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changeset 11:29dabd8db6f2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit e479a44b3c6e7a3c0facdb325892b0a6da6f0cd2
author iuc
date Thu, 02 Jun 2022 17:17:45 +0000
parents 9cd178127b19
children
files macros.xml meryl.xml test-data/output_23.mat.hist test-data/output_23.pat.hist test-data/output_23.read-db.hist
diffstat 5 files changed, 27 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Apr 28 18:11:34 2022 +0000
+++ b/macros.xml	Thu Jun 02 17:17:45 2022 +0000
@@ -1,7 +1,7 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3</token>
     <token name="@GALAXY_TOOL_VERSION@">galaxy</token>
-    <token name="@SUFFIX_VERSION@">5</token>
+    <token name="@SUFFIX_VERSION@">6</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_0196</edam_topic>
--- a/meryl.xml	Thu Apr 28 18:11:34 2022 +0000
+++ b/meryl.xml	Thu Jun 02 17:17:45 2022 +0000
@@ -94,6 +94,9 @@
                 meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_child_${i}.${read.ext} output 'child${i}.meryl' &&
             #end for
             meryl union-sum child*.meryl output child.meryl &&
+            meryl histogram child.meryl > read-db.hist &&                                          
+            tar -czf 'read-db.meryldb' child.meryl &&
+            
             ## mat specific kmers
             meryl difference mat.meryl pat.meryl output mat.only.meryl &&
             meryl histogram mat.only.meryl > mat.only.hist &&
@@ -127,17 +130,6 @@
             meryl greater-than \$VAR output pat.hapmer.meryl pat.inherited.meryl &&
             tar -czf 'pat.meryldb' pat.hapmer.meryl &&
 
-            ## shared hapmers
-            meryl intersect output shared.inherited.meryl child.meryl shared.meryl &&
-            meryl histogram shared.inherited.meryl > shared.inherited.hist &&
-            java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar shared.inherited.hist > shared.inherited.ploidy &&
-            VAR=`sed -n 2p shared.inherited.ploidy | awk '{print \$NF}'` &&
-            meryl greater-than \$VAR output shared.filt.meryl shared.inherited.meryl &&
-            
-            ## child hapmers
-            meryl union-sum output child.inherited.meryl mat.inherited.meryl pat.inherited.meryl shared.inherited.meryl &&
-            meryl difference output read.only.meryl child.meryl child.inherited.meryl &&
-            tar -czf 'read-db.meryldb' read.only.meryl &&
             echo 'K-mer size: ${size}'
         #end if
     ]]>    </command>
@@ -588,24 +580,24 @@
                 <param name="maternal_reads" value="maternal.fasta" />
                 <conditional name="options_kmer_size">
                     <param name="kmer_size" value="provide" />
-                    <param name="input_kmer_size" value="7" />
+                    <param name="input_kmer_size" value="21" />
                 </conditional>
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="1573" delta="300" />
+                    <has_size value="3362942" delta="300" />
                 </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="1779" delta="300" />
+                    <has_size value="120610" delta="300" />
                 </assert_contents>
             </output>
             <output name="pat_db_hist" file="output_23.pat.hist" />
             <output name="mat_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="1569" delta="300" />
+                    <has_size value="67883" delta="300" />
                 </assert_contents>
             </output>
             <output name="mat_db_hist" file="output_23.mat.hist" />
--- a/test-data/output_23.mat.hist	Thu Apr 28 18:11:34 2022 +0000
+++ b/test-data/output_23.mat.hist	Thu Jun 02 17:17:45 2022 +0000
@@ -0,0 +1,5 @@
+1	5634
+2	365
+3	27
+4	8
+5	1
--- a/test-data/output_23.pat.hist	Thu Apr 28 18:11:34 2022 +0000
+++ b/test-data/output_23.pat.hist	Thu Jun 02 17:17:45 2022 +0000
@@ -1,5 +1,4 @@
-10	1
-11	1
-14	1
-15	1
-19	1
+1	13695
+2	802
+3	20
+4	3
--- a/test-data/output_23.read-db.hist	Thu Apr 28 18:11:34 2022 +0000
+++ b/test-data/output_23.read-db.hist	Thu Jun 02 17:17:45 2022 +0000
@@ -0,0 +1,10 @@
+1	1020255
+2	6481
+3	421
+4	46
+5	11
+6	1
+9	1
+10	1
+126	1
+292	1