Mercurial > repos > iuc > meryl
diff meryl.xml @ 0:068920e730f4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f94b7a1d482e29e10c33205ae5394c4c4a1e74e0"
| author | iuc |
|---|---|
| date | Mon, 05 Apr 2021 15:04:36 +0000 |
| parents | |
| children | e5b18909f73d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/meryl.xml Mon Apr 05 15:04:36 2021 +0000 @@ -0,0 +1,629 @@ +<tool id='meryl' name='Meryl' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'> + <description>a genomic k-mer counter and sequence utility</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro='edam_ontology' /> + <expand macro='requirements' /> + <version_command>meryl --version</version_command> + <command detect_errors='exit_code'><![CDATA[ + #if $operation_type.command_type == 'count-kmers' + meryl + #if $operation_type.options_kmer_size.kmer_size == 'estimate' + #from math import log + $operation_type.options_kmer_size.input_kmer_size = int(log(int($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)) + #end if + $operation_type.count_operations + k=$operation_type.options_kmer_size.input_kmer_size + $operation_type.input_reads + output read-db.meryl && + echo 'K-mer size: ${$operation_type.options_kmer_size.input_kmer_size}' && + tar -zcf read-db.meryldb read-db.meryl + #elif $operation_type.command_type == 'filter-kmers' + mkdir -p ./temp_db/ && + tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ && + mv ./temp_db/* tmp.meryl && + meryl + $operation_type.filter_operations + $operation_type.N + tmp.meryl + output read-db.meryl && + tar -zcf read-db.meryldb read-db.meryl + #elif $operation_type.command_type == 'arithmetic-kmers' + mkdir -p ./temp_db/ && + tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ && + mv ./temp_db/* tmp.meryl && + meryl + $operation_type.arithmetic_operations + $operation_type.X + tmp.meryl + output read-db.meryl && + tar -zcf read-db.meryldb read-db.meryl + #elif $operation_type.command_type == 'groups-kmers' + mkdir -p ./temp_db/ && + tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ && + mv ./temp_db/* tmp_01.meryl && + tar -zxf $operation_type.input_meryldb_03 -C ./temp_db/ && + mv ./temp_db/* tmp_02.meryl && + meryl + $operation_type.groups_operations + tmp_01.meryl + tmp_02.meryl + output read-db.meryl && + tar -zcf read-db.meryldb read-db.meryl + #elif $operation_type.command_type == 'histogram-kmers' + mkdir -p ./temp_db/ && + tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ && + mv ./temp_db/* tmp.meryl && + meryl histogram tmp.meryl > read-db.hist + #elif $operation_type.command_type == 'trio-mode' + export MERQURY=\$(dirname \$(command -v merqury.sh))/../share/merqury/ && + #for $i, $read in enumerate($paternal_reads): + mkdir 'paternal{$i}.meryl' && + meryl count k=$operation_type.options_kmer_size.input_kmer_size '${read}' output 'paternal{$i}.meryl' && + #end for + meryl union-sum paternal*.meryl output pat.meryl && + #for $i, $read in enumerate($maternal_reads): + mkdir 'maternal{$i}.meryl' && + meryl count k=$operation_type.options_kmer_size.input_kmer_size '${read}' output 'maternal{$i}.meryl' && + #end for + meryl union-sum maternal*.meryl output mat.meryl && + #for $i, $read in enumerate($child_reads): + mkdir 'child{$i}.meryl' && + meryl count k=$operation_type.options_kmer_size.input_kmer_size '${read}' output 'child{$i}.meryl' && + #end for + meryl union-sum child*.meryl output child.meryl && + ## mat specific kmers + meryl difference mat.meryl pat.meryl output mat.only.meryl && + meryl histogram mat.only.meryl > mat.only.hist && + java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.only.hist > mat.only.ploidy && + VAR=`sed -n 2p mat.only.ploidy | awk '{print \$NF}'` && + meryl greater-than \$VAR output mat.only.filt.meryl mat.only.meryl && + + ## pat specific kmers + meryl difference pat.meryl mat.meryl output pat.only.meryl && + meryl histogram pat.only.meryl > pat.only.hist && + java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.only.hist > pat.only.ploidy && + VAR=`sed -n 2p pat.only.ploidy | awk '{print \$NF}'` && + meryl greater-than \$VAR output pat.only.filt.meryl pat.only.meryl && + + ## shared kmers + meryl intersect output shared.meryl mat.meryl pat.meryl && + + ## mat hapmers + meryl intersect output mat.inherited.meryl child.meryl mat.only.filt.meryl && + meryl histogram mat.inherited.meryl > mat.inherited.hist && + java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.inherited.hist > mat.inherited.ploidy && + VAR=`sed -n 2p mat.inherited.ploidy | awk '{print \$NF}'` && + meryl greater-than \$VAR output mat.hapmer.meryl mat.inherited.meryl && + tar -czf 'mat.meryldb' mat.hapmer.meryl && + + ## pat hapmers + meryl intersect output pat.inherited.meryl child.meryl pat.only.filt.meryl && + meryl histogram pat.inherited.meryl > pat.inherited.hist && + java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.inherited.hist > pat.inherited.ploidy && + VAR=`sed -n 2p pat.inherited.ploidy | awk '{print \$NF}'` && + meryl greater-than \$VAR output pat.hapmer.meryl pat.inherited.meryl && + tar -czf 'pat.meryldb' pat.hapmer.meryl && + + ## shared hapmers + meryl intersect output shared.inherited.meryl child.meryl shared.meryl && + meryl histogram shared.inherited.meryl > shared.inherited.hist && + java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar shared.inherited.hist > shared.inherited.ploidy && + VAR=`sed -n 2p shared.inherited.ploidy | awk '{print \$NF}'` && + meryl greater-than \$VAR output shared.filt.meryl shared.inherited.meryl && + + ## child hapmers + meryl