changeset 1:7de7487a7e8d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit 666539d2f4b2c8f8367f1bc3786f14a45dc639f6-dirty

--- a/eggnog_mapper.xml	Fri May 26 11:45:10 2017 -0400
+++ b/eggnog_mapper.xml	Tue Aug 08 12:40:56 2017 -0400
@@ -29,6 +29,13 @@
                 #end if
                 --Z=$db.hmm_options.Z
             #end if
+        #elif $db.mode == 'diamond':
+            ## $db.sensitive
+            ## $db.more_sensitive
+            --matrix '$db.matrix'
+            --gapopen '$db.gapopen'
+            --gapextend '$db.gapextend'
+            ## --seg '$db.seg'
         #end if
         #if $annotation_options.tax_scope:
             --tax_scope=$annotation_options.tax_scope
@@ -69,8 +76,10 @@
             <when value="hmmer">
                 <param name="database" type="select" multiple="true" min="1" label="HMM target database">
                     <options from_data_table="eggnog_mapper" >
-                        <filter type="param_value" ref="eggnog_data" key="data_dir" column="3" />
-                        <filter type="static_value" name="type" value="hmm" column="2"/>
+                        <!--
+                        -->
+                        <filter type="param_value" ref="eggnog_data" column="3" />
+                        <filter type="static_value" name="type" value="hmmer" column="2"/>
                         <validator type="no_options" message="No HMM DBs are available, request from your galaxy admin" />
                     </options>
                 </param>
@@ -92,6 +101,21 @@
             </when>
             <when value="diamond">
                 <param name="database" type="hidden" value="diamond"/>
+                <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false" label="Trigger the sensitive alignment mode with a 16x9 seed shape configuration?" help=""/>
+                <param name="more_sensitive" argument="--more-sensitive" type="boolean" truevalue="--more-sensitive" falsevalue="" checked="false" label="Trigger the more sensitive mode?" help="This mode provides some additional sensitivity compared to the sensitive mode."/>
+                <param argument="--seg" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Enable SEG masking of low complexity segments in the query?" help=""/>
+                <param argument="--matrix" type="select" label="Scoring matrix" help="In brackets are the supported values for (gap open)/(gap extend)">
+                    <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1)</option>
+                    <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1)</option>
+                    <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1)</option>
+                    <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1)</option>
+                    <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1)</option>
+                    <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1)</option>
+                    <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1)</option>
+                    <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1)</option>
+                </param>
+                <param argument="--gapopen" type="integer" value="11" label="Gap open penalty" help="" />
+                <param argument="--gapextend" type="integer" value="1" label="Gap extension penalty" help="" />
             </when>
         </conditional>
         <section name="annotation_options" expanded="false" title="Annotation Options">
@@ -246,7 +270,7 @@
             </actions>
         </data>
         <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations" from_work_dir="results.emapper.annotations">
-            <filter>output_options['no_annot'] == ''</filter>
+            <filter>not output_options['no_annot']</filter>
             <actions>
                 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_pathways,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG,functional,categories,eggNOG_HMM_model_annotation"/>
             </actions>

--- a/tool-data/eggnog_mapper.loc.sample	Fri May 26 11:45:10 2017 -0400
+++ b/tool-data/eggnog_mapper.loc.sample	Tue Aug 08 12:40:56 2017 -0400
@@ -1,9 +1,18 @@
 #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
+#
+# 
 #name	value	type	data_dir	
 #eggnog_4.5	eggnog_4.5 data	/depot/data2/galaxy/eggnog/eggnog_4.5/data
-#eggnog_4.5arcNOG	arcNOG	hmmer	/depot/data2/galaxy/eggnog/eggnog_4.5/data
-#eggnog_4.5euk	euk	hmmer	/depot/data2/galaxy/eggnog/eggnog_4.5/data
-#eggnog_4.5dmnd	eggnog_proteins.dmnd	diamond	/depot/data2/galaxy/eggnog/eggnog_4.5/data
-#
+#eggnog_4.5arcNOG	arcNOG	hmmer	eggnog_4.5
+#eggnog_4.5euk	euk	hmmer	eggnog_4.5
+#eggnog_4.5dmnd	eggnog_proteins.dmnd	diamond	eggnog_4.5