meryl: meryl.xml annotate

annotate meryl.xml @ 8:5ae3496f9ca3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 0625ea0c1df66a724d0ab3769fcaee7a07810a20"

author	iuc
date	Thu, 12 Aug 2021 13:20:54 +0000
parents	51c2360aa807
children	eadfd71dde37

rev	line source
7 51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	1 <tool id='meryl' name='Meryl' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@' profile='20.01'>
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	2 <description>a genomic k-mer counter and sequence utility</description>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	3 <macros>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	4 <import>macros.xml</import>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	5 </macros>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	6 <expand macro='edam_ontology' />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	7 <expand macro='requirements' />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	8 <version_command>meryl --version</version_command>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	9 <command detect_errors='exit_code'><![CDATA[
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	10 export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	11 #if $operation_type.command_type == 'count-kmers'
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	12 #if $operation_type.options_kmer_size.kmer_size == 'estimate'
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	13 #from math import log
2 35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	14 #set size=int(log(int($operation_type.options_kmer_size.genome_size)*(1-float($operation_type.options_kmer_size.collision_rate))/float($operation_type.options_kmer_size.collision_rate))/log(4))
35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	15 #elif $operation_type.options_kmer_size.kmer_size == 'provide'
35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	16 #set size=$operation_type.options_kmer_size.input_kmer_size
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	17 #end if
8 5ae3496f9ca3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 0625ea0c1df66a724d0ab3769fcaee7a07810a20" iuc parents: 7 diff changeset	18 ln -s '$operation_type.input_reads' ./input.${operation_type.input_reads.ext} &&
5ae3496f9ca3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 0625ea0c1df66a724d0ab3769fcaee7a07810a20" iuc parents: 7 diff changeset	19
2 35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	20 meryl
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	21 $operation_type.count_operations
2 35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	22 k=$size
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	23 memory=\$GALAXY_MEMORY_GB
2 35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	24 threads=\${GALAXY_SLOTS:-1}
8 5ae3496f9ca3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 0625ea0c1df66a724d0ab3769fcaee7a07810a20" iuc parents: 7 diff changeset	25 ./input.${operation_type.input_reads.ext}
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	26 output read-db.meryl &&
2 35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	27 echo 'K-mer size: ${size}' &&
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	28 tar -zcf read-db.meryldb read-db.meryl
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	29 #elif $operation_type.command_type == 'filter-kmers'
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	30 mkdir -p ./temp_db/ &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	31 tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	32 mv ./temp_db/* tmp.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	33 meryl
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	34 $operation_type.filter_operations
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	35 #if $operation_type.filter_type.type == 'times'
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	36 $operation_type.filter_type.N
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	37 #elif $operation_type.filter_type.type == 'frequency'
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	38 distinct=${operation_type.filter_type.distinct}
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	39 #end if
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	40 tmp.meryl
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	41 output read-db.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	42 tar -zcf read-db.meryldb read-db.meryl
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	43 #elif $operation_type.command_type == 'arithmetic-kmers'
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	44 mkdir -p ./temp_db/ &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	45 tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	46 mv ./temp_db/* tmp.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	47 meryl
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	48 $operation_type.arithmetic_operations
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	49 $operation_type.X
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	50 tmp.meryl
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	51 output read-db.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	52 tar -zcf read-db.meryldb read-db.meryl
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	53 #elif $operation_type.command_type == 'groups-kmers'
6 31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	54 #for $i,$mdb in enumerate($operation_type.input_meryldb_02)
31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	55 mkdir -p ./tmp_folder_$i/ &&
31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	56 tar -zxf $mdb -C ./tmp_folder_$i &&
31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	57 mv ./tmp_folder_$i/* db_'${i}'.meryl &&
31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	58 #end for
31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	59 meryl $operation_type.groups_operations output read-db.meryl db_* &&
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	60 tar -zcf read-db.meryldb read-db.meryl
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	61 #elif $operation_type.command_type == 'histogram-kmers'
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	62 mkdir -p ./temp_db/ &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	63 tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	64 mv ./temp_db/* tmp.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	65 meryl histogram tmp.meryl > read-db.hist
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	66 #elif $operation_type.command_type == 'print'
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	67 mkdir -p ./temp_db/ &&
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	68 tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	69 mv ./temp_db/* tmp.meryl &&
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	70 meryl print tmp.meryl > read-db.tabular
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	71 #elif $operation_type.command_type == 'trio-mode'
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	72 export MERQURY=\$(dirname \$(command -v merqury.sh))/../share/merqury/ &&
2 35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	73 #if $operation_type.options_kmer_size.kmer_size == 'estimate'
35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	74 #from math import log
35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	75 #set size=int(log(int($operation_type.options_kmer_size.genome_size)*(1-float($operation_type.options_kmer_size.collision_rate))/float($operation_type.options_kmer_size.collision_rate))/log(4))
35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	76 #elif $operation_type.options_kmer_size.kmer_size == 'provide'
35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	77 #set size=$operation_type.options_kmer_size.input_kmer_size
35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	78 #end if
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	79 #for $i, $read in enumerate($paternal_reads):
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	80 mkdir 'paternal{$i}.meryl' &&
