# HG changeset patch
# User iuc
# Date 1634901303 0
# Node ID ffd1300599a1cf8c24482184b3d3b354911d8213
# Parent  d0d4cef4f967e5674ee9ebd087cb0082062999f6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 2147ee46c226f99d16899eb29b223f0f80db5491"

diff -r d0d4cef4f967 -r ffd1300599a1 transdecoder.xml
--- a/transdecoder.xml	Mon Feb 01 20:51:40 2021 +0000
+++ b/transdecoder.xml	Fri Oct 22 11:15:03 2021 +0000
@@ -1,8 +1,11 @@
-<tool id="transdecoder" name="TransDecoder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="transdecoder" name="TransDecoder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description>finds coding regions within transcripts</description>
+    <xrefs>
+        <xref type="bio.tools">TransDecoder</xref>
+    </xrefs>
     <macros>
         <token name="@TOOL_VERSION@">5.5.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">transdecoder</requirement>
@@ -109,7 +112,7 @@
                         </when>
                     </conditional>
                     <param argument="--retain_blastp_hits" type="data" format="tabular" optional="true" label="Select BlastP result file" help="Any ORF with a blast match will be retained in the final output. (tabular outfmt6 file)"/>
-                    <param argument="--retain_pfam_hits" type="data" format="tabular" optional="true" label="Select Pfam result file" help="Domain table output file from running hmmscan to search Pfam. Any ORF with a pfam domain hit will be retained in the final output. (tabular domtblout file)"/>
+                    <param argument="--retain_pfam_hits" type="data" format="txt" optional="true" label="Select Pfam result file" help="Domain table output file from running hmmscan to search Pfam. Any ORF with a pfam domain hit will be retained in the final output. (tabular domtblout file)"/>
                     <param argument="--single_best_only" type="boolean" truevalue="--single_best_only" falsevalue="" label="Retain only the single best ORF per transcript?" help="Prioritized by homology than ORF length."/>
                     <param argument="--no_refine_starts" type="boolean" truevalue="--no_refine_starts" falsevalue="" label="Start refinement that identifies potential start codons for 5' partial ORFs using a PWM?"/>
                     <param argument="-T" type="integer" value="500" min="1" label="Set top longest ORFs to train Markov Model" help="The first (10*value) elements are selected for removing redundancies. Then number of longst ORFs of this value are selected from the non-redundant set."/>