Mercurial > repos > florianbegusch > qiime2_suite
changeset 21:a98d7ab297f1 draft
Deleted selected files
| author | florianbegusch |
|---|---|
| date | Fri, 04 Sep 2020 12:46:48 +0000 |
| parents | d93d8888f0b0 |
| children | 292c84bd5ab6 |
| files | qiime2-2020.8/qiime_vsearch_uchime-denovo.xml qiime2-2020.8/qiime_vsearch_uchime-ref.xml |
| diffstat | 2 files changed, 0 insertions(+), 210 deletions(-) [+] |
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--- 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
--- 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