annotate meryl.xml @ 1:e5b18909f73d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f25c9977e86fd2858ea9367e53afc298372a8dec"
author iuc
date Thu, 08 Apr 2021 19:22:17 +0000
parents 068920e730f4
children 35ac9de60bec
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
1 <tool id='meryl' name='Meryl' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'>
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[
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
10 #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
11 meryl
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
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
14 $operation_type.options_kmer_size.input_kmer_size = int(log(int($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))
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
15 #end if
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
16 $operation_type.count_operations
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
17 k=$operation_type.options_kmer_size.input_kmer_size
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
18 $operation_type.input_reads
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
19 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
20 echo 'K-mer size: ${$operation_type.options_kmer_size.input_kmer_size}' &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
21 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
22 #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
23 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
24 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
25 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
26 meryl
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
27 $operation_type.filter_operations
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
28 $operation_type.N
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
29 tmp.meryl
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
30 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
31 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
32 #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
33 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
34 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
35 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
36 meryl
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
37 $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
38 $operation_type.X
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
39 tmp.meryl
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
40 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
41 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
42 #elif $operation_type.command_type == 'groups-kmers'
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
43 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
44 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
45 mv ./temp_db/* tmp_01.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
46 tar -zxf $operation_type.input_meryldb_03 -C ./temp_db/ &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
47 mv ./temp_db/* tmp_02.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
48 meryl
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
49 $operation_type.groups_operations
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
50 tmp_01.meryl
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
51 tmp_02.meryl
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
52 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
53 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
54 #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
55 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
56 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
57 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
58 meryl histogram tmp.meryl > read-db.hist
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
59 #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
60 export MERQURY=\$(dirname \$(command -v merqury.sh))/../share/merqury/ &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
61 #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
62 mkdir 'paternal{$i}.meryl' &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
63 meryl count k=$operation_type.options_kmer_size.input_kmer_size '${read}' output 'paternal{$i}.meryl' &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
64 #end for
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
65 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
66 #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
67 mkdir 'maternal{$i}.meryl' &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
68 meryl count k=$operation_type.options_kmer_size.input_kmer_size '${read}' output 'maternal{$i}.meryl' &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
69 #end for
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
70 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
71 #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
72 mkdir 'child{$i}.meryl' &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
73 meryl count k=$operation_type.options_kmer_size.input_kmer_size '${read}' output 'child{$i}.meryl' &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
74 #end for
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
75 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
76 ## mat specific kmers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
77 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
78 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
79 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
80 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
81 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
82
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
83 ## pat specific kmers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
84 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
85 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
86 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
87 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
88 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
89
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
90 ## shared kmers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
91 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
92
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
93 ## mat hapmers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
94 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
95 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
96 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
97 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
98 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
99 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
100
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
101 ## pat hapmers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
102 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
103 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
104 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
105 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
106 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
107 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
108
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
109 ## shared hapmers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
110 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
111 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
112 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
113 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
114 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
115
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
116 ## child hapmers
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
117 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
118 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
119 tar -czf 'read-db.meryldb' read.only.meryl &&
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
120 echo 'K-mer size: ${$operation_type.options_kmer_size.input_kmer_size}'
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
121 #end if
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
122 ]]> </command>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
123 <inputs>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
124 <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
125 <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
126 <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
127 <option value="filter-kmers">Filter operations</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
128 <option value="arithmetic-kmers">Arithmetic operations on kmer counts</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
129 <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
130 <option value="histogram-kmers">Generate histogram dataset</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
131 <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
132 </param>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
133 <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
134 <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
135 <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
136 <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
137 <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
138 </param>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
139 <param name="input_reads" type="data" format="fastq,fasta" label="Input sequences" help="Select your reads in FASTA/FASTQ format." />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
140 <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
141 <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
142 <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
143 <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
144 </param>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
145 <when value="provide">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
146 <param name="input_kmer_size" type="integer" min="1" max="50" value="" label="K-mer 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
147 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
148 <when value="estimate">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
149 <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
150 <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
151 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
152 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
153 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
154 <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
155 <param name="filter_operations" type="select" label="Filter 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
156 <option value="less-than">Less-than: return k-mers that occur fewer than N times in the input</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
157 <option value="greater-than">Greater-than: return k-mers that occur more than N times in the input</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
158 <option value="equal-to">Equal-to: return k-mers that occur exactly N times in the input</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
159 <option value="not-equal-to">Not-equal-to: return k-mers that do not occur exactly N times in the input</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
160 </param>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
161 <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
162 <param name="N" type="integer" min="0" max="50000000000" value="" optional="true" label="Filter value" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
163 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
164 <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
165 <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
166 <option value="increase">Increase: add x to the count of each k-mer</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
167 <option value="decrease">Decrease: subsctract x from the count of each k-mer</option>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
168 <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
169 <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
170 <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
171 <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
172 </param>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
173 <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
174 <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
175 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
176 <when value="groups-kmers">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
177 <param name="groups_operations" type="select" label="Operations on sets of kmers" 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
178 <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
179 <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
180 <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
181 <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
182 <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
183 <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
184 <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
185 <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
186 <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
187 <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
188 <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
189 </param>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
190 <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
191 <param name="input_meryldb_03" 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
192 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
193 <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
194 <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
195 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
196 <when value="trio-mode">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
197 <param name="child_reads" type="data" format="fastq,fasta" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
198 <param name="paternal_reads" type="data" format="fastq,fasta" multiple="true" optional="true" label="Paternal reads" help="Select the paternal reads used for generating the assembly" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