union-sum output child.inherited.meryl mat.inherited.meryl pat.inherited.meryl shared.inherited.meryl && + meryl difference output read.only.meryl child.meryl child.inherited.meryl && + tar -czf 'read-db.meryldb' read.only.meryl && + echo 'K-mer size: ${$operation_type.options_kmer_size.input_kmer_size}' + #end if + ]]> </command> + <inputs> + <conditional name="operation_type"> + <param name="command_type" type="select" label="Operation type selector" help="Select a type of operation"> + <option value="count-kmers">Count operations</option> + <option value="filter-kmers">Filter operations</option> + <option value="arithmetic-kmers">Arithmetic operations on kmer counts</option> + <option value="groups-kmers">Operations on sets of k-mers</option> + <option value="histogram-kmers">Generate histogram dataset</option> + <option value="trio-mode">Build hap-mer dbs for trios</option> + </param> + <when value="count-kmers"> + <param name="count_operations" type="select" label="Count operations" help="Select an operation to be executed"> + <option value="count">Count: count the occurrences of canonical k-mers</option> + <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option> + <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option> + </param> + <param name="input_reads" type="data" format="fastq,fasta" label="Input sequences" help="Select your reads in FASTA/FASTQ format." /> + <conditional name="options_kmer_size"> + <param name="kmer_size" type="select" label="K-mer size selector"> + <option value="provide">Set a k-mer size</option> + <option value="estimate">Estimate the best k-mer size</option> + </param> + <when value="provide"> + <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." /> + </when> + <when value="estimate"> + <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." /> + <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." /> + </when> + </conditional> + </when> + <when value="filter-kmers"> + <param name="filter_operations" type="select" label="Filter operations" help="Select an operation to be executed"> + <option value="less-than">Less-than: return k-mers that occur fewer than N times in the input</option> + <option value="greater-than">Greater-than: return k-mers that occur more than N times in the input</option> + <option value="equal-to">Equal-to: return k-mers that occur exactly N times in the input</option> + <option value="not-equal-to">Not-equal-to: return k-mers that do not occur exactly N times in the input</option> + </param> + <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset" /> + <param name="N" type="integer" min="0" max="50000000000" value="" optional="true" label="Filter value" /> + </when> + <when value="arithmetic-kmers"> + <param name="arithmetic_operations" type="select" label="Arithmetic operations" help="Select an operation to be executed"> + <option value="increase">Increase: add x to the count of each k-mer</option> + <option value="decrease">Decrease: subsctract x from the count of each k-mer</option> + <option value="multiply">Multiply: multiply the count of each k-mer by x</option> + <option value="divide">Divide: divide the count of each k-mer by x</option> + <option value="divide-round">Divide-round: divide the count of each k-mer by x and round th results</option> + <option value="modulo">Modulo: set the count of each k-mer to the remainder of the count divided by x</option> + </param> + <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset" /> + <param name="X" type="integer" min="1" max="1000000" value="" optional="true" label="Operand" /> + </when> + <when value="groups-kmers"> + <param name="groups_operations" type="select" label="Operations on sets of kmers" help="Select an operation to be executed"> + <option value="union">Union: return k-mers that occur in any input</option> + <option value="union-min">Union-min: return k-mers that occur in any input, set the count to the minimum count</option> + <option value="union-max">Union-max: return k-mers that occur in any input, set the count to the maximum count</option> + <option value="union-sum">Union-sum: return k-mers that occur in any input, set the count to the sum of the counts</option> + <option value="intersect">Intersect: return k-mers that occur in all inputs, set the count to the count in the first input</option> + <option value="intersect-min">Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count</option> + <option value="intersect-max">Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count</option> + <option value="intersect-sum">Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts</option> + <option value="subtract">Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs</option> + <option value="difference">Difference: return k-mers that occur in the first input, but none of the other inputs</option> + <option value="symmetric-difference">Symmetric-difference: return k-mers that occur in exactly one input</option> + </param> + <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" /> + <param name="input_meryldb_03" type="data" format="meryldb" label="Input meryldb" /> + </when> + <when value="histogram-kmers"> + <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" /> + </when> + <when value="trio-mode"> + <param name="child_reads" type="data" format="fastq,fasta" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly" /> + <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" /> + <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" /> + <conditional name="options_kmer_size"> + <param