| Previous changeset 7:51c2360aa807 (2021-06-28) Next changeset 9:eadfd71dde37 (2021-10-05) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 0625ea0c1df66a724d0ab3769fcaee7a07810a20" |
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modified:
macros.xml meryl.xml |
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| diff -r 51c2360aa807 -r 5ae3496f9ca3 macros.xml --- a/macros.xml Mon Jun 28 09:32:16 2021 +0000 +++ b/macros.xml Thu Aug 12 13:20:54 2021 +0000 |
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| @@ -1,7 +1,7 @@ <macros> <token name="@TOOL_VERSION@">1.3</token> <token name="@GALAXY_TOOL_VERSION@">galaxy</token> - <token name="@SUFFIX_VERSION@">3</token> + <token name="@SUFFIX_VERSION@">4</token> <xml name="edam_ontology"> <edam_topics> <edam_topic>topic_0196</edam_topic> |
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| diff -r 51c2360aa807 -r 5ae3496f9ca3 meryl.xml --- a/meryl.xml Mon Jun 28 09:32:16 2021 +0000 +++ b/meryl.xml Thu Aug 12 13:20:54 2021 +0000 |
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| @@ -15,12 +15,14 @@ #elif $operation_type.options_kmer_size.kmer_size == 'provide' #set size=$operation_type.options_kmer_size.input_kmer_size #end if + ln -s '$operation_type.input_reads' ./input.${operation_type.input_reads.ext} && + meryl $operation_type.count_operations k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} - $operation_type.input_reads + ./input.${operation_type.input_reads.ext} output read-db.meryl && echo 'K-mer size: ${size}' && tar -zcf read-db.meryldb read-db.meryl @@ -176,17 +178,17 @@ <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" /> - + <conditional name="filter_type"> <param name="type" type="select" label="Type of filtering"> <option value="times">Return k-mers that occur N times in the input</option> <option value="frequency">Return k-mers 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 k-mers that occur N times in the input."/> + <param name="N" type="integer" min="0" max="50000000000" value="" optional="true" label="Number of times in the input" help="Return k-mers 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 k-mers that at specific frequency (e.g. frequency = 0.9998 returns top 0.02% most frequent)"/> + <param name="distinct" type="float" min="0" max="1" value="0.9998" optional="true" label="Frequency" help="Return k-mers that at specific frequency (e.g. frequency = 0.9998 returns top 0.02% most frequent)" /> </when> </conditional> </when> @@ -326,7 +328,7 @@ <param name="distinct" value="0.9998" /> </conditional> </conditional> - <output name="read_db" ftype="meryldb" > + <output name="read_db" ftype="meryldb"> <assert_contents> <has_size value="1634" delta="300" /> </assert_contents> @@ -343,7 +345,7 @@ </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> - <has_size value="2621" delta="300"/> + <has_size value="2621" delta="300" /> </assert_contents> </output> </test> @@ -617,14 +619,14 @@ <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"/> + <output name="read_db_print" file="output_25.read-db.tabular" sort="true" /> </test> <!--Test compressed files--> <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.gz" /> + <param name="input_reads" value="child.fasta.gz" ftype="fasta.gz" /> <conditional name="options_kmer_size"> <param name="kmer_size" value="provide" /> <param name="input_kmer_size" value="7" /> @@ -632,7 +634,7 @@ </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> - <has_size value="1851" delta="300" /> + <has_size value="22200" delta="300" /> </assert_contents> </output> <assert_stdout> |