 |
parents | bd342a6a5b0f |
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rev | line source |
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bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
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1 <tool id="data_manager_dram_download" name="DRAM: Download databases" version="1.3.5" tool_type="manage_data" profile="21.05"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
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2 <description>required by the DRAM suite of tools</description> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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3 <requirements> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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4 <requirement type="package" version="1.3.5">dram</requirement> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
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5 </requirements> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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6 <command detect_errors="exit_code"><![CDATA[ |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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7 python '$__tool_directory__/data_manager_dram_download.py' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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8 --out_file '$out_file' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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9 #if str($kofam_hmm_loc) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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10 --kofam_hmm_loc '$kofam_hmm_loc' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
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11 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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12 #if str($kofam_ko_list_loc) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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13 --kofam_ko_list_loc '$kofam_ko_list_loc' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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14 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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15 #if str($skip_uniref_cond.skip_uniref) == 'yes': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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16 --skip_uniref '$skip_uniref_cond.skip_uniref' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
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17 #else: |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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18 #if str($skip_uniref_cond.uniref_loc) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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19 --uniref_loc '$skip_uniref_cond.uniref_loc' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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20 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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21 --uniref_version $skip_uniref_cond.uniref_version |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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22 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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23 #if str($pfam_loc) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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24 --pfam_loc '$pfam_loc' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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25 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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26 #if str($pfam_hmm_dat) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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27 --pfam_hmm_dat '$pfam_hmm_dat' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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28 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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29 #if str($dbcan_loc) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
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30 --dbcan_loc '$dbcan_loc' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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31 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
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32 #if str($dbcan_fam_activities) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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33 --dbcan_fam_activities '$dbcan_fam_activities' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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34 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
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35 --dbcan_version $dbcan_version |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
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36 #if str($vogdb_loc) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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37 --vogdb_loc '$vogdb_loc' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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38 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
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39 #if str($vog_annotations) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
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40 --vog_annotations '$vog_annotations' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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41 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
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42 #if str($viral_loc) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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43 --viral_loc '$viral_loc' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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44 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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45 #if str($peptidase_loc) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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46 --peptidase_loc '$peptidase_loc' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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47 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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48 #if str($genome_summary_form_loc) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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49 --genome_summary_form_loc '$genome_summary_form_loc' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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50 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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51 #if str($module_step_form_loc) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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52 --module_step_form_loc '$module_step_form_loc' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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53 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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54 #if str($etc_module_database_loc) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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55 --etc_module_database_loc '$etc_module_database_loc' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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56 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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57 #if str($function_heatmap_form_loc) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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58 --function_heatmap_form_loc '$function_heatmap_form_loc' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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59 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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60 #if str($amg_database_loc) != '': |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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61 --amg_database_loc '$amg_database_loc' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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62 #end if |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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63 --threads \${GALAXY_SLOTS:-10} |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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64 --db_version '$db_version' |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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65 ]]></command> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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66 <inputs> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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67 <param argument="--kofam_hmm_loc" type="text" value="" label="Absolute path to hmm file for KOfam (profiles.tar.gz) if already installed" help="Leave blank to install"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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68 <sanitizer invalid_char=""> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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69 <valid initial="string.printable"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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70 <remove value="'"/> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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71 </valid> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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72 </sanitizer> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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73 </param> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
