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comparison qiime2/qiime_fragment-insertion_sepp.xml @ 4:914fa4daf16a draft

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Fixes
author florianbegusch
date Wed, 31 Jul 2019 03:06:00 -0400
parents 370e0b6e9826
children f190567fe3f6
comparison
equal deleted inserted replaced
3:558645416841 4:914fa4daf16a
21 #if str($pthreads): 21 #if str($pthreads):
22 --p-threads="$pthreads" 22 --p-threads="$pthreads"
23 #end if 23 #end if
24 24
25 25
26 #if $palignmentsubsetsize: 26 #if str($palignmentsubsetsize):
27 --p-alignment-subset-size=$palignmentsubsetsize 27 --p-alignment-subset-size=$palignmentsubsetsize
28 #end if 28 #end if
29 29
30 #if str($pplacementsubsetsize): 30 #if str($pplacementsubsetsize):
31 --p-placement-subset-size="$pplacementsubsetsize" 31 --p-placement-subset-size="$pplacementsubsetsize"
32 #end if
33
34 #if $pdebug:
35 --p-debug
36 #end if 32 #end if
37 33
38 --o-tree=otree 34 --o-tree=otree
39 --o-placements=oplacements 35 --o-placements=oplacements
40 ; 36 ;
45 <param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences to insert [required]" name="irepresentativesequences" optional="False" type="data"/> 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"/>
46 <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"/> 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"/>
47 <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"/> 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"/>
48 <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"/> 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"/>
49 <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"/> 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"/>
50 <param label="--p-debug: --p-no-debug Print additional run information to STDOUT for debugging. Run together with --verbose to actually see the information on STDOUT. Temporary directories will not be removed if run fails. [default: False]" name="pdebug" selected="False" type="boolean"/>
51 </inputs> 46 </inputs>
52 <outputs> 47 <outputs>
53 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/> 48 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/>
54 <data format="qza" label="${tool.name} on ${on_string}: placements.qza" name="oplacements"/> 49 <data format="qza" label="${tool.name} on ${on_string}: placements.qza" name="oplacements"/>
55 </outputs> 50 </outputs>