Mercurial > repos > iuc > meryl
changeset 4:d5d68989caec draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2"
| author | iuc |
|---|---|
| date | Fri, 30 Apr 2021 06:40:29 +0000 |
| parents | 9f7a227436d6 |
| children | d63739222f68 |
| files | macros.xml meryl.xml test-data/maternal.meryldb test-data/output_25.read-db.tabular |
| diffstat | 4 files changed, 81 insertions(+), 18 deletions(-) [+] |
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--- a/macros.xml Thu Apr 15 11:52:39 2021 +0000 +++ b/macros.xml Fri Apr 30 06:40:29 2021 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">1.2</token> - <token name="@GALAXY_TOOL_VERSION@">galaxy1</token> + <token name="@TOOL_VERSION@">1.3</token> + <token name="@GALAXY_TOOL_VERSION@">galaxy0</token> <xml name="edam_ontology"> <edam_topics> <edam_topic>topic_0196</edam_topic> @@ -12,7 +12,7 @@ <xml name="requirements"> <requirements> <requirement type="package" version="1.1">merqury</requirement> - <requirement type="package" version="1.3">meryl</requirement> + <requirement type="package" version="@TOOL_VERSION@">meryl</requirement> <requirement type="package" version="1.34">tar</requirement> </requirements> </xml>
--- a/meryl.xml Thu Apr 15 11:52:39 2021 +0000 +++ b/meryl.xml Fri Apr 30 06:40:29 2021 +0000 @@ -29,7 +29,11 @@ mv ./temp_db/* tmp.meryl && meryl $operation_type.filter_operations - $operation_type.N + #if $operation_type.filter_type.type == 'times' + $operation_type.filter_type.N + #elif $operation_type.filter_type.type == 'frequency' + distinct=${operation_type.filter_type.distinct} + #end if tmp.meryl output read-db.meryl && tar -zcf read-db.meryldb read-db.meryl @@ -60,6 +64,11 @@ 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 == 'print' + mkdir -p ./temp_db/ && + tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ && + mv ./temp_db/* tmp.meryl && + meryl print tmp.meryl > read-db.tabular #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' @@ -138,6 +147,7 @@ <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="print">Print kmer counts to a tabular file</option> <option value="trio-mode">Build hap-mer dbs for trios</option> </param> <when value="count-kmers"> @@ -163,13 +173,25 @@ </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> + <option value="less-than">Less-than: return k-mers that occur fewer than a threshold value</option> + <option value="greater-than">Greater-than: return k-mers that occur more than a threshold value</option> + <option value="equal-to">Equal-to: return k-mers that occur exactly a threshold value</option> + <option value="not-equal-to">Not-equal-to: return k-mers that do not occur exactly a threshold value</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" /> + + <conditional name="filter_type"> + <param name="type" type="select" label="Type of filtering"> + <option value="times">Return kmers that occur N times in the input</option> + <option value="frequency">Return kmers occurring at specific frequencies</option> + </param> + <when value="times"> + <param name="N" type="integer" min="0" max="50000000000" value="" optional="true" label="Number of times in the input" help="Return kmers that occur N times in the input."/> + </when> + <when value="frequency"> + <param name="distinct" type="float" min="0" max="1" value="0.9998" optional="true" label="Frequency" help="Return kmers that at specific frequency (e.g. frequency = 0.9998 returns top 0.02% most frequent)"/> + </when> + </conditional> </when> <when value="arithmetic-kmers"> <param name="arithmetic_operations" type="select" label="Arithmetic operations" help="Select an operation to be executed"> @@ -203,6 +225,9 @@ <when value="histogram-kmers"> <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" /> </when> + <when value="print"> + <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" /> @@ -225,11 +250,14 @@ </inputs> <outputs> <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb" label="${tool.name} on ${on_string}: read-db.meryldb"> - <filter>operation_type["command_type"] != "histogram-kmers"</filter> + <filter>operation_type["command_type"] != "histogram-kmers" and operation_type["command_type"] != "print"</filter> </data> <data name="read_db_hist" format="tabular" from_work_dir="read-db.hist" label="${tool.name} on ${on_string}: read-db histogram"> <filter>operation_type["command_type"] == "histogram-kmers" or operation_type["command_type"] == "trio-mode"</filter> </data> + <data name="read_db_print" format="tabular" from_work_dir="read-db.tabular" label="${tool.name} on ${on_string}: kmer counts"> + <filter>operation_type["command_type"] == "print"</filter> + </data> <data name="pat_db" format="meryldb" from_work_dir="pat.meryldb" label="${tool.name} on ${on_string}: pat.meryldb"> <filter>operation_type["command_type"] == "trio-mode"</filter> </data> @@ -268,7 +296,9 @@ <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 name="filter_type"> + <param name="N" value="100" /> + </conditional> </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> @@ -281,7 +311,9 @@ <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 name="filter_type"> + <param name="N" value="80" /> + </conditional> </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> @@ -292,9 +324,26 @@ <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="maternal.meryldb" ftype="meryldb" /> + <conditional name="filter_type"> + <param name="distinct" value="0.9998" /> + </conditional> + </conditional> + <output name="read_db" ftype="meryldb" > + <assert_contents> + <has_size value="1634" 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 name="filter_type"> + <param name="N" value="100" /> + </conditional> </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> @@ -307,7 +356,9 @@ <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 name="filter_type"> + <param name="N" value="100" /> + </conditional> </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> @@ -575,6 +626,13 @@ </conditional> <output name="read_db_hist" file="output_24.read-db.hist" /> </test> + <test expect_num_outputs="1"> + <conditional name="operation_type"> + <param name="command_type" value="print" /> + <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb" /> + </conditional> + <output name="read_db_print" file="output_25.read-db.tabular" sort="True"/> + </test> </tests> <help><![CDATA[ @@ -588,9 +646,9 @@ 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: @@ -626,9 +684,9 @@ - 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