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	81 meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} '${read}' output 'paternal{$i}.meryl' &&
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	82 #end for
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	83 meryl union-sum paternal*.meryl output pat.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	84 #for $i, $read in enumerate($maternal_reads):
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	85 mkdir 'maternal{$i}.meryl' &&
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	86 meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} '${read}' output 'maternal{$i}.meryl' &&
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	87 #end for
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	88 meryl union-sum maternal*.meryl output mat.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	89 #for $i, $read in enumerate($child_reads):
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	90 mkdir 'child{$i}.meryl' &&
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	91 meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} '${read}' output 'child{$i}.meryl' &&
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	92 #end for
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	93 meryl union-sum child*.meryl output child.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	94 ## mat specific kmers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	95 meryl difference mat.meryl pat.meryl output mat.only.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	96 meryl histogram mat.only.meryl > mat.only.hist &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	97 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.only.hist > mat.only.ploidy &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	98 VAR=`sed -n 2p mat.only.ploidy \| awk '{print \$NF}'` &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	99 meryl greater-than \$VAR output mat.only.filt.meryl mat.only.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	100
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	101 ## pat specific kmers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	102 meryl difference pat.meryl mat.meryl output pat.only.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	103 meryl histogram pat.only.meryl > pat.only.hist &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	104 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.only.hist > pat.only.ploidy &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	105 VAR=`sed -n 2p pat.only.ploidy \| awk '{print \$NF}'` &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	106 meryl greater-than \$VAR output pat.only.filt.meryl pat.only.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	107
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	108 ## shared kmers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	109 meryl intersect output shared.meryl mat.meryl pat.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	110
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	111 ## mat hapmers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	112 meryl intersect output mat.inherited.meryl child.meryl mat.only.filt.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	113 meryl histogram mat.inherited.meryl > mat.inherited.hist &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	114 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.inherited.hist > mat.inherited.ploidy &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	115 VAR=`sed -n 2p mat.inherited.ploidy \| awk '{print \$NF}'` &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	116 meryl greater-than \$VAR output mat.hapmer.meryl mat.inherited.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	117 tar -czf 'mat.meryldb' mat.hapmer.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	118
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	119 ## pat hapmers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	120 meryl intersect output pat.inherited.meryl child.meryl pat.only.filt.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	121 meryl histogram pat.inherited.meryl > pat.inherited.hist &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	122 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.inherited.hist > pat.inherited.ploidy &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	123 VAR=`sed -n 2p pat.inherited.ploidy \| awk '{print \$NF}'` &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	124 meryl greater-than \$VAR output pat.hapmer.meryl pat.inherited.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	125 tar -czf 'pat.meryldb' pat.hapmer.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	126
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	127 ## shared hapmers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	128 meryl intersect output shared.inherited.meryl child.meryl shared.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	129 meryl histogram shared.inherited.meryl > shared.inherited.hist &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	130 java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar shared.inherited.hist > shared.inherited.ploidy &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	131 VAR=`sed -n 2p shared.inherited.ploidy \| awk '{print \$NF}'` &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	132 meryl greater-than \$VAR output shared.filt.meryl shared.inherited.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	133
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	134 ## child hapmers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	135 meryl union-sum output child.inherited.meryl mat.inherited.meryl pat.inherited.meryl shared.inherited.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	136 meryl difference output read.only.meryl child.meryl child.inherited.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	137 tar -czf 'read-db.meryldb' read.only.meryl &&
2 35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	138 echo 'K-mer size: ${size}'
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	139 #end if
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	140 ]]> </command>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	141 <inputs>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	142 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	143 <param name="command_type" type="select" label="Operation type selector" help="Select a type of operation">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	144 <option value="count-kmers">Count operations</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	145 <option value="filter-kmers">Filter operations</option>
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	146 <option value="arithmetic-kmers">Arithmetic operations on k-mer counts</option>
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	147 <option value="groups-kmers">Operations on sets of k-mers</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	148 <option value="histogram-kmers">Generate histogram dataset</option>
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	149 <option value="print">Print k-mer counts to a tabular file</option>
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	150 <option value="trio-mode">Build hap-mer dbs for trios</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	151 </param>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	152 <when value="count-kmers">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	153 <param name="count_operations" type="select" label="Count operations" help="Select an operation to be executed">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	154 <option value="count">Count: count the occurrences of canonical k-mers</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	155 <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	156 <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	157 </param>
