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comparison qiime2/qiime_fragment-insertion_sepp.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_fragment-insertion_sepp" name="qiime fragment-insertion sepp" version="2019.7"> 2 <tool id="qiime_fragment-insertion_sepp" name="qiime fragment-insertion sepp"
3 <description> - Insert fragment sequences using SEPP into reference phylogenies like Greengenes 13_8</description> 3 version="2020.8">
4 <requirements> 4 <description>Insert fragment sequences using SEPP into reference phylogenies.</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 fragment-insertion sepp 9 qiime fragment-insertion sepp
9 10
10 --i-representative-sequences=$irepresentativesequences 11 --i-representative-sequences=$irepresentativesequences
11 12
12 #if str($ireferencealignment) != 'None': 13 --i-reference-database=$ireferencedatabase
13 --i-reference-alignment=$ireferencealignment
14 #end if
15 14
16 #if str($ireferencephylogeny) != 'None': 15 --p-alignment-subset-size=$palignmentsubsetsize
17 --i-reference-phylogeny=$ireferencephylogeny
18 #end if
19 16
20 #set $pthreads = '${GALAXY_SLOTS:-4}' 17 --p-placement-subset-size=$pplacementsubsetsize
21 #if str($pthreads):
22 --p-threads="$pthreads"
23 #end if
24 18
19 --p-threads=$pthreads
25 20
26 #if str($palignmentsubsetsize): 21 #if $pdebug:
27 --p-alignment-subset-size=$palignmentsubsetsize 22 --p-debug
28 #end if
29
30 #if str($pplacementsubsetsize):
31 --p-placement-subset-size="$pplacementsubsetsize"
32 #end if 23 #end if
33 24
34 --o-tree=otree 25 --o-tree=otree
26
35 --o-placements=oplacements 27 --o-placements=oplacements
28
29 #if str($examples) != 'None':
30 --examples=$examples
31 #end if
32
36 ; 33 ;
37 cp otree.qza $otree;
38 cp oplacements.qza $oplacements 34 cp oplacements.qza $oplacements
39 ]]></command>
40 <inputs>
41 <param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences to insert [required]" name="irepresentativesequences" optional="False" type="data"/>
42 <param format="qza,no_unzip.zip" label="--i-reference-alignment: ARTIFACT FeatureData[AlignedSequence] The reference multiple nucleotide alignment used to construct the reference phylogeny. [optional]" name="ireferencealignment" optional="True" type="data"/>
43 <param format="qza,no_unzip.zip" label="--i-reference-phylogeny: ARTIFACT Phylogeny[Rooted] The rooted reference phylogeny. Must be in sync with reference-alignment, i.e. each tip name must have exactly one corresponding record. [optional]" name="ireferencephylogeny" optional="True" type="data"/>
44 <param label="--p-alignment-subset-size: INTEGER Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset. The default alignment subset size is set to balance the exhaustiveness of the alignment step with the running time. [default: 1000]" name="palignmentsubsetsize" optional="True" type="integer" value="1000"/>
45 <param label="--p-placement-subset-size: INTEGER The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. The default placement subset is set to make sure the memory requirement of the pplacer step does not become prohibitively large." name="pplacementsubsetsize" optional="True" type="integer"/>
46 </inputs>
47 <outputs>
48 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/>
49 <data format="qza" label="${tool.name} on ${on_string}: placements.qza" name="oplacements"/>
50 </outputs>
51 <help><![CDATA[
52 Insert fragment sequences using SEPP into reference phylogenies like Greengenes 13_8
53 ####################################################################################
54 35
55 Perform fragment insertion of 16S sequences using the SEPP algorithm 36 ]]></command>
56 against the Greengenes 13_8 99% tree. 37 <inputs>
38 <param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences to insert into the reference tree. [required]" name="irepresentativesequences" optional="False" type="data" />
39 <param format="qza,no_unzip.zip" label="--i-reference-database: ARTIFACT SeppReferenceDatabase The reference database to insert the representative sequences into. [required]" name="ireferencedatabase" optional="False" type="data" />
40 <param label="--p-alignment-subset-size: INTEGER Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset. [default: 1000]" name="palignmentsubsetsize" optional="True" type="integer" value="1000" />
41 <param label="--p-placement-subset-size: INTEGER The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. Further reading: https://github.com/smirarab/sepp/blob/master/tutorial/s epp-tutorial.md#sample-datasets-default-parameters. [default: 5000]" name="pplacementsubsetsize" optional="True" type="integer" value="5000" />
42 <param label="--p-debug: --p-debug: / --p-no-debug Collect additional run information to STDOUT for debugging. Temporary directories will not be removed if run fails. [default: False]" name="pdebug" selected="False" type="boolean" />
43 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
44
45 </inputs>
46
47 <outputs>
48 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
49 <data format="qza" label="${tool.name} on ${on_string}: placements.qza" name="oplacements" />