name="kmer_size" type="select" label="K-mer size selector"> + <option value="provide">Set a k-mer size</option> + <option value="estimate">Estimate the best k-mer size</option> + </param> + <when value="provide"> + <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." /> + </when> + <when value="estimate"> + <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." /> + <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." /> + </when> + </conditional> + </when> + </conditional> + </inputs> + <outputs> + <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb" label="${tool.name} on ${on_string}: read-db.meryldb"> + <filter>operation_type["command_type"] != "histogram-kmers"</filter> + </data> + <data name="read_db_hist" format="tabular" from_work_dir="read-db.hist" label="${tool.name} on ${on_string}: read-db histogram"> + <filter>operation_type["command_type"] == "histogram-kmers" or operation_type["command_type"] == "trio-mode"</filter> + </data> + <data name="pat_db" format="meryldb" from_work_dir="pat.meryldb" label="${tool.name} on ${on_string}: read-db.meryl"> + <filter>operation_type["command_type"] == "trio-mode"</filter> + </data> + <data name="pat_db_hist" format="tabular" from_work_dir="pat.inherited.hist" label="${tool.name} on ${on_string}: paternal inherited histogram"> + <filter>operation_type["command_type"] == "trio-mode"</filter> + </data> + <data name="mat_db" format="meryldb" from_work_dir="mat.meryldb" label="${tool.name} on ${on_string}: mat.meryl"> + <filter>operation_type["command_type"] == "trio-mode"</filter> + </data> + <data name="mat_db_hist" format="tabular" from_work_dir="mat.inherited.hist" label="${tool.name} on ${on_string}: maternal inherited histogram"> + <filter>operation_type["command_type"] == "trio-mode"</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="count-kmers" /> + <param name="count_operation" value="count" /> + <param name="input_reads" value="child.fasta" /> + <conditional name="options_kmer_size"> + <param name="kmer_size" value="provide" /> + <param name="input_kmer_size" value="7" /> + </conditional> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="22152" delta="300" /> + </assert_contents> + </output> + <assert_stdout> + <has_line line="K-mer size: 7" /> + </assert_stdout> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="filter-kmers" /> + <param name="filter_operations" value="less-than" /> + <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> + <param name="N" value="100" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="32077" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="filter-kmers" /> + <param name="filter_operations" value="greater-than" /> + <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> + <param name="N" value="80" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="49951" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="filter-kmers" /> + <param name="filter_operations" value="equal-to" /> + <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> + <param name="N" value="100" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="2621" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="filter-kmers" /> + <param name="filter_operations" value="not-equal-to" /> + <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> + <param name="N" value="100" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="59378" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="arithmetic-kmers" /> + <param name="arithmetic_operations" value="increase" /> + <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> + <param name="X" value="100000" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="59822" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="arithmetic-kmers" /> + <param name="arithmetic_operations" value="decrease" /> + <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> + <param name="X" value="100" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="42625" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="arithmetic-kmers" /> + <param name="arithmetic_operations" value="multiply" /> + <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> + <param name="X" value="3" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="60832" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="arithmetic-kmers" /> + <param name="arithmetic_operations" value="divide" /> + <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> + <param name="X" value="2" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="56569" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="arithmetic-kmers" /> + <param name="arithmetic_operations" value="divide-round" /> + <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> + <param name="X" value="2" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="56539" delta="300" /> + </assert_contents> + </output> + </test> + <!