7 51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	158 <param name="input_reads" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Input sequences" help="Select your reads in FASTA/FASTQ format." />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	159 <conditional name="options_kmer_size">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	160 <param name="kmer_size" type="select" label="K-mer size selector">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	161 <option value="provide">Set a k-mer size</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	162 <option value="estimate">Estimate the best k-mer size</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	163 </param>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	164 <when value="provide">
2 35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	165 <param name="input_kmer_size" type="integer" min="1" max="50" value="" label="K-mer size" help="For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G).." />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	166 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	167 <when value="estimate">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	168 <param name="genome_size" type="integer" min="1000" max="70000000000" value="1000" label="Genome size" help="Haploid genome size or diploid genome size, depending on what we evaluate. In bp. Only required if the k-mer size is not provided." />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	169 <param name="collision_rate" type="float" min="0.0001" max="0.01" value="0.001" label="Tolerable collision rate" help="Tolerable collision rate. By default is 0.001." />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	170 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	171 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	172 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	173 <when value="filter-kmers">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	174 <param name="filter_operations" type="select" label="Filter operations" help="Select an operation to be executed">
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	175 <option value="less-than">Less-than: return k-mers that occur fewer than a threshold value</option>
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	176 <option value="greater-than">Greater-than: return k-mers that occur more than a threshold value</option>
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	177 <option value="equal-to">Equal-to: return k-mers that occur exactly a threshold value</option>
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	178 <option value="not-equal-to">Not-equal-to: return k-mers that do not occur exactly a threshold value</option>
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	179 </param>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	180 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset" />
8 5ae3496f9ca3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 0625ea0c1df66a724d0ab3769fcaee7a07810a20" iuc parents: 7 diff changeset	181
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	182 <conditional name="filter_type">
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	183 <param name="type" type="select" label="Type of filtering">
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	184 <option value="times">Return k-mers that occur N times in the input</option>
d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	185 <option value="frequency">Return k-mers occurring at specific frequencies</option>
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	186 </param>
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	187 <when value="times">
8 5ae3496f9ca3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 0625ea0c1df66a724d0ab3769fcaee7a07810a20" iuc parents: 7 diff changeset	188 <param name="N" type="integer" min="0" max="50000000000" value="" optional="true" label="Number of times in the input" help="Return k-mers that occur N times in the input." />
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	189 </when>
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	190 <when value="frequency">
8 5ae3496f9ca3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 0625ea0c1df66a724d0ab3769fcaee7a07810a20" iuc parents: 7 diff changeset	191 <param name="distinct" type="float" min="0" max="1" value="0.9998" optional="true" label="Frequency" help="Return k-mers that at specific frequency (e.g. frequency = 0.9998 returns top 0.02% most frequent)" />
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	192 </when>
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	193 </conditional>
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	194 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	195 <when value="arithmetic-kmers">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	196 <param name="arithmetic_operations" type="select" label="Arithmetic operations" help="Select an operation to be executed">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	197 <option value="increase">Increase: add x to the count of each k-mer</option>
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	198 <option value="decrease">Decrease: subtract x from the count of each k-mer</option>
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	199 <option value="multiply">Multiply: multiply the count of each k-mer by x</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	200 <option value="divide">Divide: divide the count of each k-mer by x</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	201 <option value="divide-round">Divide-round: divide the count of each k-mer by x and round th results</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	202 <option value="modulo">Modulo: set the count of each k-mer to the remainder of the count divided by x</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	203 </param>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	204 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	205 <param name="X" type="integer" min="1" max="1000000" value="" optional="true" label="Operand" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	206 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	207 <when value="groups-kmers">
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	208 <param name="groups_operations" type="select" label="Operations on sets of k-mers" help="Select an operation to be executed">
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	209 <option value="union">Union: return k-mers that occur in any input</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	210 <option value="union-min">Union-min: return k-mers that occur in any input, set the count to the minimum count</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	211 <option value="union-max">Union-max: return k-mers that occur in any input, set the count to the maximum count</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	212 <option value="union-sum">Union-sum: return k-mers that occur in any input, set the count to the sum of the counts</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	213 <option value="intersect">Intersect: return k-mers that occur in all inputs, set the count to the count in the first input</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	214 <option value="intersect-min">Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	215 <option value="intersect-max">Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	216 <option value="intersect-sum">Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	217 <option value="subtract">Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	218 <option value="difference">Difference: return k-mers that occur in the first input, but none of the other inputs</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	219 <option value="symmetric-difference">Symmetric-difference: return k-mers that occur in exactly one input</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	220 </param>
