Mercurial > repos > iuc > meryl
diff meryl.xml @ 11:29dabd8db6f2 draft default tip
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 |
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--- 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" />