Mercurial > repos > iuc > meryl_filter_kmers

changeset 1:fa43288f637c 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 16:44:39 +0000
parents c373ea894cfb
children
files filter-kmers.xml macros.xml
diffstat 2 files changed, 9 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/filter-kmers.xml	Thu Apr 25 21:01:48 2024 +0000
+++ b/filter-kmers.xml	Tue Oct 08 16:44:39 2024 +0000
@@ -12,7 +12,7 @@
     <command detect_errors="exit_code"><![CDATA[
     export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
     mkdir  -p ./temp_db/ &&
-    tar -zxf $input_meryldb_02 -C ./temp_db/ &&
+    tar -xmf $input_meryldb_02 --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" -C ./temp_db/ &&
     mv ./temp_db/* tmp.meryl &&
     meryl
     $filter_operations
@@ -23,7 +23,7 @@
     #end if
     tmp.meryl
     output read-db.meryl &&
-    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="filter_operations" type="select" label="Filter operations" help="Select an operation to be executed">
@@ -58,7 +58,7 @@
             <param name="filter_operations" value="less-than"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="32077" delta="1000"/>
+                    <has_size value="32382" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
@@ -71,7 +71,7 @@
             <param name="filter_operations" value="greater-than"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="49643" delta="1000"/>
+                    <has_size value="50850" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
@@ -84,7 +84,7 @@
             <param name="filter_operations" value="greater-than"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="1634" delta="1000"/>
+                    <has_size value="1880" delta="1000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
@@ -97,7 +97,7 @@
             <param name="filter_operations" value="equal-to"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="2621" delta="1000"/>
+                    <has_size value="3073" delta="1000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
@@ -110,7 +110,7 @@
             <param name="filter_operations" value="not-equal-to"/>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="59100" delta="1000"/>
+                    <has_size value="59719" delta="3000"/>
                     <expand macro="meryldb_archive_assumptions"/>
                 </assert_contents>
             </output>
--- a/macros.xml	Thu Apr 25 21:01:48 2024 +0000
+++ b/macros.xml	Tue Oct 08 16:44:39 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">