6 31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	221 <param name="input_meryldb_02" type="data" multiple="true" format="meryldb" label="Input meryldb" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	222 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	223 <when value="histogram-kmers">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	224 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	225 </when>
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	226 <when value="print">
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	227 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" />
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	228 </when>
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	229 <when value="trio-mode">
7 51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	230 <param name="child_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly" />
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	231 <param name="paternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Paternal reads" help="Select the paternal reads used for generating the assembly" />
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	232 <param name="maternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Maternal reads" help="Select the maternal reads used for generating the assembly" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	233 <conditional name="options_kmer_size">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	234 <param name="kmer_size" type="select" label="K-mer size selector">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	235 <option value="provide">Set a k-mer size</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	236 <option value="estimate">Estimate the best k-mer size</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	237 </param>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	238 <when value="provide">
2 35ac9de60bec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" iuc parents: 1 diff changeset	239 <param name="input_kmer_size" type="integer" min="1" max="50" value="" label="K-mer size" help="For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G)." />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	240 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	241 <when value="estimate">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	242 <param name="genome_size" type="integer" min="1000" max="70000000000" value="1000" label="Genome size" help="Haploid genome size or diploid genome size, depending on what we evaluate. In bp. Only required if the k-mer size is not provided." />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	243 <param name="collision_rate" type="float" min="0.0001" max="0.01" value="0.001" label="Tolerable collision rate" help="Tolerable collision rate. By default is 0.001." />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	244 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	245 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	246 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	247 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	248 </inputs>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	249 <outputs>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	250 <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb" label="${tool.name} on ${on_string}: read-db.meryldb">
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	251 <filter>operation_type["command_type"] != "histogram-kmers" and operation_type["command_type"] != "print"</filter>
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	252 </data>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	253 <data name="read_db_hist" format="tabular" from_work_dir="read-db.hist" label="${tool.name} on ${on_string}: read-db histogram">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	254 <filter>operation_type["command_type"] == "histogram-kmers" or operation_type["command_type"] == "trio-mode"</filter>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	255 </data>
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	256 <data name="read_db_print" format="tabular" from_work_dir="read-db.tabular" label="${tool.name} on ${on_string}: kmer counts">
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	257 <filter>operation_type["command_type"] == "print"</filter>
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	258 </data>
1 e5b18909f73d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f25c9977e86fd2858ea9367e53afc298372a8dec" iuc parents: 0 diff changeset	259 <data name="pat_db" format="meryldb" from_work_dir="pat.meryldb" label="${tool.name} on ${on_string}: pat.meryldb">
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	260 <filter>operation_type["command_type"] == "trio-mode"</filter>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	261 </data>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	262 <data name="pat_db_hist" format="tabular" from_work_dir="pat.inherited.hist" label="${tool.name} on ${on_string}: paternal inherited histogram">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	263 <filter>operation_type["command_type"] == "trio-mode"</filter>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	264 </data>
1 e5b18909f73d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f25c9977e86fd2858ea9367e53afc298372a8dec" iuc parents: 0 diff changeset	265 <data name="mat_db" format="meryldb" from_work_dir="mat.meryldb" label="${tool.name} on ${on_string}: mat.meryldb">
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	266 <filter>operation_type["command_type"] == "trio-mode"</filter>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	267 </data>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	268 <data name="mat_db_hist" format="tabular" from_work_dir="mat.inherited.hist" label="${tool.name} on ${on_string}: maternal inherited histogram">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	269 <filter>operation_type["command_type"] == "trio-mode"</filter>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	270 </data>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	271 </outputs>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	272 <tests>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	273 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	274 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	275 <param name="command_type" value="count-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	276 <param name="count_operation" value="count" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	277 <param name="input_reads" value="child.fasta" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	278 <conditional name="options_kmer_size">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	279 <param name="kmer_size" value="provide" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	280 <param name="input_kmer_size" value="7" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	281 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	282 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	283 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	284 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	285 <has_size value="22152" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	286 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	287 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	288 <assert_stdout>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	289 <has_line line="K-mer size: 7" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	290 </assert_stdout>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	291 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	292 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	293 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	294 <param name="command_type" value="filter-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	295 <param name="filter_operations" value="less-than" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	296 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	297 <conditional name="filter_type">
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	298 <param name="N" value="100" />
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	299 </conditional>
