Mercurial > repos > galaxyp > data_manager_eggnog_mapper_abspath

changeset 1:269f0970d762 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
author galaxyp
date Sat, 05 Sep 2020 07:24:42 +0000
parents 9d5f039c637f
children 2aec8d30ff42
files data_manager/data_manager_eggnog.py data_manager/data_manager_eggnog.xml data_manager/eggnog_macros.xml data_manager_conf.xml test-data/cached_locally/eggnog.db test-data/cached_locally/eggnog_mapper_db.loc test-data/cached_locally/eggnog_mapper_hmm_dbs.loc tool-data/eggnog_mapper_db.loc.sample tool-data/eggnog_mapper_hmm_dbs.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 11 files changed, 31 insertions(+), 208 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_eggnog.py	Mon Nov 11 11:49:47 2019 -0500
+++ b/data_manager/data_manager_eggnog.py	Sat Sep 05 07:24:42 2020 +0000
@@ -11,7 +11,7 @@
 
 
 def _get_db_version(sqlitedb_path):
-    version = '4.5'
+    version = '5.0'
     try:
         query = 'select version from version'
         conn = sqlite3.connect(sqlitedb_path)
@@ -28,7 +28,6 @@
     parser = argparse.ArgumentParser()
     parser.add_argument('--config_file')
     parser.add_argument('--install_path')
-    parser.add_argument('--dbs', default='')
     args = parser.parse_args()
 
     eggnog_db_path = os.path.join(args.install_path, 'eggnog.db')
@@ -46,19 +45,9 @@
     data_table_entry = dict(value=db_version, name=db_version,
                             path=args.install_path)
     dm_dict['data_tables'][data_table].append(data_table_entry)
-    data_table = 'eggnog_mapper_hmm_dbs'
-    dm_dict['data_tables'][data_table]\
-        = dm_dict['data_tables'].get(data_table, [])
-    if args.dbs:
-        dbs = [x.strip() for x in args.dbs.split(',')]
-        for db in dbs:
-            key = '%s_%s' % (db_version, db)
-            data_table_entry = dict(key=key, db_version=db_version,
-                                    value=db, name=db, path=db)
-            dm_dict['data_tables'][data_table].append(data_table_entry)
 
     # save info to json file
-    open(args.config_file, 'wb').write(json.dumps(dm_dict))
+    open(args.config_file, 'w').write(json.dumps(dm_dict))
 
 
 if __name__ == "__main__":
--- a/data_manager/data_manager_eggnog.xml	Mon Nov 11 11:49:47 2019 -0500
+++ b/data_manager/data_manager_eggnog.xml	Sat Sep 05 07:24:42 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="data_manager_eggnog_abspath" name="EggNOG DB Download" version="@VERSION@.1" tool_type="manage_data">
+<tool id="data_manager_eggnog_abspath" name="EggNOG DB Download" version="@VERSION@" tool_type="manage_data">
     <description>eggnog data to a specified directory</description>
     <macros>
         <import>eggnog_macros.xml</import>
@@ -10,7 +10,7 @@
 @DOWNLOAD_CMD@
     ]]></command>
     <inputs>
-        <param name="target_path" type="text" value="" label="Download Destination" 
+        <param name="target_path" type="text" value="" label="Download Destination"
             help="Full path to where the eggnod data should be installed.">
             <validator type="regex" message="Must be an absolute path">^/.*$</validator>
         </param>
@@ -18,16 +18,17 @@
     </inputs>
     <expand macro="data_manager_outputs"/>
     <tests>
-        <expand macro="data_manager_test"/>
+        <expand macro="data_manager_test">
+            <param name="target_path" value="/tmp" /> <!-- Not used in test mode -->
+        </expand>
     </tests>
     <help><![CDATA[
-This tool downloads eggnog data using download_eggnog_data.py 
-and populates the data tables: eggnog_mapper_db and eggnog_mapper_hmm_dbs.
-The data is located at: http://eggnogdb.embl.de/download/emapperdb-4.5.1/
-The optional eggNOG HMM databases: http://eggnogdb.embl.de/download/emapperdb-4.5.1/hmmdb_levels/ 
+This tool downloads eggnog data using download_eggnog_data.py
+and populates the data tables: eggnog_mapper_db.
