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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 73999800a193a91bb9b0fb9b146f74087086aaf8 |
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modified:
macros.xml normalize-by-median.xml |
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| diff -r 46f9ee5d0876 -r 6b468584d645 macros.xml --- a/macros.xml Wed Sep 09 17:59:01 2015 -0400 +++ b/macros.xml Wed Sep 09 19:37:11 2015 -0400 |
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| @@ -122,17 +122,30 @@ help="Output zero count bins (--no-zero)" /> </xml> <xml name="software-citation"> - <citation type="bibtex">@article{khmer2014, - author = "Crusoe, Michael and Edvenson, Greg and Fish, Jordan and Howe, - Adina and McDonald, Eric and Nahum, Joshua and Nanlohy, Kaben and - Ortiz-Zuazaga, Humberto and Pell, Jason and Simpson, Jared and Scott, Camille - and Srinivasan, Ramakrishnan Rajaram and Zhang, Qingpeng and Brown, C. Titus", - title = "The khmer software package: enabling efficient sequence - analysis", - year = "2014", - month = "04", - publisher = "Figshare", - url = "http://dx.doi.org/10.6084/m9.figshare.979190" + <citation type="bibtex">@article{khmer2015, + author = "Crusoe, Michael R. and Alameldin, Hussien F. and Awad, Sherine + and Bucher, Elmar and Caldwell, Adam and Cartwright, Reed and Charbonneau, + Amanda and Constantinides, Bede and Edvenson, Greg and Fay, Scott and Fenton, + Jacob and Fenzl, Thomas and Fish, Jordan and Garcia-Gutierrez, Leonor and + Garland, Phillip and Gluck, Jonathan and González, Iván and Guermond, Sarah + and Guo, Jiarong and Gupta, Aditi and Herr, Joshua R. and Howe, Adina and + Hyer, Alex and Härpfer, Andreas and Irber, Luiz and Kidd, Rhys and Lin, David + and Lippi, Justin and Mansour, Tamer and McA'Nulty, Pamela and McDonald, Eric + and Mizzi, Jessica and Murray, Kevin D. and Nahum, Joshua R. and Nanlohy, + Kaben and Nederbragt, Alexander Johan and Ortiz-Zuazaga, Humberto and Ory, + Jeramia and Pell, Jason and Pepe-Ranney, Charles and Russ, Zachary N and + Schwarz, Erich and Scott, Camille and Seaman, Josiah and Sievert, Scott and + Simpson, Jared and Skennerton, Connor T. and Spencer, James and Srinivasan, + Ramakrishnan and Standage, Daniel and Stapleton, James A. and Stein, Joe and + Steinman, Susan R and Taylor, Benjamin and Trimble, Will and Wiencko, Heather + L. and Wright, Michael and Wyss, Brian and Zhang, Qingpeng and zyme, en and + Brown, C. Titus" + title = "The khmer software package: enabling efficient nucleotide + sequence analysis", + year = "2015", + month = "08", + publisher = "F1000", + url = "http://dx.doi.org/10.12688/f1000research.6924.1" }</citation> </xml> <xml name="diginorm-citation"> |
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| diff -r 46f9ee5d0876 -r 6b468584d645 normalize-by-median.xml --- a/normalize-by-median.xml Wed Sep 09 17:59:01 2015 -0400 +++ b/normalize-by-median.xml Wed Sep 09 19:37:11 2015 -0400 |
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| @@ -1,6 +1,6 @@ <tool id="gedlab-khmer-normalize-by-median" name="Normalize By Median" - version="2.0-1"> + version="2.0-2"> <description> Filters a fastq/fasta file using digital normalization via @@ -18,8 +18,12 @@ cd output; normalize-by-median.py $paired_switch +$force_single_switch @TABLEPARAMS@ --cutoff=$cutoff +#if $unpaired_reads_filename +--unpaired-reads=$unpaired_reads_filename +#end if #if $save_countingtable --savetable=$countingtable #end if @@ -44,16 +48,27 @@ checked="false" truevalue="--paired" falsevalue="" - label="Are the inputs interleaved paired ends?" - help="(--paired) If so, then selecting this option will process the paired ends together." /> - + label="Require all sequences be properly paired?" + help="(--paired) The tool will fail if given improperly paired reads and this option is selected." /> + <param name="force_single_switch" + type="boolean" + checked="false" + truevalue="--force_single" + falsevalue="" + label="Ignore all pairing information?" + help="(--paired) By default this tool process reads in a pair-aware manner. This option disables that behavior." /> + <param name="unpaired_reads_filename" + type="" + optional="true" + label="Extra unpaired reads." + help="(--unpaired-reads) If all but one of your sequence files are interleaved paired end reads you can include one unpaired file to be processed last without regard to pairing." + /> <param name="countingtable_to_load" type="data" format="ct" optional="true" label="an optional k-mer counting table to load" help="(--loadtable) The inputs file(s) will be processed using the kmer counts in the specified k-mer counting table file as a starting point." /> - <param name="save_countingtable" type="boolean" label="Save the k-mer counting table(s) in a file" @@ -126,21 +141,22 @@ 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 `-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. +By default, Paired end reads will be considered together; if either read will +be kept, then both will be kept. (This keeps both reads from a fragment, and +helps with retention of repeats.) Unpaired reads are treated individually. + +If `--paired` is set then proper pairing is required and the tool will exit on +unpaired reads, although `--unpaired-reads` can be used to supply a file of +orphan reads to be read after the paired reads. -With `-s`/`--savetable`, the k-mer counting table -will be saved to the specified file after all sequences have been -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. `-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 `load-into-counting.py` and consumed by -`abundance-dist.py`. +`--force_single` will ignore all pairing information and treat reads +individually. + +With `-s`/`--savegraph`, the k-mer countgraph will be saved to the specified +file after all sequences have been processed. `--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 +`load-into-counting.py` and consumed by `abundance-dist.py`. ]]> </help> <citations> |