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	300 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	301 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	302 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	303 <has_size value="32077" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	304 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	305 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	306 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	307 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	308 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	309 <param name="command_type" value="filter-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	310 <param name="filter_operations" value="greater-than" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	311 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	312 <conditional name="filter_type">
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	313 <param name="N" value="80" />
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	314 </conditional>
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	315 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	316 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	317 <assert_contents>
3 9f7a227436d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit c0960aa14536ee1ef790602255abfafd687e8e69" iuc parents: 2 diff changeset	318 <has_size value="49643" delta="300" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	319 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	320 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	321 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	322 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	323 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	324 <param name="command_type" value="filter-kmers" />
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	325 <param name="filter_operations" value="greater-than" />
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	326 <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb" />
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	327 <conditional name="filter_type">
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	328 <param name="distinct" value="0.9998" />
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	329 </conditional>
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	330 </conditional>
8 5ae3496f9ca3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 0625ea0c1df66a724d0ab3769fcaee7a07810a20" iuc parents: 7 diff changeset	331 <output name="read_db" ftype="meryldb">
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	332 <assert_contents>
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	333 <has_size value="1634" delta="300" />
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	334 </assert_contents>
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	335 </output>
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	336 </test>
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	337 <test expect_num_outputs="1">
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	338 <conditional name="operation_type">
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	339 <param name="command_type" value="filter-kmers" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	340 <param name="filter_operations" value="equal-to" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	341 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	342 <conditional name="filter_type">
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	343 <param name="N" value="100" />
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	344 </conditional>
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	345 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	346 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	347 <assert_contents>
8 5ae3496f9ca3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 0625ea0c1df66a724d0ab3769fcaee7a07810a20" iuc parents: 7 diff changeset	348 <has_size value="2621" delta="300" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	349 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	350 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	351 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	352 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	353 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	354 <param name="command_type" value="filter-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	355 <param name="filter_operations" value="not-equal-to" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	356 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	357 <conditional name="filter_type">
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	358 <param name="N" value="100" />
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	359 </conditional>
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	360 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	361 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	362 <assert_contents>
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	363 <has_size value="59100" delta="300" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	364 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	365 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	366 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	367 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	368 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	369 <param name="command_type" value="arithmetic-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	370 <param name="arithmetic_operations" value="increase" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	371 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	372 <param name="X" value="100000" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	373 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	374 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	375 <assert_contents>
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	376 <has_size value="59500" delta="300" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	377 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	378 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	379 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	380 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	381 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	382 <param name="command_type" value="arithmetic-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	383 <param name="arithmetic_operations" value="decrease" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	384 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	385 <param name="X" value="100" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	386 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	387 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	388 <assert_contents>
3 9f7a227436d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit c0960aa14536ee1ef790602255abfafd687e8e69" iuc parents: 2 diff changeset	389 <has_size value="42313" delta="300" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	390 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	391 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	392 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	393 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	394 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	395 <param name="command_type" value="arithmetic-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	396 <param name="arithmetic_operations" value="multiply" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	397 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	398 <param name="X" value="3" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	399 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	400 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	401 <assert_contents>