+The data is located at: http://eggnog5.embl.de/download/emapperdb-5.0.0/
 can vary from 1G to 80G in size.
 
-The data will be downloaded to the specified directory.  This allows adding hmmdb_levels to an existing download.  
+The data will be downloaded to the specified directory.
 You should not mix eggnog data versions in the same directory.
     ]]></help>
     <expand macro="citations"/>
--- a/data_manager/eggnog_macros.xml	Mon Nov 11 11:49:47 2019 -0500
+++ b/data_manager/eggnog_macros.xml	Sat Sep 05 07:24:42 2020 +0000
@@ -1,9 +1,11 @@
 <?xml version="1.0"?>
 <macros>
-   <token name="@VERSION@">1.0.3</token>
+   <token name="@VERSION@">2.0.1</token>
+   <token name="@EGGNOG_DB_VERSION@">5.0</token>
    <xml name="citations">
         <citations>
             <citation type="doi">10.1093/nar/gkv1248</citation>
+            <citation type="doi">10.1093/molbev/msx148</citation>
         </citations>
     </xml>
     <xml name="requirements">
@@ -16,119 +18,7 @@
     </xml>
     <xml name="data_manager_params">
         <param name="test" type="hidden" value="false" />
-        <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database"/>
-        <param argument="dbs" type="select" multiple="true" label="eggNOG HMM databases to download. If none are selected only diamond can be used'">
-            <option value="arch" selected="true">Archea  arch_1 (arch)</option>
-            <option value="bact" selected="true">Bacteria bact_50 (bact)</option>
-            <option value="euk" selected="true">Eukaryote euk_500 (euk)</option>
-            <option value="NOG" selected="true">All organisms (NOG)</option>
-            <option value="aciNOG">Acidobacteria (aciNOG)</option>
-            <option value="acidNOG">Acidobacteriia (acidNOG)</option>
-            <option value="acoNOG">Aconoidasida (acoNOG)</option>
-            <option value="actNOG">Actinobacteria (actNOG)</option>
-            <option value="agaNOG">Agaricales (agaNOG)</option>
-            <option value="agarNOG">Agaricomycetes (agarNOG)</option>
-            <option value="apiNOG">Apicomplexa (apiNOG)</option>
-            <option value="aproNOG">Proteobacteria_alpha (aproNOG)</option>
-            <option value="aquNOG">Aquificae (aquNOG)</option>
-            <option value="arNOG">Archaea (arNOG)</option>
-            <option value="arcNOG">Archaeoglobi (arcNOG)</option>
-            <option value="artNOG">Arthropoda (artNOG)</option>
-            <option value="arthNOG">Arthrodermataceae (arthNOG)</option>
-            <option value="ascNOG">Ascomycota (ascNOG)</option>
-            <option value="aveNOG">Aves (aveNOG)</option>
-            <option value="bacNOG">Bacilli (bacNOG)</option>
-            <option value="bactNOG">Bacteria (bactNOG)</option>
-            <option value="bacteNOG">Bacteroidia (bacteNOG)</option>
-            <option value="basNOG">Basidiomycota (basNOG)</option>
-            <option value="bctoNOG">Bacteroidetes (bctoNOG)</option>
-            <option value="biNOG">Bilateria (biNOG)</option>
-            <option value="bproNOG">Proteobacteria_beta (bproNOG)</option>
-            <option value="braNOG">Brassicales (braNOG)</option>
-            <option value="carNOG">Carnivora (carNOG)</option>
-            <option value="chaNOG">Chaetomiaceae (chaNOG)</option>
-            <option value="chlNOG">Chlorobi (chlNOG)</option>
-            <option value="chlaNOG">Chlamydiae (chlaNOG)</option>
-            <option value="chloNOG">Chloroflexi (chloNOG)</option>
-            <option value="chlorNOG">Chloroflexi (chlorNOG)</option>
-            <option value="chloroNOG">Chlorophyta (chloroNOG)</option>
-            <option value="chorNOG">Chordata (chorNOG)</option>
-            <option value="chrNOG">Chromadorea (chrNOG)</option>
-            <option value="cloNOG">Clostridia (cloNOG)</option>
-            <option value="cocNOG">Coccidia (cocNOG)</option>
-            <option value="creNOG">Crenarchaeota (creNOG)</option>
