Mercurial > repos > florianbegusch > qiime2_all
comparison qiime_feature-table_relative-frequency.xml @ 0:09b7bcb72fa7 draft
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| author | florianbegusch |
|---|---|
| date | Thu, 24 May 2018 02:11:44 -0400 |
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| -1:000000000000 | 0:09b7bcb72fa7 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_feature-table_relative-frequency" name="qiime feature-table relative-frequency" version="2018.4"> | |
| 3 <description> - Convert to relative frequencies</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2018.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command> | |
| 8 <![CDATA[ | |
| 9 qiime feature-table relative-frequency --i-table=$itable | |
| 10 | |
| 11 #if str($cmdconfig) != 'None': | |
| 12 --cmd-config=$cmdconfig | |
| 13 #end if | |
| 14 --o-relative-frequency-table=orelativefrequencytable; | |
| 15 | |
| 16 cp orelativefrequencytable.qza $orelativefrequencytable; | |
| 17 ]]> | |
| 18 </command> | |
| 19 <inputs> | |
| 20 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table to be converted into relative frequencies. [required]" name="itable" optional="False" type="data"/> | |
| 21 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="qza" label="${tool.name} on ${on_string}: relative-frequency-table.qza" name="orelativefrequencytable"/> | |
| 25 </outputs> | |
| 26 <help> | |
| 27 <![CDATA[ | |
| 28 Rarefy table | |
| 29 ------------- | |
| 30 | |
| 31 Subsample frequencies from all samples without replacement so that the sum | |
| 32 of frequencies in each sample is equal to sampling-depth. | |
| 33 | |
| 34 Parameters | |
| 35 ---------- | |
| 36 table : FeatureTable[Frequency] | |
| 37 The feature table to be rarefied. | |
| 38 sampling_depth : Int % Range(1, None) | |
| 39 The total frequency that each sample should be rarefied to. Samples | |
| 40 where the sum of frequencies is less than the sampling depth will be | |
| 41 not be included in the resulting table. | |
| 42 | |
| 43 Returns | |
| 44 ------- | |
| 45 rarefied_table : FeatureTable[Frequency] | |
| 46 The resulting rarefied feature table. | |
| 47 ]]> | |
| 48 </help> | |
| 49 </tool> |