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	402 <has_size value="60530" delta="300" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	403 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	404 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	405 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	406 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	407 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	408 <param name="command_type" value="arithmetic-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	409 <param name="arithmetic_operations" value="divide" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	410 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	411 <param name="X" value="2" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	412 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	413 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	414 <assert_contents>
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	415 <has_size value="56200" delta="300" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	416 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	417 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	418 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	419 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	420 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	421 <param name="command_type" value="arithmetic-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	422 <param name="arithmetic_operations" value="divide-round" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	423 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	424 <param name="X" value="2" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	425 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	426 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	427 <assert_contents>
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	428 <has_size value="56100" delta="300" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	429 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	430 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	431 </test>
7 51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	432 <!-- test 12 -->
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	433 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	434 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	435 <param name="command_type" value="arithmetic-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	436 <param name="arithmetic_operations" value="modulo" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	437 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	438 <param name="X" value="3" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	439 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	440 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	441 <assert_contents>
7 51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	442 <has_size value="37501" delta="300" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	443 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	444 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	445 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	446 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	447 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	448 <param name="command_type" value="groups-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	449 <param name="groups_operations" value="union" />
6 31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	450 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	451 <param name="input_meryldb_03" value="" ftype="meryldb" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	452 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	453 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	454 <assert_contents>
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	455 <has_size value="36100" delta="300" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	456 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	457 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	458 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	459 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	460 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	461 <param name="command_type" value="groups-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	462 <param name="groups_operations" value="union-min" />
6 31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	463 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	464 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	465 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	466 <assert_contents>
3 9f7a227436d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit c0960aa14536ee1ef790602255abfafd687e8e69" iuc parents: 2 diff changeset	467 <has_size value="58925" delta="350" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	468 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	469 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	470 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	471 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	472 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	473 <param name="command_type" value="groups-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	474 <param name="groups_operations" value="union-max" />
6 31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	475 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	476 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	477 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	478 <assert_contents>
3 9f7a227436d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit c0960aa14536ee1ef790602255abfafd687e8e69" iuc parents: 2 diff changeset	479 <has_size value="58930" delta="300" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	480 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	481 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	482 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	483 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	484 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	485 <param name="command_type" value="groups-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	486 <param name="groups_operations" value="union-sum" />
6 31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	487 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	488 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	489 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	490 <assert_contents>
5 d63739222f68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" iuc parents: 4 diff changeset	491 <has_size value="58600" delta="300" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	492 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	493 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	494 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	495 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	496 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	497 <param name="command_type" value="groups-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	498 <param name="groups_operations" value="intersect" />
6 31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	499 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	500 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	501 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	502 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	503 <has_size value="14951" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	504 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	505 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	506 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	507 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	508 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	509 <param name="command_type" value="groups-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	510 <param name="groups_operations" value="intersect-min" />