-            <option value="cryNOG">Cryptosporidiidae (cryNOG)</option>
-            <option value="cyaNOG">Cyanobacteria (cyaNOG)</option>
-            <option value="cytNOG">Cytophagia (cytNOG)</option>
-            <option value="debNOG">Debaryomycetaceae (debNOG)</option>
-            <option value="defNOG">Deferribacteres (defNOG)</option>
-            <option value="dehNOG">Dehalococcoidetes (dehNOG)</option>
-            <option value="deiNOG">Deinococcusthermus (deiNOG)</option>
-            <option value="delNOG">delta/epsilon (delNOG)</option>
-            <option value="dipNOG">Diptera (dipNOG)</option>
-            <option value="dotNOG">Dothideomycetes (dotNOG)</option>
-            <option value="dproNOG">Proteobacteria_delta (dproNOG)</option>
-            <option value="droNOG">Drosophilidae (droNOG)</option>
-            <option value="eproNOG">Proteobacteria_epsilon (eproNOG)</option>
-            <option value="eryNOG">Erysipelotrichi (eryNOG)</option>
-            <option value="euNOG">Eukaryotes (euNOG)</option>
-            <option value="eurNOG">Euryarchaeota (eurNOG)</option>
-            <option value="euroNOG">Eurotiomycetes (euroNOG)</option>
-            <option value="eurotNOG">Eurotiales (eurotNOG)</option>
-            <option value="fiNOG">Fishes (fiNOG)</option>
-            <option value="firmNOG">Firmicutes (firmNOG)</option>
-            <option value="flaNOG">Flavobacteriia (flaNOG)</option>
-            <option value="fuNOG">Fungi (fuNOG)</option>
-            <option value="fusoNOG">Fusobacteria (fusoNOG)</option>
-            <option value="gproNOG">Proteobacteria_gamma (gproNOG)</option>
-            <option value="haeNOG">Haemosporida (haeNOG)</option>
-            <option value="halNOG">Halobacteria (halNOG)</option>
-            <option value="homNOG">Hominidae (homNOG)</option>
-            <option value="hymNOG">Hymenoptera (hymNOG)</option>
-            <option value="hypNOG">Hypocreales (hypNOG)</option>
-            <option value="inNOG">Insects (inNOG)</option>
-            <option value="kinNOG">Kinetoplastida (kinNOG)</option>
-            <option value="lepNOG">Lepidoptera (lepNOG)</option>
-            <option value="lilNOG">Liliopsida (lilNOG)</option>
-            <option value="maNOG">Mammals (maNOG)</option>
-            <option value="magNOG">Magnaporthales (magNOG)</option>
-            <option value="meNOG">Animals (meNOG)</option>
-            <option value="metNOG">Methanobacteria (metNOG)</option>
-            <option value="methNOG">Methanococci (methNOG)</option>
-            <option value="methaNOG">Methanomicrobia (methaNOG)</option>
-            <option value="necNOG">Nectriaceae (necNOG)</option>
-            <option value="negNOG">Negativicutes (negNOG)</option>
-            <option value="nemNOG">Nematodes (nemNOG)</option>
-            <option value="onyNOG">Onygenales (onyNOG)</option>
-            <option value="opiNOG">Opisthokonts (opiNOG)</option>
-            <option value="perNOG">Peronosporales (perNOG)</option>
-            <option value="plaNOG">Planctomycetes (plaNOG)</option>
-            <option value="pleNOG">Pleosporales (pleNOG)</option>
-            <option value="poaNOG">Poales (poaNOG)</option>
-            <option value="prNOG">Primates (prNOG)</option>
-            <option value="proNOG">Proteobacteria (proNOG)</option>
-            <option value="rhaNOG">Rhabditida (rhaNOG)</option>
-            <option value="roNOG">Rodents (roNOG)</option>
-            <option value="sacNOG">Saccharomycetaceae (sacNOG)</option>
-            <option value="saccNOG">Saccharomycetes (saccNOG)</option>
-            <option value="sorNOG">Sordariales (sorNOG)</option>
-            <option value="sordNOG">Sordariomycetes (sordNOG)</option>
-            <option value="sphNOG">Sphingobacteriia (sphNOG)</option>
-            <option value="spiNOG">Spirochaetes (spiNOG)</option>
-            <option value="spriNOG">Supraprimates (spriNOG)</option>
