Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_gneiss_add-pseudocount.xml @ 0:370e0b6e9826 draft
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| author | florianbegusch |
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| date | Wed, 17 Jul 2019 03:05:17 -0400 |
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| -1:000000000000 | 0:370e0b6e9826 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_gneiss_add-pseudocount" name="qiime gneiss add-pseudocount" version="2019.4"> | |
| 3 <description> - Add pseudocount to table</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2019.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command> | |
| 8 <![CDATA[ | |
| 9 qiime gneiss add-pseudocount --i-table=$itable | |
| 10 | |
| 11 #if $ppseudocount: | |
| 12 --p-pseudocount=$ppseudocount | |
| 13 #end if | |
| 14 | |
| 15 #if str($cmdconfig) != 'None': | |
| 16 --cmd-config=$cmdconfig | |
| 17 #end if | |
| 18 --o-composition-table=ocompositiontable; | |
| 19 | |
| 20 cp ocompositiontable.qza $ocompositiontable | |
| 21 ]]> | |
| 22 </command> | |
| 23 <inputs> | |
| 24 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table to which pseudocounts should be added. [required]" name="itable" optional="False" type="data"/> | |
| 25 <param label="--p-pseudocount: The value to add to all counts in the feature table. [default: 1]" name="ppseudocount" optional="True" type="integer" value="1"/> | |
| 26 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data format="qza" label="${tool.name} on ${on_string}: composition-table.qza" name="ocompositiontable"/> | |
| 30 </outputs> | |
| 31 <help> | |
| 32 <![CDATA[ | |
| 33 Add pseudocount to table | |
| 34 ------------------------- | |
| 35 | |
| 36 Increment all counts in table by pseudocount. | |
| 37 | |
| 38 Parameters | |
| 39 ---------- | |
| 40 table : FeatureTable[Frequency] | |
| 41 The feature table to which pseudocounts should be added. | |
| 42 pseudocount : Int, optional | |
| 43 The value to add to all counts in the feature table. | |
| 44 | |
| 45 Returns | |
| 46 ------- | |
| 47 composition_table : FeatureTable[Composition] | |
| 48 The resulting feature table. | |
| 49 ]]> | |
| 50 </help> | |
| 51 <macros> | |
| 52 <import>qiime_citation.xml</import> | |
| 53 </macros> | |
| 54 <expand macro="qiime_citation" /> | |
| 55 </tool> |