| Previous changeset 3:9f7a227436d6 (2021-04-15) Next changeset 5:d63739222f68 (2021-05-23) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 51618128e9d1a23f1f3a8c9df7f2b23a2ba3f3c2" |
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modified:
macros.xml meryl.xml |
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added:
test-data/maternal.meryldb test-data/output_25.read-db.tabular |
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| diff -r 9f7a227436d6 -r d5d68989caec macros.xml --- a/macros.xml Thu Apr 15 11:52:39 2021 +0000 +++ b/macros.xml Fri Apr 30 06:40:29 2021 +0000 |
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| @@ -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> |
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| diff -r 9f7a227436d6 -r d5d68989caec meryl.xml --- a/meryl.xml Thu Apr 15 11:52:39 2021 +0000 +++ b/meryl.xml Fri Apr 30 06:40:29 2021 +0000 |
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| b'@@ -29,7 +29,11 @@\n mv ./temp_db/* tmp.meryl &&\n meryl\n $operation_type.filter_operations\n- $operation_type.N\n+ #if $operation_type.filter_type.type == \'times\'\n+ $operation_type.filter_type.N\n+ #elif $operation_type.filter_type.type == \'frequency\'\n+ distinct=${operation_type.filter_type.distinct}\n+ #end if\n tmp.meryl\n output read-db.meryl &&\n tar -zcf read-db.meryldb read-db.meryl\n@@ -60,6 +64,11 @@\n tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&\n mv ./temp_db/* tmp.meryl &&\n meryl histogram tmp.meryl > read-db.hist\n+ #elif $operation_type.command_type == \'print\'\n+ mkdir -p ./temp_db/ &&\n+ tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&\n+ mv ./temp_db/* tmp.meryl &&\n+ meryl print tmp.meryl > read-db.tabular\n #elif $operation_type.command_type == \'trio-mode\'\n export MERQURY=\\$(dirname \\$(command -v merqury.sh))/../share/merqury/ &&\n #if $operation_type.options_kmer_size.kmer_size == \'estimate\'\n@@ -138,6 +147,7 @@\n <option value="arithmetic-kmers">Arithmetic operations on kmer counts</option>\n <option value="groups-kmers">Operations on sets of k-mers</option>\n <option value="histogram-kmers">Generate histogram dataset</option>\n+ <option value="print">Print kmer counts to a tabular file</option>\n <option value="trio-mode">Build hap-mer dbs for trios</option>\n </param>\n <when value="count-kmers">\n@@ -163,13 +173,25 @@\n </when>\n <when value="filter-kmers">\n <param name="filter_operations" type="select" label="Filter operations" help="Select an operation to be executed">\n- <option value="less-than">Less-than: return k-mers that occur fewer than N times in the input</option>\n- <option value="greater-than">Greater-than: return k-mers that occur more than N times in the input</option>\n- <option value="equal-to">Equal-to: return k-mers that occur exactly N times in the input</option>\n- <option value="not-equal-to">Not-equal-to: return k-mers that do not occur exactly N times in the input</option>\n+ <option value="less-than">Less-than: return k-mers that occur fewer than a threshold value</option>\n+ <option value="greater-than">Greater-than: return k-mers that occur more than a threshold value</option>\n+ <option value="equal-to">Equal-to: return k-mers that occur exactly a threshold value</option>\n+ <option value="not-equal-to">Not-equal-to: return k-mers that do not occur exactly a threshold value</option>\n </param>\n <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset" />\n- <param name="N" type="integer" min="0" max="50000000000" value="" optional="true" label="Filter value" />\n+ \n+ <conditional name="filter_type">\n+ <param name="type" type="select" label="Type of filtering">\n+ <option value="times">Return kmers that occur N times in the input</option>\n+ <option value="frequency">Return kmers occurring at specific frequencies</option>\n+ </param>\n+ <when value="times">\n+ <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."/>\n+ </when>\n+ <when value="frequency">\n+ <param name="distinct" type="float" min="0" max="1" value="0.9998"'..b'ns" value="less-than" />\n <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />\n- <param name="N" value="100" />\n+ <conditional name="filter_type">\n+ <param name="N" value="100" />\n+ </conditional>\n </conditional>\n <output name="read_db" ftype="meryldb">\n <assert_contents>\n@@ -281,7 +311,9 @@\n <param name="command_type" value="filter-kmers" />\n <param name="filter_operations" value="greater-than" />\n <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />\n- <param name="N" value="80" />\n+ <conditional name="filter_type">\n+ <param name="N" value="80" />\n+ </conditional>\n </conditional>\n <output name="read_db" ftype="meryldb">\n <assert_contents>\n@@ -292,9 +324,26 @@\n <test expect_num_outputs="1">\n <conditional name="operation_type">\n <param name="command_type" value="filter-kmers" />\n+ <param name="filter_operations" value="greater-than" />\n+ <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb" />\n+ <conditional name="filter_type">\n+ <param name="distinct" value="0.9998" />\n+ </conditional>\n+ </conditional>\n+ <output name="read_db" ftype="meryldb" >\n+ <assert_contents>\n+ <has_size value="1634" delta="300" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <conditional name="operation_type">\n+ <param name="command_type" value="filter-kmers" />\n <param name="filter_operations" value="equal-to" />\n <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />\n- <param name="N" value="100" />\n+ <conditional name="filter_type">\n+ <param name="N" value="100" />\n+ </conditional>\n </conditional>\n <output name="read_db" ftype="meryldb">\n <assert_contents>\n@@ -307,7 +356,9 @@\n <param name="command_type" value="filter-kmers" />\n <param name="filter_operations" value="not-equal-to" />\n <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />\n- <param name="N" value="100" />\n+ <conditional name="filter_type">\n+ <param name="N" value="100" />\n+ </conditional>\n </conditional>\n <output name="read_db" ftype="meryldb">\n <assert_contents>\n@@ -575,6 +626,13 @@\n </conditional>\n <output name="read_db_hist" file="output_24.read-db.hist" />\n </test>\n+ <test expect_num_outputs="1">\n+ <conditional name="operation_type">\n+ <param name="command_type" value="print" />\n+ <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb" />\n+ </conditional>\n+ <output name="read_db_print" file="output_25.read-db.tabular" sort="True"/>\n+ </test>\n </tests>\n <help><![CDATA[\n \n@@ -588,9 +646,9 @@\n In addition of generating count-databases, meryl can perform simple operations on it. \n \n -----\n- \n+\n .. class:: infomark\n- \n+\n **Basic functions**\n \n The functions that meryl includes are described below: \n@@ -626,9 +684,9 @@\n - Symmetric-difference: return k-mers that occur in exactly one input\n \n -----\n- \n+\n .. class:: infomark\n- \n+\n **Additional function: build hap-mers dbs for trios**\n \n In addition of the basic operations, this wrapper allows to build the hap-mers databases for trios, in accordance\n' |
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| diff -r 9f7a227436d6 -r d5d68989caec test-data/maternal.meryldb |
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| Binary file test-data/maternal.meryldb has changed |
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| diff -r 9f7a227436d6 -r d5d68989caec test-data/output_25.read-db.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_25.read-db.tabular Fri Apr 30 06:40:29 2021 +0000 |
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| @@ -0,0 +1,5 @@ +ACTAGGG 14 +CTAGACG 19 +CTAGGTC 15 +CCTAGTC 10 +CCTAGGA 11 |