diff diamond_makedb.xml @ 8:54f751e413f4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"

--- a/diamond_makedb.xml	Tue Dec 03 17:40:05 2019 -0500
+++ b/diamond_makedb.xml	Mon Mar 22 13:21:23 2021 +0000
@@ -8,7 +8,7 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
 
-    <command>
+    <command detect_errors="aggressive">
     <!-- DB has two files, *.dmnd and *.tx -->
     <![CDATA[
     diamond makedb
@@ -19,6 +19,7 @@
       #if str($tax_cond.tax_select) == 'yes':
         --taxonmap '$tax_cond.taxonmap'
         --taxonnodes '$tax_cond.taxonnodes'
+        --taxonnames '$tax_cond.taxonnames'
       #end if
     ]]>
     </command>
@@ -33,6 +34,7 @@
         <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="" />
         </when>
         <when value="no"/>
       </conditional>
@@ -53,6 +55,7 @@
                 <param name="tax_select" value="yes"/>
                 <param name="taxonmap" ftype="tabular" value="prot.accession2taxid" />
                 <param name="taxonnodes" ftype="tabular" value="nodes.dmp" />
+                <param name="taxonnames" ftype="tabular" value="names.dmp" />
             </conditional>
             <output name="outfile" value="db-wtax.dmnd" compare="sim_size" delta="2"/>
         </test>
@@ -73,7 +76,9 @@
 .. _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.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.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.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
 
 - taxonnodes: Path to the nodes.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
 ]]>