diff qiime2/qiime_phylogeny_align-to-tree-mafft-fasttree.xml @ 14:a0a8d77a991c draft

Uploaded

--- a/qiime2/qiime_phylogeny_align-to-tree-mafft-fasttree.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_phylogeny_align-to-tree-mafft-fasttree.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,53 +1,68 @@
 <?xml version="1.0" ?>
-<tool id="qiime_phylogeny_align-to-tree-mafft-fasttree" name="qiime phylogeny align-to-tree-mafft-fasttree" version="2019.7">
-	<description> - Build a phylogenetic tree using fasttree and mafft alignment</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_phylogeny_align-to-tree-mafft-fasttree" name="qiime phylogeny align-to-tree-mafft-fasttree"
+      version="2020.8">
+  <description>Build a phylogenetic tree using fasttree and mafft alignment</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime phylogeny align-to-tree-mafft-fasttree
 
 --i-sequences=$isequences
 
-#set $pnthreads = '${GALAXY_SLOTS:-4}'
-
-#if str($pnthreads):
- --p-n-threads="$pnthreads"
+#if str($pnthreads) != 'None':
+--p-n-threads=$pnthreads
 #end if
 
+--p-mask-max-gap-frequency=$pmaskmaxgapfrequency
 
-#if str($pmaskmaxgapfrequency):
- --p-mask-max-gap-frequency=$pmaskmaxgapfrequency
-#end if
+--p-mask-min-conservation=$pmaskminconservation
 
-#if str($pmaskminconservation):
- --p-mask-min-conservation=$pmaskminconservation
+#if $pparttree:
+ --p-parttree
 #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 oalignment.qza $oalignment;
-cp omaskedalignment.qza $omaskedalignment;
-cp otree.qza $otree;
 cp orootedtree.qza $orootedtree
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be used for creating a fasttree based rooted phylogenetic tree.           [required]" name="isequences" optional="False" type="data"/>
-		<param label="--p-mask-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns  regardless of gap character frequency. This value is used when masking the aligned sequences. [default: 1.0]" name="pmaskmaxgapfrequency" optional="True" type="float" min="0" max="1" exclusive_end="False" value="1.0"/>
-		<param label="--p-mask-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of  0.4 is provided, a column will only be retained  if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences. [default: 0.4]" name="pmaskminconservation" optional="True" type="float" min="0" max="1" exclusive_end="False" value="0.4"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${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[
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be used for creating a fasttree 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.                            [default: False]" name="pparttree" 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 ${on_string}: alignment.qza" name="oalignment" />
+    <data format="qza" label="${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 fasttree and mafft alignment
-############################################################
+###############################################################
 
 This pipeline will start by creating a sequence alignment using MAFFT,
 after which any alignment columns that are phylogenetically uninformative
@@ -63,6 +78,10 @@
 sequences : FeatureData[Sequence]
     The sequences to be used for creating a fasttree based rooted
     phylogenetic tree.
+n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
+    The number of threads. (Use `auto` to automatically use all available
+    cores) This value is used when aligning the sequences and creating the
+    tree with fasttree.
 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
@@ -77,6 +96,9 @@
     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.
 
 Returns
 -------
@@ -88,9 +110,9 @@
     The unrooted phylogenetic tree.
 rooted_tree : Phylogeny[Rooted]
     The rooted phylogenetic tree.
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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