Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_vsearch_cluster-features-de-novo.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
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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_cluster-features-de-novo" name="qiime vsearch cluster-features-de-novo" version="2019.7"> | 2 <tool id="qiime_vsearch_cluster-features-de-novo" name="qiime vsearch cluster-features-de-novo" |
3 <description> - De novo clustering of features.</description> | 3 version="2020.8"> |
4 <requirements> | 4 <description>De novo clustering of features.</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 cluster-features-de-novo | 9 qiime vsearch cluster-features-de-novo |
9 | 10 |
10 --i-sequences=$isequences | 11 --i-sequences=$isequences |
12 | |
11 --i-table=$itable | 13 --i-table=$itable |
12 --p-perc-identity="$ppercidentity" | |
13 | 14 |
14 #set $pthreads = '${GALAXY_SLOTS:-4}' | 15 --p-perc-identity=$ppercidentity |
15 #if str($pthreads): | 16 |
16 --p-threads="$pthreads" | 17 --p-threads=$pthreads |
18 | |
19 --o-clustered-table=oclusteredtable | |
20 | |
21 --o-clustered-sequences=oclusteredsequences | |
22 | |
23 #if str($examples) != 'None': | |
24 --examples=$examples | |
17 #end if | 25 #end if |
18 | 26 |
19 --o-clustered-table=oclusteredtable | |
20 --o-clustered-sequences=oclusteredsequences | |
21 ; | 27 ; |
22 cp oclusteredtable.qza $oclusteredtable; | |
23 cp oclusteredsequences.qza $oclusteredsequences | 28 cp oclusteredsequences.qza $oclusteredsequences |
24 ]]></command> | 29 |
25 <inputs> | 30 ]]></command> |
26 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table. [required]" name="isequences" optional="False" type="data"/> | 31 <inputs> |
27 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to be clustered. [required]" name="itable" optional="False" type="data"/> | 32 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table. [required]" name="isequences" optional="False" type="data" /> |
28 | 33 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to be clustered. [required]" name="itable" optional="False" type="data" /> |
29 <param label="--p-perc-identity: PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True) The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required]" name="ppercidentity" optional="False" min="0" max="1" value="" exclude_min="True" exclude_max="False" type="float"/> | 34 <param label="--p-perc-identity: PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True) The percent identity at which clustering should be performed. This parameter maps to vsearch\'s --id parameter. [required]" name="ppercidentity" optional="False" type="text" /> |
30 </inputs> | 35 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> |
31 <outputs> | 36 |
32 <data format="qza" label="${tool.name} on ${on_string}: clusteredtable.qza" name="oclusteredtable"/> | 37 </inputs> |
33 <data format="qza" label="${tool.name} on ${on_string}: clusteredsequences.qza" name="oclusteredsequences"/> | 38 |
34 </outputs> | 39 <outputs> |
35 <help><![CDATA[ | 40 <data format="qza" label="${tool.name} on ${on_string}: clusteredtable.qza" name="oclusteredtable" /> |
41 <data format="qza" label="${tool.name} on ${on_string}: clusteredsequences.qza" name="oclusteredsequences" /> | |
42 | |
43 </outputs> | |
44 | |
45 <help><![CDATA[ | |
36 De novo clustering of features. | 46 De novo clustering of features. |
37 ############################### | 47 ############################################################### |
38 | 48 |
39 Given a feature table and the associated feature sequences, cluster the | 49 Given a feature table and the associated feature sequences, cluster the |
40 features based on user-specified percent identity threshold of their | 50 features based on user-specified percent identity threshold of their |
41 sequences. This is not a general-purpose de novo clustering method, but | 51 sequences. This is not a general-purpose de novo clustering method, but |
42 rather is intended to be used for clustering the results of quality- | 52 rather is intended to be used for clustering the results of quality- |
56 table : FeatureTable[Frequency] | 66 table : FeatureTable[Frequency] |
57 The feature table to be clustered. | 67 The feature table to be clustered. |
58 perc_identity : Float % Range(0, 1, inclusive_start=False, inclusive_end=True) | 68 perc_identity : Float % Range(0, 1, inclusive_start=False, inclusive_end=True) |
59 The percent identity at which clustering should be performed. This | 69 The percent identity at which clustering should be performed. This |
60 parameter maps to vsearch's --id parameter. | 70 parameter maps to vsearch's --id parameter. |
71 threads : Int % Range(0, 256, inclusive_end=True), optional | |
72 The number of threads to use for computation. Passing 0 will launch one | |
73 thread per CPU core. | |
74 | |
61 Returns | 75 Returns |
62 ------- | 76 ------- |
63 clustered_table : FeatureTable[Frequency] | 77 clustered_table : FeatureTable[Frequency] |
64 The table following clustering of features. | 78 The table following clustering of features. |
65 clustered_sequences : FeatureData[Sequence] | 79 clustered_sequences : FeatureData[Sequence] |
66 Sequences representing clustered features. | 80 Sequences representing clustered features. |
67 ]]></help> | 81 ]]></help> |
68 <macros> | 82 <macros> |
69 <import>qiime_citation.xml</import> | 83 <import>qiime_citation.xml</import> |
70 </macros> | 84 </macros> |
71 <expand macro="qiime_citation"/> | 85 <expand macro="qiime_citation"/> |
72 </tool> | 86 </tool> |