Mercurial > repos > galaxyp > eggnog_mapper

changeset 7:4e4c6329f6cd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
author galaxyp
date Fri, 19 Feb 2021 18:54:25 +0000
parents 3cb37af59360
children 96cac424c870
files eggnog_macros.xml eggnog_mapper.xml test-data/cached_locally/eggnog_mapper_db.loc test-data/cached_locally/eggnog_mapper_db_versioned.loc tool-data/eggnog_mapper_db.loc.sample tool-data/eggnog_mapper_db_versioned.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 8 files changed, 48 insertions(+), 39 deletions(-) [+]
line wrap: on
line diff
--- a/eggnog_macros.xml	Sat Sep 05 07:21:28 2020 +0000
+++ b/eggnog_macros.xml	Fri Feb 19 18:54:25 2021 +0000
@@ -1,7 +1,14 @@
 <?xml version="1.0"?>
 <macros>
    <token name="@VERSION@">2.0.1</token>
-   <token name="@EGGNOG_DB_VERSION@">5.0</token>
+   <token name="@EGGNOG_DB_VERSION@">2.0</token>
+    <!--
+    # Versionning is super confusing:
+    # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5)
+    # eggnog-mapper 2.0 needs a db v2.0 (based on eggnog v5.0)
+    # db v4.5 are not compatible with eggnog-mapper 2.0
+    -->
+   <token name="@IDX_VERSION@">2.0</token>
    <xml name="citations">
         <citations>
             <citation type="doi">10.1093/nar/gkv1248</citation>
@@ -47,7 +54,7 @@
             <yield />
             <output name="out_file">
                 <assert_contents>
-                    <has_text text="eggnog_mapper_db" />
+                    <has_text text="eggnog_mapper_db_versioned" />
                     <has_text text="@EGGNOG_DB_VERSION@" />
                 </assert_contents>
             </output>
--- a/eggnog_mapper.xml	Sat Sep 05 07:21:28 2020 +0000
+++ b/eggnog_mapper.xml	Fri Feb 19 18:54:25 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@">
+<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@+galaxy1">
     <description>functional sequence annotation by orthology</description>
     <macros>
         <import>eggnog_macros.xml</import>
@@ -42,7 +42,9 @@
     <inputs>
         <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
         <param name="eggnog_data" type="select" label="Version of eggNOG Database">
-            <options from_data_table="eggnog_mapper_db"/>
+            <options from_data_table="eggnog_mapper_db_versioned">
+                <filter type="static_value" column="3" value="@IDX_VERSION@" />
+            </options>
         </param>
         <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
             label="Are these coding DNA sequences that need to be translated?"/>
@@ -243,15 +245,15 @@
             <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
             <param name="no_annot" value="true"/>
             <param name="no_file_comments" value="true"/>
-            <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
+            <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
         </test>
         <test>
             <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
             <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
             <param name="report_orthologs" value="true"/>
             <param name="no_file_comments" value="true"/>
-            <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
-            <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular"/>
+            <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
+            <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular" compare="sim_size"/>
             <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/>
         </test>
         <test>
@@ -262,8 +264,8 @@
             <section name="annotation_options">
                 <param name="tax_scope" value="651137" />
             </section>
-            <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular"/>
-            <output name="annotations" file="scoped.emapper.annotations" ftype="tabular"/>
+            <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular" compare="sim_size"/>
+            <output name="annotations" file="scoped.emapper.annotations" ftype="tabular" compare="sim_size"/>
             <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/>
         </test>
     </tests>
--- a/test-data/cached_locally/eggnog_mapper_db.loc	Sat Sep 05 07:21:28 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-#value	name	path
-5.0	eggNOG_5.0	${__HERE__}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/eggnog_mapper_db_versioned.loc	Fri Feb 19 18:54:25 2021 +0000
@@ -0,0 +1,2 @@
+#value	name	path	version
+2.0	eggNOG_2.0	${__HERE__}	2.0
--- a/tool-data/eggnog_mapper_db.loc.sample	Sat Sep 05 07:21:28 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +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://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog.db.gz
-# A complete diamond database is available from:
-#  http://eggnog5.embl.de/download/emapperdb-5.0.0/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")
-#
-#
-#db_version	name	path
-#5.0	eggnog_5.0	/path/to/directory/that/contains/eggnog.db
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/eggnog_mapper_db_versioned.loc.sample	Fri Feb 19 18:54:25 2021 +0000
@@ -0,0 +1,22 @@
+#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://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog.db.gz
+# A complete diamond database is available from:
+#  http://eggnog5.embl.de/download/emapperdb-5.0.0/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")
+#
+#
+#db_version	name	path
+#5.0	eggnog_5.0	/path/to/directory/that/contains/eggnog.db
--- a/tool_data_table_conf.xml.sample	Sat Sep 05 07:21:28 2020 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Feb 19 18:54:25 2021 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Locations of all eggnog_mapper data -->
-    <table name="eggnog_mapper_db" comment_char="#" allow_duplicate_entries="False">
-        <columns>value,name,path</columns>
-        <file path="tool-data/eggnog_mapper_db.loc" />
+    <table name="eggnog_mapper_db_versioned" comment_char="#" allow_duplicate_entries="False">
+        <columns>value,name,path,version</columns>
+        <file path="tool-data/eggnog_mapper_db_versioned.loc" />
     </table>
 </tables>
--- a/tool_data_table_conf.xml.test	Sat Sep 05 07:21:28 2020 +0000
+++ b/tool_data_table_conf.xml.test	Fri Feb 19 18:54:25 2021 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Locations of all eggnog_mapper data -->
-    <table name="eggnog_mapper_db" comment_char="#">
-        <columns>value,name,path</columns>
-        <file path="${__HERE__}/test-data/cached_locally/eggnog_mapper_db.loc" />
+    <table name="eggnog_mapper_db_versioned" comment_char="#" allow_duplicate_entries="False">
+        <columns>value,name,path,version</columns>
+        <file path="${__HERE__}/test-data/cached_locally/eggnog_mapper_db_versioned.loc" />
     </table>
 </tables>