| Previous changeset 8:f4e13769a68c (2015-09-10) Next changeset 10:69a0d7b6d0d0 (2015-09-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit a3458d38cfe23878a715b4493fffebc520f6898b |
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modified:
abundance-dist-single.xml do-partition.xml extract-partitions.xml filter-abund.xml macros.xml |
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| diff -r f4e13769a68c -r f1a4d7607ce6 abundance-dist-single.xml --- a/abundance-dist-single.xml Thu Sep 10 16:33:21 2015 -0400 +++ b/abundance-dist-single.xml Thu Sep 10 18:49:27 2015 -0400 |
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| @@ -1,6 +1,6 @@ <tool id="gedlab-khmer-abundance-dist-single" name="Abundance Distribution (all-in-one)" - version="2.0-1"> + version="2.0-2"> <description> Calculate abundance distribution of the k-mers in a given @@ -24,7 +24,6 @@ #if $save_countingtable --savetable=$optional_output_countingtable #end if ---report-total-kmers --squash @THREADS@ $input_sequence_filename |
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| diff -r f4e13769a68c -r f1a4d7607ce6 do-partition.xml --- a/do-partition.xml Thu Sep 10 16:33:21 2015 -0400 +++ b/do-partition.xml Thu Sep 10 18:49:27 2015 -0400 |
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| @@ -46,7 +46,7 @@ </inputs> <outputs> <data name="information" - format="text" + format="txt" label="${tool.name} summary for #echo ','.join(map(str, $inputs ))#" /> <expand macro="output_sequences" /> </outputs> |
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| diff -r f4e13769a68c -r f1a4d7607ce6 extract-partitions.xml --- a/extract-partitions.xml Thu Sep 10 16:33:21 2015 -0400 +++ b/extract-partitions.xml Thu Sep 10 18:49:27 2015 -0400 |
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| @@ -50,7 +50,7 @@ </inputs> <outputs> <data name="distribution" - format="text" + format="txt" label="Partition size distribution from ${tool.name}" /> <expand macro="output_sequences" /> </outputs> |
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| diff -r f4e13769a68c -r f1a4d7607ce6 filter-abund.xml --- a/filter-abund.xml Thu Sep 10 16:33:21 2015 -0400 +++ b/filter-abund.xml Thu Sep 10 18:49:27 2015 -0400 |
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| @@ -1,6 +1,6 @@ <tool id="gedlab-khmer-filter-abund" name="Filter by abundance" - version="2.0-2"> + version="2.0-3"> <description> Trims fastq/fasta sequences at k-mers of a given abundance @@ -25,7 +25,6 @@ #for input in $inputs $input #end for ---out $output ]]> </command> @@ -46,8 +45,7 @@ <expand macro="input_counting_table_filename" /> </inputs> <outputs> - <!-- <expand macro="output_sequences" /> --> - <expand macro="output_sequences_single" /> + <expand macro="output_sequences" /> </outputs> <tests> <test> @@ -55,11 +53,11 @@ <param name="input_counting_table_filename" value="test-abund-read-2.ct" ftype="ct" /> <output name="output"> - <!-- <discover_dataset name="test-abund-read-2.fa.abundfilt"> --> + <discover_dataset name="test-abund-read-2.fa.abundfilt"> <assert_contents> <has_text text="GGTTGACGGGGCTCAGGG" /> </assert_contents> - <!-- </discover_dataset> --> + </discover_dataset> </output> </test> <test> @@ -68,11 +66,11 @@ value="test-abund-read-2.ct" ftype="ct" /> <param name="cutoff" value="1" /> <output name="output"> - <!-- <discover_dataset name="test-abund-read-2.fa.abundfilt"> --> + <discover_dataset name="test-abund-read-2.fa.abundfilt"> <assert_contents> <has_text text="GGTTGACGGGGCTCAGGG" /> </assert_contents> - <!-- </discover_dataset> --> + </discover_dataset> </output> </test> </tests> |
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| diff -r f4e13769a68c -r f1a4d7607ce6 macros.xml --- a/macros.xml Thu Sep 10 16:33:21 2015 -0400 +++ b/macros.xml Thu Sep 10 18:49:27 2015 -0400 |
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| @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.0rc1">khmer</requirement> + <requirement type="package" version="2.0">khmer</requirement> </requirements> </xml> <xml name="version"> |