-            <option value="strNOG">Streptophyta (strNOG)</option>
-            <option value="synNOG">Synergistetes (synNOG)</option>
-            <option value="tenNOG">Tenericutes (tenNOG)</option>
-            <option value="thaNOG">Thaumarchaeota (thaNOG)</option>
-            <option value="theNOG">Thermoplasmata (theNOG)</option>
-            <option value="therNOG">Thermotogae (therNOG)</option>
-            <option value="thermNOG">Thermococci (thermNOG)</option>
-            <option value="treNOG">Tremellales (treNOG)</option>
-            <option value="veNOG">Vertebrates (veNOG)</option>
-            <option value="verNOG">Verrucomicrobia (verNOG)</option>
-            <option value="verrNOG">Verrucomicrobiae (verrNOG)</option>
-            <option value="virNOG">Viridiplantae (virNOG)</option>
-        </param>
+        <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database" help="Takes ~9Gb, you most probably want it."/>
     </xml>
     <xml name="data_manager_outputs">
         <outputs>
@@ -141,33 +31,26 @@
 #import os.path
 #set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally')
 #end if
-#if $dbs:
-#set $eggnogdbs = ' '.join(str($dbs).split(','))
-#else
-#set $eggnogdbs = 'none'
-#end if
 mkdir -p '${install_path}' &&
-download_eggnog_data.py 
-  $diamond_database -y -q 
+download_eggnog_data.py
+  $diamond_database -y -q
 #if $test == 'true'
   -s
 #end if
-  --data_dir '$install_path' 
-  $eggnogdbs &&
-python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' --dbs '$dbs'
+  --data_dir '$install_path' &&
+python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path'
     ]]></token>
     <xml name="data_manager_test">
-        <!--
         <test>
             <param name="test" value="true"/>
-            <param name="diamond_database" value="false"/>
-            <param name="dbs" value="thaNOG"/>
+            <param name="diamond_database" value="true"/>
+            <yield />
             <output name="out_file">
                 <assert_contents>
                     <has_text text="eggnog_mapper_db" />
+                    <has_text text="@EGGNOG_DB_VERSION@" />
                 </assert_contents>
             </output>
         </test>
-        -->
     </xml>
 </macros>
--- a/data_manager_conf.xml	Mon Nov 11 11:49:47 2019 -0500
+++ b/data_manager_conf.xml	Sat Sep 05 07:24:42 2020 +0000
@@ -8,14 +8,5 @@
         <column name="path" />  <!-- Absolute path specified by the Data Manager Tool -->
       </output>
     </data_table>
-    <data_table name="eggnog_mapper_hmm_dbs">  <!-- Defines a Data Table to be modified. -->
-      <output> <!-- Handle the output of the Data Manager Tool -->
-        <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool -->
-        <column name="db_version" /> <!-- columns that are going to be specified by the Data Manager Tool -->
-        <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
-        <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
-        <column name="path" /> <!-- columns that are going to be specified by the Data Manager Tool -->
-      </output>
-    </data_table>
   </data_manager>
 </data_managers>
Binary file test-data/cached_locally/eggnog.db has changed
--- a/test-data/cached_locally/eggnog_mapper_db.loc	Mon Nov 11 11:49:47 2019 -0500
+++ b/test-data/cached_locally/eggnog_mapper_db.loc	Sat Sep 05 07:24:42 2020 +0000
@@ -1,2 +1,2 @@
 #value	name	path
-4.5	eggNOG_4.5	${__HERE__}
+5.0	eggNOG_5.0	${__HERE__}
--- a/test-data/cached_locally/eggnog_mapper_hmm_dbs.loc	Mon Nov 11 11:49:47 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-#key	db_version	value	name	path
-4.5_ENOG411CB2I	4.5	ENOG411CB2I	ENOG411CB2I	${__HERE__}/hmmdb_levels/ENOG411CB2I/ENOG411CB2I
--- a/tool-data/eggnog_mapper_db.loc.sample	Mon Nov 11 11:49:47 2019 -0500
+++ b/tool-data/eggnog_mapper_db.loc.sample	Sat Sep 05 07:24:42 2020 +0000
@@ -1,25 +1,22 @@
 #This is a sample file distributed with Galaxy that enables tools
-#to use a directory of eggnog_mapper data files. 
