Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_vsearch_dereplicate-sequences.xml @ 14:a0a8d77a991c draft
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| author | florianbegusch |
|---|---|
| date | Thu, 03 Sep 2020 09:51:29 +0000 |
| parents | f190567fe3f6 |
| children |
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| 13:887cd4ad8e16 | 14:a0a8d77a991c |
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| 1 <?xml version="1.0" ?> | 1 <?xml version="1.0" ?> |
| 2 <tool id="qiime_vsearch_dereplicate-sequences" name="qiime vsearch dereplicate-sequences" version="2019.7"> | 2 <tool id="qiime_vsearch_dereplicate-sequences" name="qiime vsearch dereplicate-sequences" |
| 3 <description> - Dereplicate sequences.</description> | 3 version="2020.8"> |
| 4 <requirements> | 4 <description>Dereplicate sequences.</description> |
| 5 <requirement type="package" version="2019.7">qiime2</requirement> | 5 <requirements> |
| 6 </requirements> | 6 <requirement type="package" version="2020.8">qiime2</requirement> |
| 7 <command><![CDATA[ | 7 </requirements> |
| 8 <command><![CDATA[ | |
| 8 qiime vsearch dereplicate-sequences | 9 qiime vsearch dereplicate-sequences |
| 9 | 10 |
| 10 --i-sequences=$isequences | 11 --i-sequences=$isequences |
| 11 | 12 |
| 12 #if $pderepprefix: | 13 #if $pderepprefix: |
| 13 --p-derep-prefix | 14 --p-derep-prefix |
| 14 #end if | 15 #end if |
| 15 | 16 |
| 16 --o-dereplicated-table=odereplicatedtable | 17 --o-dereplicated-table=odereplicatedtable |
| 18 | |
| 17 --o-dereplicated-sequences=odereplicatedsequences | 19 --o-dereplicated-sequences=odereplicatedsequences |
| 20 | |
| 21 #if str($examples) != 'None': | |
| 22 --examples=$examples | |
| 23 #end if | |
| 24 | |
| 18 ; | 25 ; |
| 19 cp odereplicatedtable.qza $odereplicatedtable; | |
| 20 cp odereplicatedsequences.qza $odereplicatedsequences | 26 cp odereplicatedsequences.qza $odereplicatedsequences |
| 21 ]]></command> | 27 |
| 22 <inputs> | 28 ]]></command> |
| 23 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality] The sequences to be dereplicated. [required]" name="isequences" optional="False" type="data"/> | 29 <inputs> |
| 24 <param label="--p-derep-prefix: --p-no-derep-prefix Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant. [default: False]" name="pderepprefix" selected="False" type="boolean"/> | 30 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality] The sequences to be dereplicated. [required]" name="isequences" optional="False" type="data" /> |
| 25 </inputs> | 31 <param label="--p-derep-prefix: --p-derep-prefix: / --p-no-derep-prefix Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant. [default: False]" name="pderepprefix" selected="False" type="boolean" /> |
| 26 <outputs> | 32 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> |
| 27 <data format="qza" label="${tool.name} on ${on_string}: dereplicatedtable.qza" name="odereplicatedtable"/> | 33 |
| 28 <data format="qza" label="${tool.name} on ${on_string}: dereplicatedsequences.qza" name="odereplicatedsequences"/> | 34 </inputs> |
| 29 </outputs> | 35 |
| 30 <help><![CDATA[ | 36 <outputs> |
| 37 <data format="qza" label="${tool.name} on ${on_string}: dereplicatedtable.qza" name="odereplicatedtable" /> | |
| 38 <data format="qza" label="${tool.name} on ${on_string}: dereplicatedsequences.qza" name="odereplicatedsequences" /> | |
| 39 | |
| 40 </outputs> | |
| 41 | |
| 42 <help><![CDATA[ | |
| 31 Dereplicate sequences. | 43 Dereplicate sequences. |
| 32 ###################### | 44 ############################################################### |
| 33 | 45 |
| 34 Dereplicate sequence data and create a feature table and feature | 46 Dereplicate sequence data and create a feature table and feature |
| 35 representative sequences. Feature identifiers in the resulting artifacts | 47 representative sequences. Feature identifiers in the resulting artifacts |
| 36 will be the sha1 hash of the sequence defining each feature. If clustering | 48 will be the sha1 hash of the sequence defining each feature. If clustering |
| 37 of features into OTUs is desired, the resulting artifacts can be passed to | 49 of features into OTUs is desired, the resulting artifacts can be passed to |
| 51 ------- | 63 ------- |
| 52 dereplicated_table : FeatureTable[Frequency] | 64 dereplicated_table : FeatureTable[Frequency] |
| 53 The table of dereplicated sequences. | 65 The table of dereplicated sequences. |
| 54 dereplicated_sequences : FeatureData[Sequence] | 66 dereplicated_sequences : FeatureData[Sequence] |
| 55 The dereplicated sequences. | 67 The dereplicated sequences. |
| 56 ]]></help> | 68 ]]></help> |
| 57 <macros> | 69 <macros> |
| 58 <import>qiime_citation.xml</import> | 70 <import>qiime_citation.xml</import> |
| 59 </macros> | 71 </macros> |
| 60 <expand macro="qiime_citation"/> | 72 <expand macro="qiime_citation"/> |
| 61 </tool> | 73 </tool> |