74 <param argument="--kofam_ko_list_loc" type="text" value="" label="Absolute path to KOfam ko list file (ko_list.gz) if already installed" help="Leave blank to install"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
75 <sanitizer invalid_char=""> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
76 <valid initial="string.printable"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
77 <remove value="'"/> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
78 </valid> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
79 </sanitizer> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
80 </param> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
81 |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
82 <conditional name="skip_uniref_cond"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
83 <param argument="--skip_uniref" type="select" label="Skip downloading and processing uniref?" help="Choosing Yes saves time and memory and does not impact DRAM distillation"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
84 <option value="no" selected="true">No</option> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
85 <option value="yes">Yes</option> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
86 </param> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
87 <when value="no"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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changeset
|
88 <param argument="--uniref_loc" type="text" value="" label="Absolute path to uniref (uniref90.fasta.gz) if already installed" help="Leave blank to install"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
89 <sanitizer invalid_char=""> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
90 <valid initial="string.printable"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
91 <remove value="'"/> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
92 </valid> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
93 </sanitizer> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
94 </param> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
|
95 <param argument="--uniref_version" type="integer" value="90" label="UniRef version to download" help="Ignored if uniref is not downloaded and processed"/> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
96 </when> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
97 <when value="yes"/> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
98 </conditional> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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|
99 <param argument="--pfam_loc" type="text" value="" label="Absolute path to pfam-A full file (Pfam-A.full.gz) if already installed" help="Leave blank to install"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
100 <sanitizer invalid_char=""> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
101 <valid initial="string.printable"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
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102 <remove value="'"/> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
103 </valid> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
104 </sanitizer> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
105 </param> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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|
106 <param argument="--pfam_hmm_dat" type="text" value="" label="Absolute path to pfam hmm .dat file to get PF descriptions (Pfam-A.hmm.dat.gz) if already installed" help="Leave blank to install"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
107 <sanitizer invalid_char=""> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
108 <valid initial="string.printable"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
|
109 <remove value="'"/> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
110 </valid> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
111 </sanitizer> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
112 </param> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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|
113 <param argument="--dbcan_loc" type="text" value="" label="Absolute path to dbCAN file (dbCAN-HMMdb-V9.txt) if already installed" help="Leave blank to install"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
114 <sanitizer invalid_char=""> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
115 <valid initial="string.printable"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
116 <remove value="'"/> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
|
117 </valid> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
|
118 </sanitizer> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
|
119 </param> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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|
120 <param argument="--dbcan_fam_activities" type="text" value="" label="Absolute path to CAZY family activities file (CAZyDB.07302020.fam-activities.txt) if already installed" help="Leave blank to install"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
121 <sanitizer invalid_char=""> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
122 <valid initial="string.printable"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
123 <remove value="'"/> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
|
124 </valid> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
|
125 </sanitizer> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
|
126 </param> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
|
127 <param argument="--dbcan_version" type="integer" value="10" label="Version of dbCAN to use"/> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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128 <param argument="--vogdb_loc" type="text" value="" label="Absolute path to hmm file for vogdb (vog.hmm.tar.gz) if already installed" help="Leave blank to install"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
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129 <sanitizer invalid_char=""> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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130 <valid initial="string.printable"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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131 <remove value="'"/> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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132 </valid> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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133 </sanitizer> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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134 </param> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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|
135 <param argument="--vog_annotations" type="text" value="" label="Absolute path to vogdb annotations file (vog.annotations.tsv.gz) if already installed" help="Leave blank to install"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
136 <sanitizer invalid_char=""> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
137 <valid initial="string.printable"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
|
138 <remove value="'"/> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
|
139 </valid> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
|
140 </sanitizer> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
141 </param> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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|
142 <param argument="--viral_loc" type="text" value="" label="Absolute path to merged viral protein faa file (viral.x.protein.faa.gz) if already installed" help="Leave blank to install"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
143 <sanitizer invalid_char=""> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
144 <valid initial="string.printable"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
diff
changeset
|
145 <remove value="'"/> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
|
146 </valid> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
parents:
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changeset
|
147 </sanitizer> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
iuc
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148 </param> |
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149 <param argument="--peptidase_loc" type="text" value="" label="Absolute path to MEROPS peptidase fasta file (pepunit.lib) if already installed" help="Leave blank to install"> |