+#to use a directory of eggnog_mapper data files.
 #
 # eggnog-mapper requires the following files to be installed in the data directory:
 #  https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz
-#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz
-#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz
-# In addition individual HMM DBs can be installed from:
-#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/
+#  http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog.db.gz
 # A complete diamond database is available from:
-#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz
+#  http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog_proteins.dmnd.gz
 #
-# The python script download_eggnog_data.py, 
+# The python script download_eggnog_data.py,
 # included with eggnog_mapper, can be used to download the files to the correct directory
 #
 # The near-equivalence of columns "value" and "db" is needed for the tests to work,
 # and for the setting of --data_dir to the parent directory of eggnog.db
-# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. 
+# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky.
 # See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases
-# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, 
+# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de,
 # value and db should be the same (in the example, both should be "thaNOG")
 #
 #
-#db_version	name	path	
-#4.5.1	eggnog_4.5.1	/path/to/directory/that/contains/eggnog.db
+#db_version	name	path
+#5.0	eggnog_5.0	/path/to/directory/that/contains/eggnog.db
--- a/tool-data/eggnog_mapper_hmm_dbs.loc.sample	Mon Nov 11 11:49:47 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of eggnog_mapper data files. 
-#
-# eggnog-mapper requires the following files to be installed in the data directory:
-#  https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz
-#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog.db.gz
-#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/OG_fasta.tar.gz
-# In addition individual HMM DBs can be installed from:
-#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/hmmdb_levels/
-# A complete diamond database is available from:
-#  http://eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/eggnog_proteins.dmnd.gz
-#
-# The python script download_eggnog_data.py, 
-# included with eggnog_mapper, can be used to download the files to the correct directory
-#
-# The near-equivalence of columns "value" and "db" is needed for the tests to work,
-# and for the setting of --data_dir to the parent directory of eggnog.db
-# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. 
-# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases
-# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, 
-# value and db should be the same (in the example, both should be "thaNOG")
-#
-#
-#key	db_version	value	name	path
-#4.5.1_NOG	4.5.1	NOG	Full eggNOG database (NOG)	
-#4.5.1_euk	4.5.1	euk	Eukaryotes (euk)	
-#4.5.1_aproNOG	4.5.1	aproNOG	Proteobacteria_alpha (aproNOG)	
-#4.5.1_aproNOG	4.5.1	ENOG411CB2I	ENOG411CB2I (custom)	/path/to/custom/hmmdb/ENOG411CB2I
--- a/tool_data_table_conf.xml.sample	Mon Nov 11 11:49:47 2019 -0500
+++ b/tool_data_table_conf.xml.sample	Sat Sep 05 07:24:42 2020 +0000
@@ -4,8 +4,4 @@
         <columns>value,name,path</columns>
         <file path="tool-data/eggnog_mapper_db.loc" />
     </table>
-    <table name="eggnog_mapper_hmm_dbs" comment_char="#" allow_duplicate_entries="False">
-        <columns>key,db_version,value,name,path</columns>
-        <file path="tool-data/eggnog_mapper_hmm_dbs.loc" />
-    </table>
 </tables>
--- a/tool_data_table_conf.xml.test	Mon Nov 11 11:49:47 2019 -0500
+++ b/tool_data_table_conf.xml.test	Sat Sep 05 07:24:42 2020 +0000
@@ -4,8 +4,4 @@
         <columns>value,name,path</columns>
         <file path="${__HERE__}/test-data/cached_locally/eggnog_mapper_db.loc" />
     </table>
-    <table name="eggnog_mapper_hmm_dbs" comment_char="#">
-        <columns>key,db_version,value,name,path</columns>
-        <file path="${__HERE__}/test-data/cached_locally/eggnog_mapper_hmm_dbs.loc" />
-    </table>
 </tables>