Mercurial > repos > iuc > meryl_groups_kmers

changeset 1:c4758f3bf36e 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 16:44:04 +0000
parents 9f9d2625f6c3
children
files groups-kmers.xml macros.xml
diffstat 2 files changed, 15 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/groups-kmers.xml	Thu Apr 25 21:02:11 2024 +0000
+++ b/groups-kmers.xml	Tue Oct 08 16:44:04 2024 +0000
@@ -13,11 +13,11 @@
     export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
     #for $i,$mdb in enumerate($input_meryldb_02)
         mkdir -p ./tmp_folder_$i/ &&
-        tar -zxf $mdb -C ./tmp_folder_$i &&
+        tar -xmf $mdb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" -C ./tmp_folder_$i &&
         mv ./tmp_folder_$i/* db_'${i}'.meryl &&
     #end for
     meryl $groups_operations output read-db.meryl db_*  &&
-    tar -zcf read-db.meryldb read-db.meryl
+    tar -cf read-db.meryldb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" read-db.meryl
     ]]></command>
     <inputs>
         <param name="groups_operations" type="select" label="Operations on sets of k-mers" help="Select an operation to be executed">
@@ -44,7 +44,7 @@
             <param name="groups_operations" value="union"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="36100" delta="1000"/>
+                    <has_size value="34918" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
@@ -54,7 +54,7 @@
             <param name="groups_operations" value="union-min"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="58925" delta="1000"/>
+                    <has_size value="59637" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
@@ -64,7 +64,7 @@
             <param name="groups_operations" value="union-max"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="58930" delta="1000"/>
+                    <has_size value="60705" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
@@ -74,7 +74,7 @@
             <param name="groups_operations" value="union-sum"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="58600" delta="1000"/>
+                    <has_size value="61311" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
@@ -84,7 +84,7 @@
             <param name="groups_operations" value="intersect"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="14951" delta="1000"/>
+                    <has_size value="16003" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
@@ -94,7 +94,7 @@
             <param name="groups_operations" value="intersect-min"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="14957" delta="1000"/>
+                    <has_size value="15413" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
@@ -104,7 +104,7 @@
             <param name="groups_operations" value="intersect-max"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="14956" delta="1000"/>
+                    <has_size value="15424" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
@@ -114,7 +114,7 @@
             <param name="groups_operations" value="intersect-sum"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="14953" delta="1000"/>
+                    <has_size value="15965" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
@@ -124,7 +124,7 @@
             <param name="groups_operations" value="subtract"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="23999" delta="1000"/>
+                    <has_size value="25728" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
@@ -134,7 +134,7 @@
             <param name="groups_operations" value="difference"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="24016" delta="1000"/>
+                    <has_size value="24666" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
@@ -144,7 +144,7 @@
             <param name="groups_operations" value="symmetric-difference"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="57455" delta="1000"/>
+                    <has_size value="60385" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
--- a/macros.xml	Thu Apr 25 21:02:11 2024 +0000
+++ b/macros.xml	Tue Oct 08 16:44:04 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">