| Previous changeset 4:d5d68989caec (2021-04-30) Next changeset 6:31fa26c0692b (2021-06-08) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c" |
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modified:
macros.xml meryl.xml test-data/output_25.read-db.tabular |
| b |
| diff -r d5d68989caec -r d63739222f68 macros.xml --- a/macros.xml Fri Apr 30 06:40:29 2021 +0000 +++ b/macros.xml Sun May 23 18:09:41 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.3</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 d5d68989caec -r d63739222f68 meryl.xml --- a/meryl.xml Fri Apr 30 06:40:29 2021 +0000 +++ b/meryl.xml Sun May 23 18:09:41 2021 +0000 |
| [ |
| b'@@ -7,6 +7,7 @@\n <expand macro=\'requirements\' />\n <version_command>meryl --version</version_command>\n <command detect_errors=\'exit_code\'><![CDATA[\n+ export GALAXY_MEMORY_GB=\\$((\\${GALAXY_MEMORY_MB:-8192}/1024)) &&\n #if $operation_type.command_type == \'count-kmers\'\n #if $operation_type.options_kmer_size.kmer_size == \'estimate\'\n #from math import log\n@@ -17,7 +18,7 @@\n meryl\n $operation_type.count_operations\n k=$size\n- memory=\\${GALAXY_MEMORY_GB:-1}\n+ memory=\\$GALAXY_MEMORY_GB\n threads=\\${GALAXY_SLOTS:-1}\n $operation_type.input_reads\n output read-db.meryl &&\n@@ -79,17 +80,17 @@\n #end if\n #for $i, $read in enumerate($paternal_reads):\n mkdir \'paternal{$i}.meryl\' &&\n- meryl count k=$size memory=\\${GALAXY_MEMORY_GB:-1} threads=\\${GALAXY_SLOTS:-1} \'${read}\' output \'paternal{$i}.meryl\' &&\n+ meryl count k=$size memory=\\$GALAXY_MEMORY_GB threads=\\${GALAXY_SLOTS:-1} \'${read}\' output \'paternal{$i}.meryl\' &&\n #end for\n meryl union-sum paternal*.meryl output pat.meryl &&\n #for $i, $read in enumerate($maternal_reads):\n mkdir \'maternal{$i}.meryl\' &&\n- meryl count k=$size memory=\\${GALAXY_MEMORY_GB:-1} threads=\\${GALAXY_SLOTS:-1} \'${read}\' output \'maternal{$i}.meryl\' &&\n+ meryl count k=$size memory=\\$GALAXY_MEMORY_GB threads=\\${GALAXY_SLOTS:-1} \'${read}\' output \'maternal{$i}.meryl\' &&\n #end for\n meryl union-sum maternal*.meryl output mat.meryl &&\n #for $i, $read in enumerate($child_reads):\n mkdir \'child{$i}.meryl\' &&\n- meryl count k=$size memory=\\${GALAXY_MEMORY_GB:-1} threads=\\${GALAXY_SLOTS:-1} \'${read}\' output \'child{$i}.meryl\' &&\n+ meryl count k=$size memory=\\$GALAXY_MEMORY_GB threads=\\${GALAXY_SLOTS:-1} \'${read}\' output \'child{$i}.meryl\' &&\n #end for\n meryl union-sum child*.meryl output child.meryl &&\n ## mat specific kmers\n@@ -144,10 +145,10 @@\n <param name="command_type" type="select" label="Operation type selector" help="Select a type of operation">\n <option value="count-kmers">Count operations</option>\n <option value="filter-kmers">Filter operations</option>\n- <option value="arithmetic-kmers">Arithmetic operations on kmer counts</option>\n+ <option value="arithmetic-kmers">Arithmetic operations on k-mer 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="print">Print k-mer 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@@ -182,21 +183,21 @@\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+ <option value="times">Return k-mers that occur N times in the input</option>\n+ <option value="frequency">Return k-mers 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+ '..b' <when value="arithmetic-kmers">\n <param name="arithmetic_operations" type="select" label="Arithmetic operations" help="Select an operation to be executed">\n <option value="increase">Increase: add x to the count of each k-mer</option>\n- <option value="decrease">Decrease: subsctract x from the count of each k-mer</option>\n+ <option value="decrease">Decrease: subtract x from the count of each k-mer</option>\n <option value="multiply">Multiply: multiply the count of each k-mer by x</option>\n <option value="divide">Divide: divide the count of each k-mer by x</option>\n <option value="divide-round">Divide-round: divide the count of each k-mer by x and round th results</option>\n@@ -206,7 +207,7 @@\n <param name="X" type="integer" min="1" max="1000000" value="" optional="true" label="Operand" />\n </when>\n <when value="groups-kmers">\n- <param name="groups_operations" type="select" label="Operations on sets of kmers" help="Select an operation to be executed">\n+ <param name="groups_operations" type="select" label="Operations on sets of k-mers" help="Select an operation to be executed">\n <option value="union">Union: return k-mers that occur in any input</option>\n <option value="union-min">Union-min: return k-mers that occur in any input, set the count to the minimum count</option>\n <option value="union-max">Union-max: return k-mers that occur in any input, set the count to the maximum count</option>\n@@ -362,7 +363,7 @@\n </conditional>\n <output name="read_db" ftype="meryldb">\n <assert_contents>\n- <has_size value="59378" delta="300" />\n+ <has_size value="59100" delta="300" />\n </assert_contents>\n </output>\n </test>\n@@ -375,7 +376,7 @@\n </conditional>\n <output name="read_db" ftype="meryldb">\n <assert_contents>\n- <has_size value="59822" delta="300" />\n+ <has_size value="59500" delta="300" />\n </assert_contents>\n </output>\n </test>\n@@ -401,7 +402,7 @@\n </conditional>\n <output name="read_db" ftype="meryldb">\n <assert_contents>\n- <has_size value="60531" delta="300" />\n+ <has_size value="60530" delta="300" />\n </assert_contents>\n </output>\n </test>\n@@ -414,7 +415,7 @@\n </conditional>\n <output name="read_db" ftype="meryldb">\n <assert_contents>\n- <has_size value="56569" delta="300" />\n+ <has_size value="56200" delta="300" />\n </assert_contents>\n </output>\n </test>\n@@ -427,7 +428,7 @@\n </conditional>\n <output name="read_db" ftype="meryldb">\n <assert_contents>\n- <has_size value="56539" delta="300" />\n+ <has_size value="56100" delta="300" />\n </assert_contents>\n </output>\n </test>\n@@ -454,7 +455,7 @@\n </conditional>\n <output name="read_db" ftype="meryldb">\n <assert_contents>\n- <has_size value="36417" delta="300" />\n+ <has_size value="36100" delta="300" />\n </assert_contents>\n </output>\n </test>\n@@ -493,7 +494,7 @@\n </conditional>\n <output name="read_db" ftype="meryldb">\n <assert_contents>\n- <has_size value="59004" delta="350" />\n+ <has_size value="58600" delta="300" />\n </assert_contents>\n </output>\n </test>\n' |
| b |
| diff -r d5d68989caec -r d63739222f68 test-data/output_25.read-db.tabular --- a/test-data/output_25.read-db.tabular Fri Apr 30 06:40:29 2021 +0000 +++ b/test-data/output_25.read-db.tabular Sun May 23 18:09:41 2021 +0000 |
| b |
| @@ -1,5 +1,5 @@ ACTAGGG 14 +CCTAGTC 10 +CCTAGGA 11 CTAGACG 19 CTAGGTC 15 -CCTAGTC 10 -CCTAGGA 11 |