diff diamond.xml @ 7:62c9df8382c2 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"

--- a/diamond.xml	Thu Sep 27 06:30:30 2018 -0400
+++ b/diamond.xml	Tue Dec 03 17:40:05 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="bg_diamond" name="Diamond" version="@VERSION@.0">
+<tool id="bg_diamond" name="Diamond" version="@VERSION@.0" profile="19.01">
     <description>alignment tool for short sequences against a protein database</description>
     <macros>
         <import>macros.xml</import>
@@ -64,7 +64,7 @@
         --subject-cover '$subject_cover'
         --block-size '$block_size'
         #if str($unal) == '1':
-            --unal 1 --un '$unalqueries' 
+            --unal 1 --un '$unalqueries'
         #end if
         $no_self_hits
         #if $tax_cond.tax_select == 'file':
@@ -103,7 +103,7 @@
                     <option value="26">Pachysolen tannophilus Nuclear Code</option>
                 </param>
                 <param argument="--min-orf" name="min_orf" type="integer" value="1" label="ignore translated sequences without an open reading frame of at least this length" help="By default this feature is disabled for sequences of length below 30, set to 20 for sequences of length below 100, and set to 40 otherwise. Setting this option to 1 will disable this feature" />
-    
+
                 <param name="query_strand" argument="--strand" type="select" label="query strands to search" help="">
                     <option value="both" selected="True">Both</option>
                     <option value="plus">Plus</option>
@@ -165,7 +165,7 @@
         <param argument="--masking" type="boolean" truevalue="1" falsevalue="0" checked="true" label="enable masking of low complexity regions?" help="Masked residues appear in the output as X"/>
         <conditional name="tax_cond">
             <param name="tax_select" type="select" label="Restrict search taxonomically?" help="Any taxonomic rank can be used, and only reference sequences matching one of the specified taxon ids will be searched against">
-                <option value="no">No</option>
+                <option value="no" selected="True">No</option>
                 <option value="list">list of taxids entered manually</option>
                 <option value="file">list of taxids from single column tabular file</option>
             </param>
@@ -179,7 +179,7 @@
         </conditional>
         <conditional name="filter_score">
             <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)">
-                <option value="evalue">Maximum e-value to report alignments</option>
+                <option value="evalue" selected="True">Maximum e-value to report alignments</option>
                 <option value="min-score">Minimum bit score to report alignments</option>
             </param>
             <when value="evalue">