--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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@@ -0,0 +1,155 @@
+<?xml version="1.0" ?>
+<tool id="qiime_phylogeny_align-to-tree-mafft-raxml" name="qiime phylogeny align-to-tree-mafft-raxml"
+      version="2020.8">
+  <description>Build a phylogenetic tree using raxml and mafft alignment.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime phylogeny align-to-tree-mafft-raxml
+
+--i-sequences=$isequences
+
+#if str($pnthreads) != 'None':
+--p-n-threads=$pnthreads
+#end if
+
+--p-mask-max-gap-frequency=$pmaskmaxgapfrequency
+
+--p-mask-min-conservation=$pmaskminconservation
+
+#if $pparttree:
+ --p-parttree
+#end if
+
+#if str($psubstitutionmodel) != 'None':
+--p-substitution-model=$psubstitutionmodel
+#end if
+
+#if str($pseed):
+  --p-seed=$pseed
+#end if
+#if str($praxmlversion) != 'None':
+--p-raxml-version=$praxmlversion
+#end if
+
+--o-alignment=oalignment
+
+--o-masked-alignment=omaskedalignment
+
+--o-tree=otree
+
+--o-rooted-tree=orootedtree
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp orootedtree.qza $orootedtree
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be used for creating a iqtree based rooted phylogenetic tree.           [required]" name="isequences" optional="False" type="data" />
+    <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="Int % Range(1">Int % Range(1</option>
+      <option value="None">None</option>
+    </param>
+    <param exclude_max="False" label="--p-mask-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns  regardless of gap character frequency. This value is used when masking the aligned sequences. [default: 1.0]" max="1" min="0" name="pmaskmaxgapfrequency" optional="True" type="float" value="1.0" />
+    <param exclude_max="False" label="--p-mask-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of  0.4 is provided, a column will only be retained  if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences. [default: 0.4]" max="1" min="0" name="pmaskminconservation" optional="True" type="float" value="0.4" />
+    <param label="--p-parttree: --p-parttree: / --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default. NOTE: if using this option, it is recomended that only the CAT-based substitution models of RAxML be considered for this pipeline. [default: False]" name="pparttree" selected="False" type="boolean" />
+    <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="GTRGAMMA">GTRGAMMA</option>
+      <option value="GTRGAMMAI">GTRGAMMAI</option>
+      <option value="GTRCAT">GTRCAT</option>
+      <option value="GTRCATI">GTRCATI</option>
+    </param>
+    <param label="--p-seed: INTEGER        Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]" name="pseed" optional="False" type="text" />
+    <param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="Standard">Standard</option>
+      <option value="SSE3">SSE3</option>
+      <option value="AVX2">AVX2</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment" />
+    <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" />
+    <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
+    <data format="qza" label="${tool.name} on ${on_string}: rootedtree.qza" name="orootedtree" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Build a phylogenetic tree using raxml and mafft alignment.
+###############################################################
+
+This pipeline will start by creating a sequence alignment using MAFFT,
+after which any alignment columns that are phylogenetically uninformative
+or ambiguously aligned will be removed (masked). The resulting masked
+alignment will be used to infer a phylogenetic tree using RAxML, under the
+specified substitution model, and then subsequently rooted at its midpoint.
+Output files from each step of the pipeline will be saved. This includes
+both the unmasked and masked MAFFT alignment from q2-alignment methods, and
+both the rooted and unrooted phylogenies from q2-phylogeny methods.
+
+Parameters
+----------
+sequences : FeatureData[Sequence]
+    The sequences to be used for creating a iqtree based rooted
+    phylogenetic tree.
+n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
+    The number of threads. (Use `all` to automatically use all available
+    cores. This value is used when aligning the sequences and creating the
+    tree with iqtree.
+mask_max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
+    The maximum relative frequency of gap characters in a column for the
+    column to be retained. This relative frequency must be a number between
+    0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
+    gap characters, and 1.0 retains all columns  regardless of gap
+    character frequency. This value is used when masking the aligned
+    sequences.
+mask_min_conservation : Float % Range(0, 1, inclusive_end=True), optional
+    The minimum relative frequency of at least one non-gap character in a
+    column for that column to be retained. This relative frequency must be
+    a number between 0.0 and 1.0 (inclusive). For example, if a value of
+    0.4 is provided, a column will only be retained  if it contains at
+    least one character that is present in at least 40% of the sequences.
+    This value is used when masking the aligned sequences.
+parttree : Bool, optional
+    This flag is required if the number of sequences being aligned are
+    larger than 1000000. Disabled by default. NOTE: if using this option,
+    it is recomended that only the CAT-based substitution models of RAxML
+    be considered for this pipeline.
+substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional
+    Model of Nucleotide Substitution.
+seed : Int, optional
+    Random number seed for the parsimony starting tree. This allows you to
+    reproduce tree results. If not supplied then one will be randomly
+    chosen.
+raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional
+    Select a specific CPU optimization of RAxML to use. The SSE3 versions
+    will run approximately 40% faster than the standard version. The AVX2
+    version will run 10-30% faster than the SSE3 version.
+
+Returns
+-------
+alignment : FeatureData[AlignedSequence]
+    The aligned sequences.
+masked_alignment : FeatureData[AlignedSequence]
+    The masked alignment.
+tree : Phylogeny[Unrooted]
+    The unrooted phylogenetic tree.
+rooted_tree : Phylogeny[Rooted]
+    The rooted phylogenetic tree.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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