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comparison meryl.xml @ 11:c6e9752d4104 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 17:17:09 +0000
parents f361d6eb1046
children
comparison
equal deleted inserted replaced
10:f361d6eb1046 11:c6e9752d4104
92 mkdir 'child${i}.meryl' && 92 mkdir 'child${i}.meryl' &&
93 ln -s '$read' ./input_child_${i}.${read.ext} && 93 ln -s '$read' ./input_child_${i}.${read.ext} &&
94 meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_child_${i}.${read.ext} output 'child${i}.meryl' && 94 meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_child_${i}.${read.ext} output 'child${i}.meryl' &&
95 #end for 95 #end for
96 meryl union-sum child*.meryl output child.meryl && 96 meryl union-sum child*.meryl output child.meryl &&
97 meryl histogram child.meryl > read-db.hist &&
98 tar -czf 'read-db.meryldb' child.meryl &&
99
97 ## mat specific kmers 100 ## mat specific kmers
98 meryl difference mat.meryl pat.meryl output mat.only.meryl && 101 meryl difference mat.meryl pat.meryl output mat.only.meryl &&
99 meryl histogram mat.only.meryl > mat.only.hist && 102 meryl histogram mat.only.meryl > mat.only.hist &&
100 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.only.hist > mat.only.ploidy && 103 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.only.hist > mat.only.ploidy &&
101 VAR=`sed -n 2p mat.only.ploidy | awk '{print \$NF}'` && 104 VAR=`sed -n 2p mat.only.ploidy | awk '{print \$NF}'` &&
125 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.inherited.hist > pat.inherited.ploidy && 128 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.inherited.hist > pat.inherited.ploidy &&
126 VAR=`sed -n 2p pat.inherited.ploidy | awk '{print \$NF}'` && 129 VAR=`sed -n 2p pat.inherited.ploidy | awk '{print \$NF}'` &&
127 meryl greater-than \$VAR output pat.hapmer.meryl pat.inherited.meryl && 130 meryl greater-than \$VAR output pat.hapmer.meryl pat.inherited.meryl &&
128 tar -czf 'pat.meryldb' pat.hapmer.meryl && 131 tar -czf 'pat.meryldb' pat.hapmer.meryl &&
129 132
130 ## shared hapmers
131 meryl intersect output shared.inherited.meryl child.meryl shared.meryl &&
132 meryl histogram shared.inherited.meryl > shared.inherited.hist &&
133 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar shared.inherited.hist > shared.inherited.ploidy &&
134 VAR=`sed -n 2p shared.inherited.ploidy | awk '{print \$NF}'` &&
135 meryl greater-than \$VAR output shared.filt.meryl shared.inherited.meryl &&
136
137 ## child hapmers
138 meryl union-sum output child.inherited.meryl mat.inherited.meryl pat.inherited.meryl shared.inherited.meryl &&
139 meryl difference output read.only.meryl child.meryl child.inherited.meryl &&
140 tar -czf 'read-db.meryldb' read.only.meryl &&
141 echo 'K-mer size: ${size}' 133 echo 'K-mer size: ${size}'
142 #end if 134 #end if
143 ]]> </command> 135 ]]> </command>
144 <inputs> 136 <inputs>
145 <conditional name="operation_type"> 137 <conditional name="operation_type">
586 <param name="child_reads" value="child.fasta" /> 578 <param name="child_reads" value="child.fasta" />
587 <param name="paternal_reads" value="paternal.fasta" /> 579 <param name="paternal_reads" value="paternal.fasta" />
588 <param name="maternal_reads" value="maternal.fasta" /> 580 <param name="maternal_reads" value="maternal.fasta" />
589 <conditional name="options_kmer_size"> 581 <conditional name="options_kmer_size">
590 <param name="kmer_size" value="provide" /> 582 <param name="kmer_size" value="provide" />
591 <param name="input_kmer_size" value="7" /> 583 <param name="input_kmer_size" value="21" />
592 </conditional> 584 </conditional>
593 </conditional> 585 </conditional>
594 <output name="read_db" ftype="meryldb"> 586 <output name="read_db" ftype="meryldb">
595 <assert_contents> 587 <assert_contents>
596 <has_size value="1573" delta="300" /> 588 <has_size value="3362942" delta="300" />
597 </assert_contents> 589 </assert_contents>
598 </output> 590 </output>
599 <output name="read_db_hist" file="output_23.read-db.hist" /> 591 <output name="read_db_hist" file="output_23.read-db.hist" />
600 <output name="pat_db" ftype="meryldb"> 592 <output name="pat_db" ftype="meryldb">
601 <assert_contents> 593 <assert_contents>
602 <has_size value="1779" delta="300" /> 594 <has_size value="120610" delta="300" />
603 </assert_contents> 595 </assert_contents>
604 </output> 596 </output>
605 <output name="pat_db_hist" file="output_23.pat.hist" /> 597 <output name="pat_db_hist" file="output_23.pat.hist" />
606 <output name="mat_db" ftype="meryldb"> 598 <output name="mat_db" ftype="meryldb">
607 <assert_contents> 599 <assert_contents>
608 <has_size value="1569" delta="300" /> 600 <has_size value="67883" delta="300" />
609 </assert_contents> 601 </assert_contents>
610 </output> 602 </output>
611 <output name="mat_db_hist" file="output_23.mat.hist" /> 603 <output name="mat_db_hist" file="output_23.mat.hist" />
612 </test> 604 </test>
613 <test expect_num_outputs="1"> 605 <test expect_num_outputs="1">