| Previous changeset 1:e5b18909f73d (2021-04-08) Next changeset 3:9f7a227436d6 (2021-04-15) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 9c098f0bdeca38de2f282a85a20e9e6fb3fd4929" |
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modified:
macros.xml meryl.xml |
| b |
| diff -r e5b18909f73d -r 35ac9de60bec macros.xml --- a/macros.xml Thu Apr 08 19:22:17 2021 +0000 +++ b/macros.xml Fri Apr 09 13:21:51 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.2</token> - <token name="@GALAXY_TOOL_VERSION@">galaxy0</token> + <token name="@GALAXY_TOOL_VERSION@">galaxy1</token> <xml name="edam_ontology"> <edam_topics> <edam_topic>topic_0196</edam_topic> |
| b |
| diff -r e5b18909f73d -r 35ac9de60bec meryl.xml --- a/meryl.xml Thu Apr 08 19:22:17 2021 +0000 +++ b/meryl.xml Fri Apr 09 13:21:51 2021 +0000 |
| [ |
| @@ -8,16 +8,20 @@ <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)) + #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)) + #elif $operation_type.options_kmer_size.kmer_size == 'provide' + #set size=$operation_type.options_kmer_size.input_kmer_size #end if + meryl $operation_type.count_operations - k=$operation_type.options_kmer_size.input_kmer_size + k=$size + memory=\${GALAXY_MEMORY_GB:-1} + threads=\${GALAXY_SLOTS:-1} $operation_type.input_reads output read-db.meryl && - echo 'K-mer size: ${$operation_type.options_kmer_size.input_kmer_size}' && + echo 'K-mer size: ${size}' && tar -zcf read-db.meryldb read-db.meryl #elif $operation_type.command_type == 'filter-kmers' mkdir -p ./temp_db/ && @@ -58,19 +62,25 @@ meryl histogram tmp.meryl > read-db.hist #elif $operation_type.command_type == 'trio-mode' export MERQURY=\$(dirname \$(command -v merqury.sh))/../share/merqury/ && + #if $operation_type.options_kmer_size.kmer_size == 'estimate' + #from math import log + #set size=int(log(int($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)) + #elif $operation_type.options_kmer_size.kmer_size == 'provide' + #set size=$operation_type.options_kmer_size.input_kmer_size + #end if #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' && + meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${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' && + meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${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' && + meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'child{$i}.meryl' && #end for meryl union-sum child*.meryl output child.meryl && ## mat specific kmers @@ -117,7 +127,7 @@ 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}' + echo 'K-mer size: ${size}' #end if ]]> </command> <inputs> @@ -143,7 +153,7 @@ <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." /> + <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).." /> </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." /> @@ -203,7 +213,7 @@ <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." /> + <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)." /> </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." /> |