# HG changeset patch
# User iuc
# Date 1656086218 0
# Node ID c7d4789dd859588e2ecde90a9a9edccb9cb4e4aa
# Parent  341c8de8b5fba76b0c03f32a12166e8a5ba9cb51
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit de05aab169e4fc4ee7130411d0081741bb246ce2

diff -r 341c8de8b5fb -r c7d4789dd859 kc-align.xml
--- a/kc-align.xml	Tue Aug 31 09:10:27 2021 +0000
+++ b/kc-align.xml	Fri Jun 24 15:56:58 2022 +0000
@@ -1,12 +1,27 @@
-<tool id="kc-align" name="Kc-Align" version="1.0.2" python_template_version="3.5">
+<tool id="kc-align" name="Kc-Align" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.2</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+    </macros>
     <xrefs>
-        <xref type="bio.tools">kallisto</xref>
+        <xref type="bio.tools">kc-align</xref>
     </xrefs>
     <requirements>
-        <requirement type="package" version="1.0.2">kcalign</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">kcalign</requirement>
     </requirements>
     <command detect_errors="exit_code">
         <![CDATA[
+        ## number of slots needs to be one or divisible by three
+        SLOTS=\${GALAXY_SLOTS:-1};
+        while [ \$SLOTS -gt 1 ]; 
+        do
+            if ! (( \$SLOTS % 3 )) ; then break; fi; 
+            ((SLOTS--));
+        done;
+        if [[ "\${GALAXY_SLOTS:-1}" -ne "\$SLOTS" ]]; then
+            >&2 echo "Warning: using only \$SLOTS threads (instead of the configured \${GALAXY_SLOTS:-1}), since it needs to be 1 or a multiple of three. Please contact your Galaxy Admin";
+        fi;
+
         kc-align
             --mode '$position.mode'
             --reference '$ref'
@@ -20,7 +35,7 @@
                 -d '$position.dist'
             #end if
             $compress
-            -th \${GALAXY_SLOTS:-1}
+            -th "\$SLOTS"
 
     ]]></command>
     <inputs>