# HG changeset patch
# User iuc
# Date 1637317744 0
# Node ID 904fb55e91564e2b4de813c9fb0d25b443635a22
# Parent  0ff17c7a18cd10943455528db2990445b1cf42bd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 61ba7fa8ac35d0f0a15bfbef268738187861e74c"

diff -r 0ff17c7a18cd -r 904fb55e9156 macros.xml
--- a/macros.xml	Mon May 03 08:51:01 2021 +0000
+++ b/macros.xml	Fri Nov 19 10:29:04 2021 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">2.4.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">2.5.4</token>
+    <token name="@VERSION_SUFFIX@">0</token>
 
     <xml name="citations">
         <citations>
diff -r 0ff17c7a18cd -r 904fb55e9156 orthofinder_only_groups.xml
--- a/orthofinder_only_groups.xml	Mon May 03 08:51:01 2021 +0000
+++ b/orthofinder_only_groups.xml	Fri Nov 19 10:29:04 2021 +0000
@@ -1,11 +1,14 @@
 <tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>finds orthogroups in a set of proteomes</description>
+    <xrefs>
+        <xref type="bio.tools">OrthoFinder</xref>
+    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">orthofinder</requirement>
-        <requirement type="package" version="2.34">util-linux</requirement>
+        <requirement type="package" version="2.36">util-linux</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #import re
@@ -47,6 +50,7 @@
         #if $init.start == "fasta":
             -f .
             -S $init.search.search_program
+            $init.input_type
         #elif $init.start == "blast":
             -b .
         #end if
@@ -79,16 +83,21 @@
     <inputs>
         <!-- Control where Orthofinder starts -->
         <conditional name="init">
-            <param name="start" type="select" label="Orthofinder starting point" help="OrthoFinder can be run in 2 steps. Choose 'From fasta proteomes' to run OrthoFinder from scratch or 'From blast results' if you have all the blast results from a previous OrthoFinder run.">
-                <option value="fasta" selected="true">From fasta proteomes</option>
+            <param name="start" type="select" label="Orthofinder starting point" help="OrthoFinder can be run in 2 steps. Choose 'From fasta files' to run OrthoFinder from scratch or 'From blast results' if you have all the blast results from a previous OrthoFinder run.">
+                <option value="fasta" selected="true">From fasta files</option>
                 <option value="blast">From blast results</option>
             </param>
 
             <when value="fasta">
-                <param name="input_fasta" type="data" format="fasta" multiple="true" label="Select input fasta proteomes" help="One fasta file per species; species and sequences names in the results will remain the same than in the input files."/>
+                <param name="input_fasta" type="data" format="fasta" multiple="true" label="Select input fasta files" help="One fasta file per species; species and sequence names in the results will remain the same than in the input files."/>
+                <param name="input_type" type="select" label="Input contains nucleotide or amino acid sequences?">
+                    <option value="">Amino acid</option>
+                    <option value="-d">Nucleotide</option>
+                </param>
                 <conditional name="search">
                     <param name="search_program" type="select" label="Sequence search program">
                         <option value="diamond" selected="true">Diamond (faster)</option>
+                        <option value="diamond_ultra_sens">Diamond ultra-sensitive</option>
                         <option value="blast">Blast</option>
                         <option value="blast_gz">Blast_gz - blast results gzipped</option>
                     </param>
@@ -96,6 +105,7 @@
                         <param name="keepblastout" type="boolean" checked="true" label="Do you want to get the blast results?" help="Used to re-run OrthoFinder from pre-computed blast results"/>
                     </when>
                     <when value="diamond"></when>
+                    <when value="diamond_ultra_sens"></when>
                     <when value="blast_gz"></when>
                 </conditional>
             </when>
@@ -768,7 +778,7 @@
 ----------
 Parameters
 ----------
-    - Sequence search program : You can choose either blast, blast_gz, or diamond (diamond is faster)
+    - Sequence search program : You can choose either blast, blast_gz, diamond, or diamond ultra-sensitive (diamond is faster)
     - Get the blast results : Check "Yes" if, while using blast as the sequence search program, you want to retrieve the blast output files
     - Inflation : the inflation parameter; modify this parameter is not recommended.