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comparison meryl.xml @ 2:35ac9de60bec draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929"
author iuc
date Fri, 09 Apr 2021 13:21:51 +0000
parents e5b18909f73d
children 9f7a227436d6
comparison
equal deleted inserted replaced
1:e5b18909f73d 2:35ac9de60bec
6 <expand macro='edam_ontology' /> 6 <expand macro='edam_ontology' />
7 <expand macro='requirements' /> 7 <expand macro='requirements' />
8 <version_command>meryl --version</version_command> 8 <version_command>meryl --version</version_command>
9 <command detect_errors='exit_code'><![CDATA[ 9 <command detect_errors='exit_code'><![CDATA[
10 #if $operation_type.command_type == 'count-kmers' 10 #if $operation_type.command_type == 'count-kmers'
11 meryl
12 #if $operation_type.options_kmer_size.kmer_size == 'estimate' 11 #if $operation_type.options_kmer_size.kmer_size == 'estimate'
13 #from math import log 12 #from math import log
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)) 13 #set size=int(log(int($operation_type.options_kmer_size.genome_size)*(1-float($operation_type.options_kmer_size.collision_rate))/float($operation_type.options_kmer_size.collision_rate))/log(4))
14 #elif $operation_type.options_kmer_size.kmer_size == 'provide'
15 #set size=$operation_type.options_kmer_size.input_kmer_size
15 #end if 16 #end if
17 meryl
16 $operation_type.count_operations 18 $operation_type.count_operations
17 k=$operation_type.options_kmer_size.input_kmer_size 19 k=$size
20 memory=\${GALAXY_MEMORY_GB:-1}
21 threads=\${GALAXY_SLOTS:-1}
18 $operation_type.input_reads 22 $operation_type.input_reads
19 output read-db.meryl && 23 output read-db.meryl &&
20 echo 'K-mer size: ${$operation_type.options_kmer_size.input_kmer_size}' && 24 echo 'K-mer size: ${size}' &&
21 tar -zcf read-db.meryldb read-db.meryl 25 tar -zcf read-db.meryldb read-db.meryl
22 #elif $operation_type.command_type == 'filter-kmers' 26 #elif $operation_type.command_type == 'filter-kmers'
23 mkdir -p ./temp_db/ && 27 mkdir -p ./temp_db/ &&
24 tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ && 28 tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&
25 mv ./temp_db/* tmp.meryl && 29 mv ./temp_db/* tmp.meryl &&
56 tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ && 60 tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&
57 mv ./temp_db/* tmp.meryl && 61 mv ./temp_db/* tmp.meryl &&
58 meryl histogram tmp.meryl > read-db.hist 62 meryl histogram tmp.meryl > read-db.hist
59 #elif $operation_type.command_type == 'trio-mode' 63 #elif $operation_type.command_type == 'trio-mode'
60 export MERQURY=\$(dirname \$(command -v merqury.sh))/../share/merqury/ && 64 export MERQURY=\$(dirname \$(command -v merqury.sh))/../share/merqury/ &&
65 #if $operation_type.options_kmer_size.kmer_size == 'estimate'
66 #from math import log
67 #set size=int(log(int($operation_type.options_kmer_size.genome_size)*(1-float($operation_type.options_kmer_size.collision_rate))/float($operation_type.options_kmer_size.collision_rate))/log(4))
68 #elif $operation_type.options_kmer_size.kmer_size == 'provide'
69 #set size=$operation_type.options_kmer_size.input_kmer_size
70 #end if
61 #for $i, $read in enumerate($paternal_reads): 71 #for $i, $read in enumerate($paternal_reads):
62 mkdir 'paternal{$i}.meryl' && 72 mkdir 'paternal{$i}.meryl' &&
63 meryl count k=$operation_type.options_kmer_size.input_kmer_size '${read}' output 'paternal{$i}.meryl' && 73 meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'paternal{$i}.meryl' &&
64 #end for 74 #end for
65 meryl union-sum paternal*.meryl output pat.meryl && 75 meryl union-sum paternal*.meryl output pat.meryl &&
66 #for $i, $read in enumerate($maternal_reads): 76 #for $i, $read in enumerate($maternal_reads):
67 mkdir 'maternal{$i}.meryl' && 77 mkdir 'maternal{$i}.meryl' &&
68 meryl count k=$operation_type.options_kmer_size.input_kmer_size '${read}' output 'maternal{$i}.meryl' && 78 meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'maternal{$i}.meryl' &&