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150 <sanitizer invalid_char=""> |
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151 <valid initial="string.printable"> |
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152 <remove value="'"/> |
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153 </valid> |
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154 </sanitizer> |
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155 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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156 <param argument="--genome_summary_form_loc" type="text" value="" label="Absolute path to genome summary form file (genome_summary_form.YYYYMMDD.tsv) if already installed" help="Leave blank to install"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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157 <sanitizer invalid_char=""> |
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158 <valid initial="string.printable"> |
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159 <remove value="'"/> |
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160 </valid> |
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161 </sanitizer> |
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162 </param> |
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163 <param argument="--module_step_form_loc" type="text" value="" label="Absolute path to module step form file (module_step_form.YYYYMMDD.tsv) if already installed" help="Leave blank to install"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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164 <sanitizer invalid_char=""> |
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165 <valid initial="string.printable"> |
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166 <remove value="'"/> |
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167 </valid> |
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168 </sanitizer> |
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169 </param> |
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170 <param argument="--etc_module_database_loc" type="text" value="" label="Absolute path to etc module database file (etc_mdoule_database.YYYYMMDD.tsv) if already installed" help="Leave blank to install"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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171 <sanitizer invalid_char=""> |
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172 <valid initial="string.printable"> |
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173 <remove value="'"/> |
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174 </valid> |
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175 </sanitizer> |
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176 </param> |
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177 <param argument="--function_heatmap_form_loc" type="text" value="" label="Absolute path to function heatmap form file (function_heatmap_form.YYYYMMDD.tsv) if already installed" help="Leave blank to install"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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178 <sanitizer invalid_char=""> |
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179 <valid initial="string.printable"> |
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180 <remove value="'"/> |
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181 </valid> |
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182 </sanitizer> |
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183 </param> |
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184 <param argument="--amg_database_loc" type="text" value="" label="Absolute path to amg database file (amg_database.YYYYMMDD.tsv) if already installed" help="Leave blank to install"> |
bd342a6a5b0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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185 <sanitizer invalid_char=""> |
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186 <valid initial="string.printable"> |
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187 <remove value="'"/> |
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188 </valid> |
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189 </sanitizer> |
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190 </param> |
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191 <param argument="--db_version" type="text" value="1.3.5" label="Version of DRAM databases to install"> |
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192 <sanitizer invalid_char=""> |
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193 <valid initial="string.printable"> |
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194 <remove value="'"/> |
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195 </valid> |
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196 </sanitizer> |
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197 </param> |
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198 </inputs> |
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199 <outputs> |
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200 <data name="out_file" format="data_manager_json"/> |
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201 </outputs> |
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202 <tests> |
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203 <test expect_failure="true"> |
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204 <param name="kofam_hmm_loc" value="profiles.tar.gz"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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205 <param name="kofam_ko_list_loc" value="ko_list.gz"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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206 <param name="skip_uniref" value="yes"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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207 <param name="pfam_loc" value="Pfam-A.full.gz"/> |
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208 <param name="pfam_hmm_dat" value="Pfam-A.hmm.dat.gz"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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209 <param name="dbcan_loc" value="dbCAN-HMMdb-V9.txt"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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210 <param name="dbcan_fam_activities" value="CAZyDB.07302020.fam-activities.txt"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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211 <param name="vogdb_loc" value="vog.hmm.tar.gz"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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212 <param name="vog_annotations" value="vog.annotations.tsv.gz"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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213 <param name="viral_loc" value="viral.x.protein.faa.gz"/> |
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214 <param name="peptidase_loc" value="pepunit.lib"/> |
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215 <param name="genome_summary_form_loc" value="genome_summary_form.20220715.tsv"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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216 <param name="module_step_form_loc" value="module_step_form.20220715.tsv"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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217 <param name="etc_module_database_loc" value="etc_mdoule_database.20220715.tsv"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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218 <param name="function_heatmap_form_loc" value="function_heatmap_form.20220715.tsv"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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219 <param name="amg_database_loc" value="amg_database.20220715.tsv"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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220 <assert_stderr> |
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221 <has_text text="Database location does not exist"/> |
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222 </assert_stderr> |
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223 </test> |
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224 </tests> |
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225 <help> |
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226 This tool downloads and processes DRAM databases for annotation and makes them available to corresponding versions |
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227 of the DRAM suite of tools. |
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228 |
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229 See https://github.com/WrightonLabCSU/DRAM/wiki for details about DRAM. |
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230 </help> |
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231 <citations> |
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232 <citation type="doi">10.1093/nar/gkaa621</citation> |
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233 </citations> |
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234 </tool> |
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235 |