--- a/diamond_makedb.xml	Sat Nov 27 09:48:10 2021 +0000
+++ b/diamond_makedb.xml	Fri Apr 22 13:51:34 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bg_diamond_makedb" name="Diamond makedb" version="@TOOL_VERSION@" profile="19.01">
+<tool id="bg_diamond_makedb" name="Diamond makedb" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
     <description>Build database from a FASTA file</description>
     <macros>
         <import>macros.xml</import>
@@ -32,9 +32,12 @@
           <option value="no" selected="true">No</option>
         </param>
         <when value="yes">
-          <param argument="--taxonmap" type="data" format="tabular" label="protein accession to taxid mapping file" help="" />
-          <param argument="--taxonnodes" type="data" format="tabular" label="taxonomy nodes.dmp from NCBI" help="" />
-          <param argument="--taxonnames" type="data" format="tabular" label="taxonomy names.dmp from NCBI" help="" />
+          <param argument="--taxonmap" type="data" format="tabular" 
+            label="Protein accession to taxid mapping file" 
+            help="Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. 
+              A custom file following the same format may be supplied here. Note that the first line of this file is assumed to contain headings and will be ignored" />
+          <param argument="--taxonnodes" type="data" format="tabular" label="Taxonomy nodes.dmp from NCBI" help="This parameter is optional and needs to be supplied in order to provide taxonomy features" />
+          <param argument="--taxonnames" type="data" format="tabular" label="Taxonomy names.dmp from NCBI" help="This parameter is optional and needs to be supplied in order to provide taxonomy features" />
         </when>
         <when value="no"/>
       </conditional>
@@ -76,7 +79,7 @@
 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
 
 
-- taxonmap: Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. The file can be downloaded from NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.gz
+- taxonmap: Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. The file can be downloaded from NCBI: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz
 
 - taxonnames: Path to the names.dmp file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip