Mercurial > repos > florianbegusch > qiime2_suite

changeset 8:d66c7509e8f9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Tue, 13 Aug 2019 07:57:53 -0400
parents 85b520815e85
children f190567fe3f6
files qiime2/qiime_demux_filter-samples.xml qiime2/qiime_diversity_alpha-phylogenetic-alt.xml qiime2/qiime_feature-classifier_classify-hybrid-vsearch-sklearn.xml
diffstat 3 files changed, 0 insertions(+), 224 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2/qiime_demux_filter-samples.xml	Tue Aug 13 07:53:59 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_demux_filter-samples" name="qiime demux filter-samples" version="2019.7">
-	<description> - Filter samples out of demultiplexed data.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
-qiime demux filter-samples 
-    
---i-demux=$idemux
-
-
-#if $input_files_mmetadatafile:
-#def list_dict_to_string(list_dict):
-  #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
-  #for d in list_dict[1:]:
-	  #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
-  #end for
-  #return $file_list
-#end def
-  --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
-#end if
-
-
-
-#if '__sq__' in str($pwhere):
-  #set $pwhere_temp = $pwhere.replace('__sq__', "'")
-  #set $pwhere = $pwhere_temp
-#end if
-
-
-#if str($pwhere):
- --p-where="$pwhere"
-#end if
-
-
-#if $pexcludeids:
- --p-exclude-ids
-#end if
-
-#if str($citations) != 'None':
- --citations=$citations
-#end if
-
-
---o-filtered-demux=ofiltereddemux
-
-;
-cp ofiltereddemux.qza $ofiltereddemux
-	]]></command>
-	<inputs>
-
-		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
-			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. Sample metadata file containing individual_id_column.  [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
-		</repeat>
-
-		<param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] The demultiplexed data from which samples should be filtered.                                    [required]" name="idemux" optional="False" type="data"/>
-		<param label="--p-where: TEXT       Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained.                                 [optional]" name="pwhere" optional="True" type="text"/>
-		<param label="--p-exclude-ids: --p-no-exclude-ids Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data.       [default: False]" name="pexcludeids" selected="False" type="boolean"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: filtereddemux.qza" name="ofiltereddemux"/>
-	</outputs>
-	<help><![CDATA[
-
-	]]></help>
-<macros>
-    <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
--- a/qiime2/qiime_diversity_alpha-phylogenetic-alt.xml	Tue Aug 13 07:53:59 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_diversity_alpha-phylogenetic-alt" name="qiime diversity alpha-phylogenetic-alt" version="2019.7">
-	<description> - Alpha diversity (phylogenetic) - alternative implementation</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
-qiime diversity alpha-phylogenetic-alt
-
---i-table=$itable
---i-phylogeny=$iphylogeny
-
---p-metric=$pmetric
-
---o-alpha-diversity=oalphadiversity
-
-;
-cp oalphadiversity.qza $oalphadiversity
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples for which alpha diversity should be computed.       [required]" name="itable" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                  [required]" name="iphylogeny" optional="False" type="data"/>
-		<param label="--p-metric: " name="pmetric" optional="False" type="select">
-			<option value="faith_pd">faith_pd</option>
-		</param>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: alphadiversity.qza" name="oalphadiversity"/>
-	</outputs>
-	<help><![CDATA[
-
-	]]></help>
-<macros>
-    <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
--- a/qiime2/qiime_feature-classifier_classify-hybrid-vsearch-sklearn.xml	Tue Aug 13 07:53:59 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,116 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_feature-classifier_classify-hybrid-vsearch-sklearn" name="qiime feature-classifier classify-hybrid-vsearch-sklearn" version="2019.7">
-	<description> -  ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
-qiime feature-classifier classify-hybrid-vsearch-sklearn
-    
---i-query=$iquery
---i-reference-reads=$ireferencereads
---i-reference-taxonomy=$ireferencetaxonomy
---i-classifier=$iclassifier
-
-#if str($pmaxaccepts) != 'None':
- --p-maxaccepts=$pmaxaccepts
-#end if
-
-#if str($ppercidentity):
- --p-perc-identity=$ppercidentity
-#end if
-
-#if str($pquerycov):
- --p-query-cov=$pquerycov
-#end if
-
-#if str($pstrand) != 'None':
- --p-strand=$pstrand
-#end if
-
-#if str($pminconsensus):
- --p-min-consensus=$pminconsensus
-#end if
-
-#if str($pconfidence) != 'None':
- --p-confidence=$pconfidence
-#end if
-
-#if str($preadorientation) != 'None':
- --p-read-orientation=$preadorientation
-#end if
-
-#set $pthreads = '${GALAXY_SLOTS:-4}'
-
-#if str($pthreads):
-
-#if str($pthreads):
- --p-threads="$pthreads"
-#end if
-
-#end if
-
-
-#if $pprefilter:
- --p-prefilter
-#end if
-
-#if str($psamplesize):
- --p-sample-size=$psamplesize
-#end if
-
-#if str($prandseed):
- --p-randseed=$prandseed
-#end if
-
-
---o-classification=oclassification
-
-;
-cp oclassification.qza $oclassification
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically.        [required]" name="iquery" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] reference sequences.                        [required]" name="ireferencereads" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] reference taxonomy labels.                  [required]" name="ireferencetaxonomy" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-classifier: ARTIFACT TaxonomicClassifier Pre-trained sklearn taxonomic classifier for classifying the reads.                      [required]" name="iclassifier" optional="False" type="data"/>
-		<param label="--p-maxaccepts: " name="pmaxaccepts" 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 label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Percent sequence similarity to use for PREFILTER. Reject match if percent identity to query is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled. [default: 0.5]" name="ppercidentity" optional="True" type="float" value="0.5"/>
-		<param label="--p-query-cov: PROPORTION Range(0.0, 1.0, inclusive_end=True) Query coverage threshold to use for PREFILTER. Reject match if query alignment coverage per high-scoring pair is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled.                            [default: 0.8]" name="pquerycov" optional="True" type="float" value="0.8"/>
-		<param label="--p-strand: " name="pstrand" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="both">both</option>
-			<option value="plus">plus</option>
-		</param>
-		<param label="--p-min-consensus: NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment.   [default: 0.51]" name="pminconsensus" optional="True" type="float" value="0.51"/>
-		<param label="--p-confidence: " name="pconfidence" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="Float % Range(0">Float % Range(0</option>
-			<option value="1">1</option>
-			<option value="inclusive_end=True">inclusive_end=True</option>
-		</param>
-		<param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="same">same</option>
-			<option value="reverse-complement">reverse-complement</option>
-			<option value="auto">auto</option>
-		</param>
-		<param label="--p-prefilter: --p-no-prefilter Toggle positive filter of query sequences on or off. [default: True]" name="pprefilter" selected="False" type="boolean"/>
-		<param label="--p-sample-size: INTEGER Range(1, None)      Randomly extract the given number of sequences from the reference database to use for prefiltering. This parameter is ignored if `prefilter` is disabled. [default: 1000]" name="psamplesize" optional="True" type="integer" value="1000"/>
-		<param label="--p-randseed: INTEGER  Use integer as a seed for the pseudo-random generator Range(0, None)      used during prefiltering. A given seed always produces the same output, which is useful for replicability. Set to 0 to use a pseudo-random seed. This parameter is ignored if `prefilter` is disabled.    [default: 0]" name="prandseed" optional="True" type="integer" value="0"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
-	</outputs>
-	<help><![CDATA[
-
-	]]></help>
-<macros>
-    <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>