# HG changeset patch
# User florianbegusch
# Date 1599223608 0
# Node ID a98d7ab297f1d3f2bee91629f1261248ba2a915a
# Parent  d93d8888f0b0b2ddf4ea5ee9c55363442d8f97b6
Deleted selected files

diff -r d93d8888f0b0 -r a98d7ab297f1 qiime2-2020.8/qiime_vsearch_uchime-denovo.xml
--- a/qiime2-2020.8/qiime_vsearch_uchime-denovo.xml	Fri Sep 04 12:44:24 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_vsearch_uchime-denovo" name="qiime vsearch uchime-denovo"
-      version="2020.8">
-  <description>De novo chimera filtering with vsearch.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime vsearch uchime-denovo
-
---i-sequences=$isequences
-
---i-table=$itable
-
---p-dn=$pdn
-
---p-mindiffs=$pmindiffs
-
---p-mindiv=$pmindiv
-
---p-minh=$pminh
-
---p-xn=$pxn
-
---o-chimeras=ochimeras
-
---o-nonchimeras=ononchimeras
-
---o-stats=ostats
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp ostats.qza $ostats
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data" />
-    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table (used for computing total feature abundances).                              [required]" name="itable" optional="False" type="data" />
-    <param label="--p-dn: NUMBER           No vote pseudo-count, corresponding to the Range(0.0, None)      parameter n in the chimera scoring function. [default: 1.4]" min="0.0" name="pdn" optional="True" type="float" value="1.4" />
-    <param label="--p-mindiffs: INTEGER    Minimum number of differences per segment. Range(1, None)                                                [default: 3]" min="1" name="pmindiffs" optional="True" type="integer" value="3" />
-    <param label="--p-mindiv: NUMBER       Minimum divergence from closest parent. Range(0.0, None)                                            [default: 0.8]" min="0.0" name="pmindiv" optional="True" type="float" value="0.8" />
-    <param exclude_max="False" label="--p-minh: PROPORTION Range(0.0, 1.0, inclusive_end=True) Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity.                         [default: 0.28]" max="1.0" min="0.0" name="pminh" optional="True" type="float" value="0.28" />
-    <param exclude_min="True" label="--p-xn: NUMBER Range(1.0, None, inclusive_start=False) No vote weight, corresponding to the parameter beta in the scoring function.              [default: 8.0]" max="None" min="1.0" name="pxn" optional="True" type="float" value="8.0" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras" />
-    <data format="qza" label="${tool.name} on ${on_string}: nonchimeras.qza" name="ononchimeras" />
-    <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats" />
-    
-  </outputs>
-
-  <help><![CDATA[
-De novo chimera filtering with vsearch.
-###############################################################
-
-Apply the vsearch uchime_denovo method to identify chimeric feature
-sequences. The results of this method can be used to filter chimeric
-features from the corresponding feature table. For additional details,
-please refer to the vsearch documentation.
-
-Parameters
-----------
-sequences : FeatureData[Sequence]
-    The feature sequences to be chimera-checked.
-table : FeatureTable[Frequency]
-    Feature table (used for computing total feature abundances).
-dn : Float % Range(0.0, None), optional
-    No vote pseudo-count, corresponding to the parameter n in the chimera
-    scoring function.
-mindiffs : Int % Range(1, None), optional
-    Minimum number of differences per segment.
-mindiv : Float % Range(0.0, None), optional
-    Minimum divergence from closest parent.
-minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
-    Minimum score (h). Increasing this value tends to reduce the number of
-    false positives and to decrease sensitivity.
-xn : Float % Range(1.0, None, inclusive_start=False), optional
-    No vote weight, corresponding to the parameter beta in the scoring
-    function.
-
-Returns
--------
-chimeras : FeatureData[Sequence]
-    The chimeric sequences.
-nonchimeras : FeatureData[Sequence]
-    The non-chimeric sequences.