199 <param name="maternal_reads" type="data" format="fastq,fasta" multiple="true" optional="true" label="Maternal reads" help="Select the maternal reads used for generating the assembly" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
200 <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
201 <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
202 <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
203 <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
204 </param>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
205 <when value="provide">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
206 <param name="input_kmer_size" type="integer" min="1" max="50" value="" label="K-mer 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
207 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
208 <when value="estimate">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
209 <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
210 <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
211 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
212 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
213 </when>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
214 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
215 </inputs>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
216 <outputs>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
217 <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb" label="${tool.name} on ${on_string}: read-db.meryldb">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
218 <filter>operation_type["command_type"] != "histogram-kmers"</filter>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
219 </data>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
220 <data name="read_db_hist" format="tabular" from_work_dir="read-db.hist" label="${tool.name} on ${on_string}: read-db histogram">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
221 <filter>operation_type["command_type"] == "histogram-kmers" or operation_type["command_type"] == "trio-mode"</filter>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
222 </data>
1
e5b18909f73d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f25c9977e86fd2858ea9367e53afc298372a8dec"
iuc
parents: 0
diff changeset
223 <data name="pat_db" format="meryldb" from_work_dir="pat.meryldb" label="${tool.name} on ${on_string}: pat.meryldb">
0
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
224 <filter>operation_type["command_type"] == "trio-mode"</filter>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
225 </data>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
226 <data name="pat_db_hist" format="tabular" from_work_dir="pat.inherited.hist" label="${tool.name} on ${on_string}: paternal inherited histogram">
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
227 <filter>operation_type["command_type"] == "trio-mode"</filter>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
228 </data>
1
e5b18909f73d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f25c9977e86fd2858ea9367e53afc298372a8dec"
iuc
parents: 0
diff changeset
229 <data name="mat_db" format="meryldb" from_work_dir="mat.meryldb" label="${tool.name} on ${on_string}: mat.meryldb">
0
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
230 <filter>operation_type["command_type"] == "trio-mode"</filter>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
231 </data>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
232 <data name="mat_db_hist" format="tabular" from_work_dir="mat.inherited.hist" label="${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
233 <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
234 </data>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
235 </outputs>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
236 <tests>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
237 <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
238 <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
239 <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
240 <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
241 <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
242 <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
243 <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
244 <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
245 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
246 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
247 <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
248 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
249 <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
250 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
251 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
252 <assert_stdout>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
253 <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
254 </assert_stdout>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
255 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
256 <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
257 <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
258 <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
259 <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
260 <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
261 <param name="N" value="100" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
262 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
263 <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
264 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
265 <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
266 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
267 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
268 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
269 <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
270 <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
271 <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
272 <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
273 <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
274 <param name="N" value="80" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
275 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
276 <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
277 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
278 <has_size value="49951" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
279 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
280 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
281 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
282 <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
283 <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
284 <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
285 <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
286 <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
287 <param name="N" value="100" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
288 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
289 <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
290 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
291 <has_size value="2621" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
292 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
293 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
294 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
295 <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
296 <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
297 <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
298 <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
299 <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
300 <param name="N" value="100" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
301 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
302 <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
303 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
304 <has_size value="59378" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
305 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
306 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
307 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
308 <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
309 <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
310 <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
311 <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
312 <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
313 <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
314 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
315 <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
316 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
317 <has_size value="59822" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
318 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
319 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
320 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
321 <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
322 <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
323 <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
324 <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
325 <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
326 <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
327 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
328 <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
329 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
330 <has_size value="42625" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
331 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
332 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
333 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
334 <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
335 <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
336 <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
337 <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
338 <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
339 <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
340 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
341 <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
342 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
343 <has_size value="60832" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
344 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
345 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
346 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
347 <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
348 <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
349 <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
350 <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
351 <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
352 <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
353 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
354 <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
355 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
356 <has_size value="56569" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
357 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
358 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
359 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
360 <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
361 <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
362 <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
363 <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
364 <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
365 <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
366 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
367 <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
368 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
369 <has_size value="56539" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
370 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
371 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
372 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
373 <!-- test 11 -->
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
374 <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
375 <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
376 <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
377 <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
378 <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
379 <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
380 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
381 <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
382 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
383 <has_size value="37542" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
384 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
385 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
386 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
387 <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
388 <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
389 <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
390 <param name="groups_operations" value="union" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
391 <param name="input_meryldb_02" value="output_02.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
392 <param name="input_meryldb_03" value="output_03.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
393 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
394 <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
395 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
396 <has_size value="36417" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
397 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
398 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
399 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
400 <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
401 <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
402 <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
403 <param name="groups_operations" value="union-min" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
404 <param name="input_meryldb_02" value="output_02.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
405 <param name="input_meryldb_03" value="output_03.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
406 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
