Mercurial > repos > iuc > kc_align

diff kc-align.xml @ 10:97476dfde728 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit de05aab169e4fc4ee7130411d0081741bb246ce2
author iuc
date Fri, 24 Jun 2022 15:57:35 +0000
parents 0c0288a9d92c
children
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--- a/kc-align.xml	Mon Oct 12 18:09:09 2020 +0000
+++ b/kc-align.xml	Fri Jun 24 15:57:35 2022 +0000
@@ -1,9 +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">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'
@@ -17,7 +35,7 @@
                 -d '$position.dist'
             #end if
             $compress
-            -th \${GALAXY_SLOTS:-1}
+            -th "\$SLOTS"
 
     ]]></command>
     <inputs>