6 31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	511 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	512 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	513 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	514 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	515 <has_size value="14957" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	516 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	517 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	518 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	519 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	520 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	521 <param name="command_type" value="groups-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	522 <param name="groups_operations" value="intersect-max" />
6 31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	523 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	524 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	525 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	526 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	527 <has_size value="14956" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	528 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	529 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	530 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	531 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	532 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	533 <param name="command_type" value="groups-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	534 <param name="groups_operations" value="intersect-sum" />
6 31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	535 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	536 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	537 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	538 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	539 <has_size value="14953" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	540 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	541 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	542 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	543 <!-- test 20 -->
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	544 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	545 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	546 <param name="command_type" value="groups-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	547 <param name="groups_operations" value="subtract" />
6 31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	548 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	549 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	550 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	551 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	552 <has_size value="23999" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	553 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	554 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	555 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	556 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	557 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	558 <param name="command_type" value="groups-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	559 <param name="groups_operations" value="difference" />
6 31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	560 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	561 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	562 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	563 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	564 <has_size value="24016" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	565 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	566 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	567 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	568 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	569 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	570 <param name="command_type" value="groups-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	571 <param name="groups_operations" value="symmetric-difference" />
6 31fa26c0692b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3" iuc parents: 5 diff changeset	572 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	573 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	574 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	575 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	576 <has_size value="57455" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	577 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	578 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	579 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	580 <test expect_num_outputs="6">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	581 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	582 <param name="command_type" value="trio-mode" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	583 <param name="child_reads" value="child.fasta" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	584 <param name="paternal_reads" value="paternal.fasta" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	585 <param name="maternal_reads" value="maternal.fasta" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	586 <conditional name="options_kmer_size">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	587 <param name="kmer_size" value="provide" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	588 <param name="input_kmer_size" value="7" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	589 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	590 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	591 <output name="read_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	592 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	593 <has_size value="1573" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	594 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	595 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	596 <output name="read_db_hist" file="output_23.read-db.hist" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	597 <output name="pat_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	598 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	599 <has_size value="1779" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	600 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	601 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	602 <output name="pat_db_hist" file="output_23.pat.hist" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	603 <output name="mat_db" ftype="meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	604 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	605 <has_size value="1569" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	606 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	607 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	608 <output name="mat_db_hist" file="output_23.mat.hist" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	609 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	610 <test expect_num_outputs="1">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	611 <conditional name="operation_type">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	612 <param name="command_type" value="histogram-kmers" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	613 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	614 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	615 <output name="read_db_hist" file="output_24.read-db.hist" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	616 </test>
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	617 <test expect_num_outputs="1">
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	618 <conditional name="operation_type">
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	619 <param name="command_type" value="print" />
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	620 <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb" />
d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	621 </conditional>
8 5ae3496f9ca3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 0625ea0c1df66a724d0ab3769fcaee7a07810a20" iuc parents: 7 diff changeset	622 <output name="read_db_print" file="output_25.read-db.tabular" sort="true" />