-- test 11 --> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="arithmetic-kmers" /> + <param name="arithmetic_operations" value="modulo" /> + <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> + <param name="X" value="3" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="37542" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="groups-kmers" /> + <param name="groups_operations" value="union" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="36417" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="groups-kmers" /> + <param name="groups_operations" value="union-min" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="59226" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="groups-kmers" /> + <param name="groups_operations" value="union-max" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="59234" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="groups-kmers" /> + <param name="groups_operations" value="union-sum" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="59004" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="groups-kmers" /> + <param name="groups_operations" value="intersect" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="14951" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="groups-kmers" /> + <param name="groups_operations" value="intersect-min" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="14957" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="groups-kmers" /> + <param name="groups_operations" value="intersect-max" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="14956" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="groups-kmers" /> + <param name="groups_operations" value="intersect-sum" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="14953" delta="300" /> + </assert_contents> + </output> + </test> + <!-- test 20 --> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="groups-kmers" /> + <param name="groups_operations" value="subtract" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="23999" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="groups-kmers" /> + <param name="groups_operations" value="difference" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="24016" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="groups-kmers" /> + <param name="groups_operations" value="symmetric-difference" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="57455" delta="300" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="6"> + <conditional name="operation_type"> + <param name="command_type" value="trio-mode" /> + <param name="child_reads" value="child.fasta" /> + <param name="paternal_reads" value="paternal.fasta" /> + <param name="maternal_reads" value="maternal.fasta" /> + <conditional name="options_kmer_size"> + <param name="kmer_size" value="provide" /> + <param name="input_kmer_size" value="7" /> + </conditional> + </conditional> + <output name="read_db" ftype="meryldb"> + <assert_contents> + <has_size value="1573" delta="300" /> + </assert_contents> + </output> + <output name="read_db_hist" file="output_23.read-db.hist" /> + <output name="pat_db" ftype="meryldb"> + <assert_contents> + <has_size value="1779" delta="300" /> + </assert_contents> + </output> + <output name="pat_db_hist" file="output_23.pat.hist" /> + <output name="mat_db" ftype="meryldb"> + <assert_contents> + <has_size value="1569" delta="300" /> + </assert_contents> + </output> + <output name="mat_db_hist" file="output_23.mat.hist" /> + </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="histogram-kmers" /> + <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> + </conditional> + <output name="read_db_hist" file="output_24.read-db.hist" /> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**Purpose** + +Meryl is the k-mer counter. It is built into the Celera assembler and is also available as a stand-alone application. +Meryl uses a sorting-based approach that sorts the k-mers in lexicographical order. + +In addition of generating count-databases, meryl can perform simple operations on it. + +----- + +.. class:: infomark + +**Basic functions** + +The functions that meryl includes are described below: + + :: + + COUNT OPERATIONS + - Count: count the occurrences of canonical k-mers + - Count-forward: count the occurreces of forward k-mers + - Count-reverse: count the occurreces of reverse k-mers + FILTERING OPERATIONS + - Less-than: return k-mers that occur fewer than N times in the input + - Greater-than: return k-mers that occur more than N times in the input + - Equal-to: return k-mers that occur exactly N times in the input + - Not-equal-to: return k-mers that do not occur exactly N times in the input + ARITHMETIC OPERATIONS + - Increase: add x to the count of each k-mer + - Decrease: subsctract x from the count of each k-mer + - Multiply: multiply the count of each k-mer by x + - Divide: divide the count of each k-mer by x + - Divide-round: divide the count of each k-mer by x and round th results + - Modulo: set the count of each k-mer to the remainder of the count divided by x + OPERATIONS ON SETS + - Union-min: return k-mers that occur in any input, set the count to the minimum count + - Union-max: return k-mers that occur in any input, set the count to the maximum count + - Union-sum: return k-mers that occur in any input, set the count to the sum of the counts + - Intersect: return k-mers that occur in all inputs, set the count to the count in the first input + - Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count + - Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count + - Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts + - Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs + - Difference: return k-mers that occur in the first input, but none of the other inputs + - Symmetric-difference: return k-mers that occur in exactly one input + +----- + +.. class:: infomark + +**Additional function: build hap-mers dbs for trios** + +In addition of the basic operations, this wrapper allows to build the hap-mers databases for trios, in accordance +with `merqury's recommended guidelines. <https://github.com/marbl/merqury/wiki/1.-Prepare-meryl-dbs#3-build-hap-mer-dbs-for-trios>`_ + + ]]> </help> + <expand macro="citations" /> +</tool>