69 #end for 79 #end for
70 meryl union-sum maternal*.meryl output mat.meryl && 80 meryl union-sum maternal*.meryl output mat.meryl &&
71 #for $i, $read in enumerate($child_reads): 81 #for $i, $read in enumerate($child_reads):
72 mkdir 'child{$i}.meryl' && 82 mkdir 'child{$i}.meryl' &&
73 meryl count k=$operation_type.options_kmer_size.input_kmer_size '${read}' output 'child{$i}.meryl' && 83 meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'child{$i}.meryl' &&
74 #end for 84 #end for
75 meryl union-sum child*.meryl output child.meryl && 85 meryl union-sum child*.meryl output child.meryl &&
76 ## mat specific kmers 86 ## mat specific kmers
77 meryl difference mat.meryl pat.meryl output mat.only.meryl && 87 meryl difference mat.meryl pat.meryl output mat.only.meryl &&
78 meryl histogram mat.only.meryl > mat.only.hist && 88 meryl histogram mat.only.meryl > mat.only.hist &&
115 125
116 ## child hapmers 126 ## child hapmers
117 meryl union-sum output child.inherited.meryl mat.inherited.meryl pat.inherited.meryl shared.inherited.meryl && 127 meryl union-sum output child.inherited.meryl mat.inherited.meryl pat.inherited.meryl shared.inherited.meryl &&
118 meryl difference output read.only.meryl child.meryl child.inherited.meryl && 128 meryl difference output read.only.meryl child.meryl child.inherited.meryl &&
119 tar -czf 'read-db.meryldb' read.only.meryl && 129 tar -czf 'read-db.meryldb' read.only.meryl &&
120 echo 'K-mer size: ${$operation_type.options_kmer_size.input_kmer_size}' 130 echo 'K-mer size: ${size}'
121 #end if 131 #end if
122 ]]> </command> 132 ]]> </command>
123 <inputs> 133 <inputs>
124 <conditional name="operation_type"> 134 <conditional name="operation_type">
125 <param name="command_type" type="select" label="Operation type selector" help="Select a type of operation"> 135 <param name="command_type" type="select" label="Operation type selector" help="Select a type of operation">
141 <param name="kmer_size" type="select" label="K-mer size selector"> 151 <param name="kmer_size" type="select" label="K-mer size selector">
142 <option value="provide">Set a k-mer size</option> 152 <option value="provide">Set a k-mer size</option>
143 <option value="estimate">Estimate the best k-mer size</option> 153 <option value="estimate">Estimate the best k-mer size</option>
144 </param> 154 </param>
145 <when value="provide"> 155 <when value="provide">
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." /> 156 <param name="input_kmer_size" type="integer" min="1" max="50" value="" label="K-mer size" help="For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G).." />
147 </when> 157 </when>
148 <when value="estimate"> 158 <when value="estimate">
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." /> 159 <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." />
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." /> 160 <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." />
151 </when> 161 </when>
201 <param name="kmer_size" type="select" label="K-mer size selector"> 211 <param name="kmer_size" type="select" label="K-mer size selector">
202 <option value="provide">Set a k-mer size</option> 212 <option value="provide">Set a k-mer size</option>
203 <option value="estimate">Estimate the best k-mer size</option> 213 <option value="estimate">Estimate the best k-mer size</option>
204 </param> 214 </param>
205 <when value="provide"> 215 <when value="provide">
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." /> 216 <param name="input_kmer_size" type="integer" min="1" max="50" value="" label="K-mer size" help="For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G)." />
207 </when> 217 </when>
208 <when value="estimate"> 218 <when value="estimate">
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." /> 219 <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." />
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." /> 220 <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." />
211 </when> 221 </when>