| Previous changeset 1:9e66f77aa094 (2015-07-07) Next changeset 3:93a451fcde49 (2015-07-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty |
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modified:
count-median.xml do-partition.xml filter-abund.xml normalize-by-median.xml |
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| diff -r 9e66f77aa094 -r 5c565b7edfd0 count-median.xml --- a/count-median.xml Tue Jul 07 12:53:33 2015 -0400 +++ b/count-median.xml Tue Jul 07 12:57:38 2015 -0400 |
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| @@ -55,7 +55,7 @@ fields are separated by spaces. For khmer 1.x count-median.py will split sequence names at the first space which means that some sequence formats (e.g. paired FASTQ in Casava 1.8 format) will yield uninformative names. Use -:option:`--csv` to fix this behavior. +`--csv` to fix this behavior. </help> <citations> <expand macro="software-citation" /> |
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| diff -r 9e66f77aa094 -r 5c565b7edfd0 do-partition.xml --- a/do-partition.xml Tue Jul 07 12:53:33 2015 -0400 +++ b/do-partition.xml Tue Jul 07 12:57:38 2015 -0400 |
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| @@ -66,11 +66,11 @@ Load in a set of sequences, partition them, merge the partitions, and annotate the original sequences files with the partition information. -This script combines the functionality of :program:`load-graph.py`, -:program:`partition-graph.py`, :program:`merge-partitions.py`, and -:program:`annotate-partitions.py` into one script. This is convenient +This script combines the functionality of `load-graph.py`, +`partition-graph.py`, `merge-partitions.py`, and +`annotate-partitions.py` into one script. This is convenient but should probably not be used for large data sets, because -:program:`do-partition.py` doesn't provide save/resume functionality. +`do-partition.py` doesn't provide save/resume functionality. ]]> </help> <citations> |
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| diff -r 9e66f77aa094 -r 5c565b7edfd0 filter-abund.xml --- a/filter-abund.xml Tue Jul 07 12:53:33 2015 -0400 +++ b/filter-abund.xml Tue Jul 07 12:57:38 2015 -0400 |
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| @@ -82,7 +82,7 @@ Trimmed sequences will be placed in ${input_sequence_filename}.abundfilt for each input sequence file. If the input sequences are from RNAseq or -metagenome sequencing then :option:`--variable-coverage` should be used. +metagenome sequencing then `--variable-coverage` should be used. ]]> </help> <citations> |
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| diff -r 9e66f77aa094 -r 5c565b7edfd0 normalize-by-median.xml --- a/normalize-by-median.xml Tue Jul 07 12:53:33 2015 -0400 +++ b/normalize-by-median.xml Tue Jul 07 12:57:38 2015 -0400 |
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| @@ -126,21 +126,21 @@ Discard sequences based on whether or not their median k-mer abundance lies above a specified cutoff. Kept sequences will be placed in <fileN>.keep. -Paired end reads will be considered together if :option:`-p` is set. If +Paired end reads will be considered together if `-p` is set. If either read will be kept, then both will be kept. This should result in keeping (or discarding) each sequencing fragment. This helps with retention of repeats, especially. -With :option:`-s`/:option:`--savetable`, the k-mer counting table +With `-s`/`--savetable`, the k-mer counting table will be saved to the specified file after all sequences have been -processed. With :option:`-d`, the k-mer counting table will be -saved every d files for multifile runs; if :option:`-s` is set, +processed. With `-d`, the k-mer counting table will be +saved every d files for multifile runs; if `-s` is set, the specified name will be used, and if not, the name `backup.ct` -will be used. :option:`-l`/:option:`--loadtable` will load the +will be used. `-l`/`--loadtable` will load the specified k-mer counting table before processing the specified files. Note that these tables are are in the same format as those -produced by :program:`load-into-counting.py` and consumed by -:program:`abundance-dist.py`. +produced by `load-into-counting.py` and consumed by +`abundance-dist.py`. ]]> </help> <citations> |