| Previous changeset 10:9cd178127b19 (2022-04-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit e479a44b3c6e7a3c0facdb325892b0a6da6f0cd2 |
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modified:
macros.xml meryl.xml test-data/output_23.mat.hist test-data/output_23.pat.hist test-data/output_23.read-db.hist |
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| diff -r 9cd178127b19 -r 29dabd8db6f2 macros.xml --- a/macros.xml Thu Apr 28 18:11:34 2022 +0000 +++ b/macros.xml Thu Jun 02 17:17:45 2022 +0000 |
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| @@ -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> |
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| diff -r 9cd178127b19 -r 29dabd8db6f2 meryl.xml --- a/meryl.xml Thu Apr 28 18:11:34 2022 +0000 +++ b/meryl.xml Thu Jun 02 17:17:45 2022 +0000 |
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| @@ -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" /> |
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| diff -r 9cd178127b19 -r 29dabd8db6f2 test-data/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 |
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| @@ -0,0 +1,5 @@ +1 5634 +2 365 +3 27 +4 8 +5 1 |
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| diff -r 9cd178127b19 -r 29dabd8db6f2 test-data/output_23.pat.hist --- 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 |
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| @@ -1,5 +1,4 @@ -10 1 -11 1 -14 1 -15 1 -19 1 +1 13695 +2 802 +3 20 +4 3 |
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| diff -r 9cd178127b19 -r 29dabd8db6f2 test-data/output_23.read-db.hist --- 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 |
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| @@ -0,0 +1,10 @@ +1 1020255 +2 6481 +3 421 +4 46 +5 11 +6 1 +9 1 +10 1 +126 1 +292 1 |