50
51 </outputs>
52
53 <help><![CDATA[
54 Insert fragment sequences using SEPP into reference phylogenies.
55 ###############################################################
56
57 Perform fragment insertion of sequences using the SEPP algorithm.
57 58
58 Parameters 59 Parameters
59 ---------- 60 ----------
60 representative_sequences : FeatureData[Sequence] 61 representative_sequences : FeatureData[Sequence]
61 The sequences to insert 62 The sequences to insert into the reference tree.
63 reference_database : SeppReferenceDatabase
64 The reference database to insert the representative sequences into.
62 alignment_subset_size : Int, optional 65 alignment_subset_size : Int, optional
63 Each placement subset is further broken into subsets of at most these 66 Each placement subset is further broken into subsets of at most these
64 many sequences and a separate HMM is trained on each subset. The 67 many sequences and a separate HMM is trained on each subset.
65 default alignment subset size is set to balance the exhaustiveness of
66 the alignment step with the running time.
67 placement_subset_size : Int, optional 68 placement_subset_size : Int, optional
68 The tree is divided into subsets such that each subset includes at most 69 The tree is divided into subsets such that each subset includes at most
69 these many subsets. The placement step places the fragment on only one 70 these many subsets. The placement step places the fragment on only one
70 subset, determined based on alignment scores. The default placement 71 subset, determined based on alignment scores. Further reading:
71 subset is set to make sure the memory requirement of the pplacer step
72 does not become prohibitively large. Further reading:
73 https://github.com/smirarab/sepp/blob/master/tutorial/sepp- 72 https://github.com/smirarab/sepp/blob/master/tutorial/sepp-
74 tutorial.md#sample-datasets-default-parameters 73 tutorial.md#sample-datasets-default-parameters.
75 reference_alignment : FeatureData[AlignedSequence], optional 74 threads : Int, optional
76 The reference multiple nucleotide alignment used to construct the 75 The number of threads to use.
77 reference phylogeny.
78 reference_phylogeny : Phylogeny[Rooted], optional
79 The rooted reference phylogeny. Must be in sync with reference-
80 alignment, i.e. each tip name must have exactly one corresponding
81 record.
82 debug : Bool, optional 76 debug : Bool, optional
83 Print additional run information to STDOUT for debugging. Run together 77 Collect additional run information to STDOUT for debugging. Temporary
84 with --verbose to actually see the information on STDOUT. Temporary
85 directories will not be removed if run fails. 78 directories will not be removed if run fails.
86 79
87 Returns 80 Returns
88 ------- 81 -------
89 tree : Phylogeny[Rooted] 82 tree : Phylogeny[Rooted]
90 The tree with inserted feature data 83 The tree with inserted feature data.
91 placements : Placements 84 placements : Placements
92 \ 85 Information about the feature placements within the reference tree.
93 ]]></help> 86 ]]></help>
94 <macros> 87 <macros>
95 <import>qiime_citation.xml</import> 88 <import>qiime_citation.xml</import>
96 </macros> 89 </macros>
97 <expand macro="qiime_citation"/> 90 <expand macro="qiime_citation"/>
98 </tool> 91 </tool>