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

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13:887cd4ad8e16

<?xml version="1.0" ?>
<tool id="qiime_fragment-insertion_sepp" name="qiime fragment-insertion sepp" version="2019.7">
	<description> - Insert fragment sequences using SEPP into reference phylogenies like Greengenes 13_8</description>
	<requirements>
		<requirement type="package" version="2019.7">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime fragment-insertion sepp

--i-representative-sequences=$irepresentativesequences

#if str($ireferencealignment) != 'None':
 --i-reference-alignment=$ireferencealignment
#end if

#if str($ireferencephylogeny) != 'None':
 --i-reference-phylogeny=$ireferencephylogeny
#end if

#set $pthreads = '${GALAXY_SLOTS:-4}'
#if str($pthreads):
 --p-threads="$pthreads"
#end if


#if str($palignmentsubsetsize):
 --p-alignment-subset-size=$palignmentsubsetsize
#end if

#if str($pplacementsubsetsize):
 --p-placement-subset-size="$pplacementsubsetsize"
#end if

--o-tree=otree
--o-placements=oplacements
;
cp otree.qza $otree;
cp oplacements.qza $oplacements
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences to insert                      [required]" name="irepresentativesequences" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-reference-alignment: ARTIFACT FeatureData[AlignedSequence] The reference multiple nucleotide alignment used to construct the reference phylogeny.           [optional]" name="ireferencealignment" optional="True" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-reference-phylogeny: ARTIFACT Phylogeny[Rooted]  The rooted reference phylogeny. Must be in sync with reference-alignment, i.e. each tip name must have exactly one corresponding record.            [optional]" name="ireferencephylogeny" optional="True" type="data"/>
		<param label="--p-alignment-subset-size: INTEGER Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset. The default alignment subset size is set to balance the exhaustiveness of the alignment step with the running time.   [default: 1000]" name="palignmentsubsetsize" optional="True" type="integer" value="1000"/>
		<param label="--p-placement-subset-size: INTEGER The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. The default placement subset is set to make sure the memory requirement of the pplacer step does not become prohibitively large." name="pplacementsubsetsize" optional="True" type="integer"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree"/>
		<data format="qza" label="${tool.name} on ${on_string}: placements.qza" name="oplacements"/>
	</outputs>
	<help><![CDATA[
Insert fragment sequences using SEPP into reference phylogenies like Greengenes 13_8
####################################################################################

Perform fragment insertion of 16S sequences using the SEPP algorithm
against the Greengenes 13_8 99% tree.

Parameters
----------
representative_sequences : FeatureData[Sequence]
    The sequences to insert
alignment_subset_size : Int, optional
    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.
placement_subset_size : Int, optional
    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. Further reading:
    https://github.com/smirarab/sepp/blob/master/tutorial/sepp-
    tutorial.md#sample-datasets-default-parameters
reference_alignment : FeatureData[AlignedSequence], optional
    The reference multiple nucleotide alignment used to construct the
    reference phylogeny.
reference_phylogeny : Phylogeny[Rooted], optional
    The rooted reference phylogeny. Must be in sync with reference-
    alignment, i.e. each tip name must have exactly one corresponding
    record.
debug : Bool, optional
    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.

Returns
-------
tree : Phylogeny[Rooted]
    The tree with inserted feature data
placements : Placements
	\
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>

14:a0a8d77a991c

<?xml version="1.0" ?>
<tool id="qiime_fragment-insertion_sepp" name="qiime fragment-insertion sepp"
      version="2020.8">
  <description>Insert fragment sequences using SEPP into reference phylogenies.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime fragment-insertion sepp

--i-representative-sequences=$irepresentativesequences

--i-reference-database=$ireferencedatabase

--p-alignment-subset-size=$palignmentsubsetsize

--p-placement-subset-size=$pplacementsubsetsize

--p-threads=$pthreads

#if $pdebug:
 --p-debug
#end if

--o-tree=otree

--o-placements=oplacements

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp oplacements.qza $oplacements

  ]]></command>
  <inputs>
    <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" />
    <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" />
    <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" />
    <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" />
    <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" />
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
    <data format="qza" label="${tool.name} on ${on_string}: placements.qza" name="oplacements" />
    
  </outputs>

  <help><![CDATA[
Insert fragment sequences using SEPP into reference phylogenies.
###############################################################

Perform fragment insertion of sequences using the SEPP algorithm.

Parameters
----------
representative_sequences : FeatureData[Sequence]
    The sequences to insert into the reference tree.
reference_database : SeppReferenceDatabase
    The reference database to insert the representative sequences into.
alignment_subset_size : Int, optional
    Each placement subset is further broken into subsets of at most these
    many sequences and a separate HMM is trained on each subset.
placement_subset_size : Int, optional
    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/sepp-
    tutorial.md#sample-datasets-default-parameters.
threads : Int, optional
    The number of threads to use.
debug : Bool, optional
    Collect additional run information to STDOUT for debugging. Temporary
    directories will not be removed if run fails.

Returns
-------
tree : Phylogeny[Rooted]
    The tree with inserted feature data.
placements : Placements
    Information about the feature placements within the reference tree.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>