Mercurial > repos > iuc > hmmer_nhmmer

diff nhmmer.xml @ 8:2ec5e1ad1da7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 061757dd7b3bfe66b7738fd54bd6c5e135d9afe8
author iuc
date Mon, 06 Nov 2023 20:23:30 +0000
parents b28e8ed99424
children 54b92ae4f75b
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--- a/nhmmer.xml	Wed Jul 21 14:11:12 2021 +0000
+++ b/nhmmer.xml	Mon Nov 06 20:23:30 2023 +0000
@@ -1,9 +1,10 @@
 <?xml version="1.0"?>
-<tool id="hmmer_nhmmer" name="nhmmer" version="@TOOL_VERSION@+galaxy0">
+<tool id="hmmer_nhmmer" name="nhmmer" version="@TOOL_VERSION@+galaxy1">
   <description>search a DNA model or alignment against a DNA database (BLASTN-like)</description>
   <macros>
     <import>macros.xml</import>
   </macros>
+  <expand macro="bio_tools"/>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
   <command><![CDATA[
@@ -12,8 +13,7 @@
 
 @OFORMAT_WITH_OPTS@
 @HSSI@
-@THRESHOLDS_NODOM@
-@CUT@
+@THRESHOLDS@
 @ACCEL_HEUR@
 @FORMAT_SELECTOR@
 @ADV_OPTS@
@@ -30,8 +30,7 @@
     <param name="seqfile" type="data" format="fasta" label="Target sequence file"/>
     <expand macro="oformat_with_opts_dfam_alisc"/>
     <expand macro="hssi"/>
-    <expand macro="thresholds_nodom"/>
-    <expand macro="cut" />
+    <expand macro="thresholds_cut_xml"/>
     <expand macro="accel_heur_xml"/>
     <expand macro="format_selector_noprot"/>
     <expand macro="adv_opts"/>