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	623 </test>
7 51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	624 <!--Test compressed files-->
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	625 <test expect_num_outputs="1">
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	626 <conditional name="operation_type">
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	627 <param name="command_type" value="count-kmers" />
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	628 <param name="count_operation" value="count" />
8 5ae3496f9ca3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 0625ea0c1df66a724d0ab3769fcaee7a07810a20" iuc parents: 7 diff changeset	629 <param name="input_reads" value="child.fasta.gz" ftype="fasta.gz" />
7 51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	630 <conditional name="options_kmer_size">
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	631 <param name="kmer_size" value="provide" />
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	632 <param name="input_kmer_size" value="7" />
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	633 </conditional>
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	634 </conditional>
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	635 <output name="read_db" ftype="meryldb">
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	636 <assert_contents>
8 5ae3496f9ca3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 0625ea0c1df66a724d0ab3769fcaee7a07810a20" iuc parents: 7 diff changeset	637 <has_size value="22200" delta="300" />
7 51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	638 </assert_contents>
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	639 </output>
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	640 <assert_stdout>
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	641 <has_line line="K-mer size: 7" />
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	642 </assert_stdout>
51c2360aa807 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8" iuc parents: 6 diff changeset	643 </test>
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	644 </tests>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	645 <help><![CDATA[
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	646
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	647 .. class:: infomark
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	648
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	649 Purpose
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	650
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	651 Meryl is the k-mer counter. It is built into the Celera assembler and is also available as a stand-alone application.
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	652 Meryl uses a sorting-based approach that sorts the k-mers in lexicographical order.
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	653
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	654 In addition of generating count-databases, meryl can perform simple operations on it.
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	655
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	656 -----
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	657
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	658 .. class:: infomark
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	659
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	660 Basic functions
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	661
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	662 The functions that meryl includes are described below:
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	663
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	664 ::
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	665
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	666 COUNT OPERATIONS
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	667 - Count: count the occurrences of canonical k-mers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	668 - Count-forward: count the occurreces of forward k-mers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	669 - Count-reverse: count the occurreces of reverse k-mers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	670 FILTERING OPERATIONS
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	671 - Less-than: return k-mers that occur fewer than N times in the input
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	672 - Greater-than: return k-mers that occur more than N times in the input
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	673 - Equal-to: return k-mers that occur exactly N times in the input
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	674 - Not-equal-to: return k-mers that do not occur exactly N times in the input
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	675 ARITHMETIC OPERATIONS
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	676 - Increase: add x to the count of each k-mer
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	677 - Decrease: subsctract x from the count of each k-mer
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	678 - Multiply: multiply the count of each k-mer by x
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	679 - Divide: divide the count of each k-mer by x
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	680 - Divide-round: divide the count of each k-mer by x and round th results
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	681 - Modulo: set the count of each k-mer to the remainder of the count divided by x
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	682 OPERATIONS ON SETS
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	683 - Union-min: return k-mers that occur in any input, set the count to the minimum count
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	684 - Union-max: return k-mers that occur in any input, set the count to the maximum count
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	685 - Union-sum: return k-mers that occur in any input, set the count to the sum of the counts
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	686 - Intersect: return k-mers that occur in all inputs, set the count to the count in the first input
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	687 - Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	688 - Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	689 - Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	690 - Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	691 - Difference: return k-mers that occur in the first input, but none of the other inputs
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	692 - Symmetric-difference: return k-mers that occur in exactly one input
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	693
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	694 -----
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	695
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	696 .. class:: infomark
4 d5d68989caec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" iuc parents: 3 diff changeset	697
0 068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	698 Additional function: build hap-mers dbs for trios
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	699
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	700 In addition of the basic operations, this wrapper allows to build the hap-mers databases for trios, in accordance
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	701 with `merqury's recommended guidelines. <https://github.com/marbl/merqury/wiki/1.-Prepare-meryl-dbs#3-build-hap-mer-dbs-for-trios>`_
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	702
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	703 ]]> </help>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	704 <expand macro="citations" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0" iuc parents: diff changeset	705 </tool>

Mercurial > repos > iuc > meryl

annotate meryl.xml @ 8:5ae3496f9ca3 draft