Mercurial > repos > iuc > meryl_trio_mode

changeset 1:47e9001da01b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
author iuc
date Tue, 08 Oct 2024 16:43:34 +0000
parents c85aec7804a4
children
files macros.xml trio-mode.xml
diffstat 2 files changed, 8 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Apr 25 21:01:24 2024 +0000
+++ b/macros.xml	Tue Oct 08 16:43:34 2024 +0000
@@ -1,7 +1,7 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3</token>
     <token name="@GALAXY_TOOL_VERSION@">galaxy</token>
-    <token name="@SUFFIX_VERSION@">6</token>
+    <token name="@SUFFIX_VERSION@">7</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
@@ -16,6 +16,7 @@
             <requirement type="package" version="1.1">merqury</requirement>
             <requirement type="package" version="@TOOL_VERSION@">meryl</requirement>
             <requirement type="package" version="1.34">tar</requirement>
+            <requirement type="package" version="2.8">pigz</requirement>
         </requirements>
     </xml>
     <xml name="meryldb_archive_assumptions">
--- a/trio-mode.xml	Thu Apr 25 21:01:24 2024 +0000
+++ b/trio-mode.xml	Tue Oct 08 16:43:34 2024 +0000
@@ -37,7 +37,7 @@
     #end for
     meryl union-sum child*.meryl output child.meryl &&
     meryl histogram child.meryl > read-db.hist &&                                          
-    tar -czf 'read-db.meryldb' child.meryl &&
+    tar -cf read-db.meryldb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" child.meryl &&
     
     ## mat specific kmers
     meryl difference mat.meryl pat.meryl output mat.only.meryl &&
@@ -62,7 +62,7 @@
     java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.inherited.hist > mat.inherited.ploidy &&
     VAR=`sed -n 2p mat.inherited.ploidy | awk '{print \$NF}'` &&
     meryl greater-than \$VAR output mat.hapmer.meryl mat.inherited.meryl &&
-    tar -czf 'mat.meryldb' mat.hapmer.meryl &&
+    tar -cf mat.meryldb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" mat.hapmer.meryl &&
 
     ## pat hapmers
     meryl intersect output pat.inherited.meryl child.meryl pat.only.filt.meryl &&
@@ -70,7 +70,7 @@
     java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.inherited.hist > pat.inherited.ploidy &&
     VAR=`sed -n 2p pat.inherited.ploidy | awk '{print \$NF}'` &&
     meryl greater-than \$VAR output pat.hapmer.meryl pat.inherited.meryl &&
-    tar -czf 'pat.meryldb' pat.hapmer.meryl &&
+    tar -cf pat.meryldb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" pat.hapmer.meryl &&
 
     echo 'K-mer size: ${size}'
     ]]></command>
@@ -111,21 +111,21 @@
             <param name="child_reads" value="child.fasta"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="3362942" delta="2000"/>
+                    <has_size value="3373562" delta="6000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
             <output name="read_db_hist" file="output_23.read-db.hist"/>
             <output name="pat_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="120610" delta="400"/>
+                    <has_size value="124859" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
             <output name="pat_db_hist" file="output_23.pat.hist"/>
             <output name="mat_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="67883" delta="300"/>
+                    <has_size value="71220" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>