407 <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
408 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
409 <has_size value="59226" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
410 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
411 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
412 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
413 <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
414 <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
415 <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
416 <param name="groups_operations" value="union-max" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
417 <param name="input_meryldb_02" value="output_02.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
418 <param name="input_meryldb_03" value="output_03.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
419 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
420 <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
421 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
422 <has_size value="59234" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
423 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
424 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
425 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
426 <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
427 <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
428 <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
429 <param name="groups_operations" value="union-sum" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
430 <param name="input_meryldb_02" value="output_02.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
431 <param name="input_meryldb_03" value="output_03.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
432 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
433 <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
434 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
435 <has_size value="59004" delta="300" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
436 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
437 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
438 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
439 <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
440 <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
441 <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
442 <param name="groups_operations" value="intersect" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
443 <param name="input_meryldb_02" value="output_02.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
444 <param name="input_meryldb_03" value="output_03.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
445 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
446 <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
447 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
448 <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
449 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
450 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
451 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
452 <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
453 <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
454 <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
455 <param name="groups_operations" value="intersect-min" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
456 <param name="input_meryldb_02" value="output_02.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
457 <param name="input_meryldb_03" value="output_03.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
458 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
459 <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
460 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
461 <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
462 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
463 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
464 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
465 <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
466 <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
467 <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
468 <param name="groups_operations" value="intersect-max" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
469 <param name="input_meryldb_02" value="output_02.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
470 <param name="input_meryldb_03" value="output_03.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
471 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
472 <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
473 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
474 <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
475 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
476 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
477 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
478 <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
479 <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
480 <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
481 <param name="groups_operations" value="intersect-sum" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
482 <param name="input_meryldb_02" value="output_02.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
483 <param name="input_meryldb_03" value="output_03.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
484 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
485 <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
486 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
487 <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
488 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
489 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
490 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
491 <!-- test 20 -->
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
492 <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
493 <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
494 <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
495 <param name="groups_operations" value="subtract" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
496 <param name="input_meryldb_02" value="output_02.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
497 <param name="input_meryldb_03" value="output_03.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
498 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
499 <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
500 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
501 <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
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 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
504 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
505 <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
506 <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
507 <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
508 <param name="groups_operations" value="difference" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
509 <param name="input_meryldb_02" value="output_02.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
510 <param name="input_meryldb_03" value="output_03.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
511 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
512 <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
513 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
514 <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
515 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
516 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
517 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
518 <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
519 <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
520 <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
521 <param name="groups_operations" value="symmetric-difference" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
522 <param name="input_meryldb_02" value="output_02.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
523 <param name="input_meryldb_03" value="output_03.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
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="57455" 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="6">
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="trio-mode" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
534 <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
535 <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
536 <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
537 <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
538 <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
539 <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
540 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
541 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
542 <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
543 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
544 <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
545 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
546 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
547 <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
548 <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
549 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
550 <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
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 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
553 <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
554 <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
555 <assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
556 <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
557 </assert_contents>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
558 </output>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
559 <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
560 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
561 <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
562 <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
563 <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
564 <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
565 </conditional>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
566 <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
567 </test>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
568 </tests>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
569 <help><![CDATA[
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
570
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
571 .. class:: infomark
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
572
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
573 **Purpose**
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
574
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
575 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
576 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
577
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
578 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
579
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
580 -----
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
581
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
582 .. class:: infomark
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
583
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
584 **Basic functions**
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
585
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
586 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
587
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
588 ::
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
589
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
590 COUNT OPERATIONS
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
591 - 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
592 - 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
593 - 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
594 FILTERING OPERATIONS
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
595 - 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
596 - 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
597 - 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
598 - 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
599 ARITHMETIC OPERATIONS
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
600 - 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
601 - 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
602 - 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
603 - 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
604 - 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
605 - 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
606 OPERATIONS ON SETS
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
607 - 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
608 - 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
609 - 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
610 - 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
611 - 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
612 - 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
613 - 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
614 - 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
615 - 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
616 - 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
617
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
618 -----
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
619
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
620 .. class:: infomark
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
621
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
622 **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
623
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
624 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
625 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
626
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
627 ]]> </help>
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
628 <expand macro="citations" />
068920e730f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
iuc
parents:
diff changeset
629 </tool>