comparison qiime2/qiime_taxa_filter-seqs.xml @ 14:a0a8d77a991c draft

Uploaded

13:887cd4ad8e16

<?xml version="1.0" ?>
<tool id="qiime_taxa_filter-seqs" name="qiime taxa filter-seqs" version="2019.7">
	<description> - Taxonomy-based feature sequence filter.</description>
	<requirements>
		<requirement type="package" version="2019.7">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime taxa filter-seqs


#if str( $id_to_taxonomy_fp.selector ) == 'history'
	#set $tax = $id_to_taxonomy_fp.taxonomy_fp
	--i-taxonomy '$tax'
#else:
	#set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
	--i-taxonomy '$tax'
#end if


--i-sequences=$isequences

#if str($pinclude):
 --p-include="$pinclude"
#end if

#if str($pexclude):
 --p-exclude="$pexclude"
#end if

#if str($pquerydelimiter):
 --p-query-delimiter="$pquerydelimiter"
#end if

#if str($pmode) != 'None':
 --p-mode=$pmode
#end if

--o-filtered-sequences=ofilteredsequences
;
cp ofilteredsequences.qza $ofilteredsequences
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] Feature sequences to be filtered.         [required]" name="isequences" optional="False" type="data"/>

		<conditional name="id_to_taxonomy_fp" optional="True">
		   <param name="selector" type="select" label="Reference taxonomy to query">
			  <option value="cached">Public databases</option>
			  <option value="history">Databases from your history</option>
		   </param>
		   <when value="cached">
			  <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
				 <options from_data_table="qiime_taxonomy" />
			  </param>
		   </when>
		   <when value="history">
			  <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
		   </when>
		</conditional>

		<param label="--p-include: TEXT        One or more search terms that indicate which taxa should be included in the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included.       [optional]" name="pinclude" optional="True" type="text"/>
		<param label="--p-exclude: TEXT        One or more search terms that indicate which taxa should be excluded from the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded.        [optional]" name="pexclude" optional="True" type="text"/>
		<param label="--p-query-delimiter: TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations.                [default: ',']" name="pquerydelimiter" optional="True" type="text" value=","/>
		<param label="--p-mode: " name="pmode" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="exact">exact</option>
			<option value="contains">contains</option>
		</param>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: filteredsequences.qza" name="ofilteredsequences"/>
	</outputs>
	<help><![CDATA[
Taxonomy-based feature sequence filter.
#######################################

This method filters sequences based on their taxonomic annotations.
Features can be retained in the result by specifying one or more include
search terms, and can be filtered out of the result by specifying one or
more exclude search terms. If both include and exclude are provided, the

Returns
-------
filtered_sequences : FeatureData[Sequence]
    The taxonomy-filtered feature sequences.
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>

14:a0a8d77a991c

<?xml version="1.0" ?>
<tool id="qiime_taxa_filter-seqs" name="qiime taxa filter-seqs"
      version="2020.8">
  <description>Taxonomy-based feature sequence filter.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime taxa filter-seqs

--i-sequences=$isequences

--i-taxonomy=$itaxonomy

#if str($pinclude):
  --p-include=$pinclude
#end if
#if str($pexclude):
  --p-exclude=$pexclude
#end if
#if str($pquerydelimiter):
  --p-query-delimiter=$pquerydelimiter
#end if
#if str($pmode) != 'None':
--p-mode=$pmode
#end if

--o-filtered-sequences=ofilteredsequences

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp ofilteredsequences.qza $ofilteredsequences

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] Feature sequences to be filtered.         [required]" name="isequences" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature sequences. All features in the feature sequences must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature sequences will be ignored.                                  [required]" name="itaxonomy" optional="False" type="data" />
    <param label="--p-include: TEXT        One or more search terms that indicate which taxa should be included in the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included.       [optional]" name="pinclude" optional="False" type="text" />
    <param label="--p-exclude: TEXT        One or more search terms that indicate which taxa should be excluded from the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded.        [optional]" name="pexclude" optional="False" type="text" />
    <param label="--p-query-delimiter: TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations.                [default: \',\']" name="pquerydelimiter" optional="False" type="text" value="\',\'" />
    <param label="--p-mode: " name="pmode" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="exact">exact</option>
      <option value="contains">contains</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}: filteredsequences.qza" name="ofilteredsequences" />
    
  </outputs>

  <help><![CDATA[
Taxonomy-based feature sequence filter.
###############################################################

This method filters sequences based on their taxonomic annotations.
Features can be retained in the result by specifying one or more include
search terms, and can be filtered out of the result by specifying one or
more exclude search terms. If both include and exclude are provided, the

Returns
-------
filtered_sequences : FeatureData[Sequence]
    The taxonomy-filtered feature sequences.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>