-stats : UchimeStats
-    Summary statistics from chimera checking.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file
diff -r d93d8888f0b0 -r a98d7ab297f1 qiime2-2020.8/qiime_vsearch_uchime-ref.xml
--- a/qiime2-2020.8/qiime_vsearch_uchime-ref.xml	Fri Sep 04 12:44:24 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,110 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_vsearch_uchime-ref" name="qiime vsearch uchime-ref"
-      version="2020.8">
-  <description>Reference-based chimera filtering with vsearch.</description>
-  <requirements>
-    <requirement type="package" version="2020.8">qiime2</requirement>
-  </requirements>
-  <command><![CDATA[
-qiime vsearch uchime-ref
-
---i-sequences=$isequences
-
---i-table=$itable
-
---i-reference-sequences=$ireferencesequences
-
---p-dn=$pdn
-
---p-mindiffs=$pmindiffs
-
---p-mindiv=$pmindiv
-
---p-minh=$pminh
-
---p-xn=$pxn
-
---p-threads=$pthreads
-
---o-chimeras=ochimeras
-
---o-nonchimeras=ononchimeras
-
---o-stats=ostats
-
-#if str($examples) != 'None':
---examples=$examples
-#end if
-
-;
-cp ostats.qza $ostats
-
-  ]]></command>
-  <inputs>
-    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data" />
-    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table (used for computing total feature abundances).                              [required]" name="itable" optional="False" type="data" />
-    <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] The non-chimeric reference sequences.     [required]" name="ireferencesequences" optional="False" type="data" />
-    <param label="--p-dn: NUMBER           No vote pseudo-count, corresponding to the Range(0.0, None)      parameter n in the chimera scoring function. [default: 1.4]" min="0.0" name="pdn" optional="True" type="float" value="1.4" />
-    <param label="--p-mindiffs: INTEGER    Minimum number of differences per segment. Range(1, None)                                                [default: 3]" min="1" name="pmindiffs" optional="True" type="integer" value="3" />
-    <param label="--p-mindiv: NUMBER       Minimum divergence from closest parent. Range(0.0, None)                                            [default: 0.8]" min="0.0" name="pmindiv" optional="True" type="float" value="0.8" />
-    <param exclude_max="False" label="--p-minh: PROPORTION Range(0.0, 1.0, inclusive_end=True) Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity.                         [default: 0.28]" max="1.0" min="0.0" name="pminh" optional="True" type="float" value="0.28" />
-    <param exclude_min="True" label="--p-xn: NUMBER Range(1.0, None, inclusive_start=False) No vote weight, corresponding to the parameter beta in the scoring function.              [default: 8.0]" max="None" min="1.0" name="pxn" optional="True" type="float" value="8.0" />
-    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
-    
-  </inputs>
-
-  <outputs>
-    <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras" />
-    <data format="qza" label="${tool.name} on ${on_string}: nonchimeras.qza" name="ononchimeras" />
-    <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats" />
-    
-  </outputs>
-
-  <help><![CDATA[
-Reference-based chimera filtering with vsearch.
-###############################################################
-
-Apply the vsearch uchime_ref method to identify chimeric feature sequences.
-The results of this method can be used to filter chimeric features from the
-corresponding feature table. For additional details, please refer to the
-vsearch documentation.
-
-Parameters
-----------
-sequences : FeatureData[Sequence]
-    The feature sequences to be chimera-checked.
-table : FeatureTable[Frequency]
-    Feature table (used for computing total feature abundances).
-reference_sequences : FeatureData[Sequence]
-    The non-chimeric reference sequences.
-dn : Float % Range(0.0, None), optional
-    No vote pseudo-count, corresponding to the parameter n in the chimera
-    scoring function.
-mindiffs : Int % Range(1, None), optional
-    Minimum number of differences per segment.
-mindiv : Float % Range(0.0, None), optional
-    Minimum divergence from closest parent.
-minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
-    Minimum score (h). Increasing this value tends to reduce the number of
-    false positives and to decrease sensitivity.
-xn : Float % Range(1.0, None, inclusive_start=False), optional
-    No vote weight, corresponding to the parameter beta in the scoring
-    function.
-threads : Int % Range(0, 256, inclusive_end=True), optional
-    The number of threads to use for computation. Passing 0 will launch one
-    thread per CPU core.
-
-Returns
--------
-chimeras : FeatureData[Sequence]
-    The chimeric sequences.
-nonchimeras : FeatureData[Sequence]
-    The non-chimeric sequences.
-stats : UchimeStats
-    Summary statistics from chimera checking.
-  ]]></help>
-  <macros>
-    <import>qiime_citation.xml</import>
-  </macros>
-  <expand macro="qiime_citation"/>
-</tool>
\ No newline at end of file