comparison qiime2/qiime_feature-classifier_extract-reads.xml @ 6:de4c22a52df4 draft

Fixes

5:a025a4a89e07

	<description> - Extract reads from reference</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime feature-classifier extract-reads

--i-sequences=$isequences
--p-f-primer="$pfprimer"
--p-r-primer="$prprimer"

#if str($ptrunclen):
 --p-trunc-len=$ptrunclen

--o-reads=oreads
;
cp oreads.qza $oreads
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] [required]" name="isequences" optional="False" type="data"/>
		<param label="--p-f-primer: TEXT       forward primer sequence                   [required]" name="pfprimer" optional="False" type="text"/>
		<param label="--p-r-primer: TEXT       reverse primer sequence                   [required]" name="prprimer" optional="False" type="text"/>
		<param label="--p-trunc-len: INTEGER   read is cut to trunc-len if trunc-len is positive. Applied before trim-left.               [default: 0]" name="ptrunclen" optional="True" type="integer" value="0"/>
		<param label="--p-trim-left: INTEGER   trim-left nucleotides are removed from the 5' end if trim-left is positive. Applied after trunc-len. [default: 0]" name="ptrimleft" optional="True" type="integer" value="0"/>
		<param label="--p-identity: NUMBER     minimum combined primer match identity threshold. [default: 0.8]" name="pidentity" optional="True" type="float" value="0.8"/>

6:de4c22a52df4

	<description> - Extract reads from reference</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[


#if str( $input_sequences.selector ) == 'history'
	#set $seq = $input_sequences.i_sequences

#else:
	qiime tools import --type 'FeatureData[Sequence]' --input-path '$input_sequences.i_sequences.fields.path' --output-path database.qza;
	#set $seq = 'database.qza'
#end if


qiime feature-classifier extract-reads

--i-sequences=$seq

--p-f-primer="$pfprimer"
--p-r-primer="$prprimer"

#if str($ptrunclen):
 --p-trunc-len=$ptrunclen

--o-reads=oreads
;
cp oreads.qza $oreads
	]]></command>
	<inputs>
		<conditional name="input_sequences" optional="False">
		   <param name="selector" type="select" label="--i-sequences: FeatureData[Sequence] [required] - Reference sequences to query">
			  <option value="cached">Public databases</option>
			  <option value="history">Databases from your history</option>
		   </param>
		   <when value="cached">
			  <param name="i_sequences" label="--i-sequences: FeatureData[Sequence] [required] - Reference sequences" type="select" optional="True">
				 <options from_data_table="qiime_rep_set" />
			  </param>
		   </when>
		   <when value="history">
			  <param name="i_sequences" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
		   </when>
		</conditional>

		<param label="--p-f-primer: TEXT       forward primer sequence                   [required]" name="pfprimer" optional="False" type="text"/>
		<param label="--p-r-primer: TEXT       reverse primer sequence                   [required]" name="prprimer" optional="False" type="text"/>
		<param label="--p-trunc-len: INTEGER   read is cut to trunc-len if trunc-len is positive. Applied before trim-left.               [default: 0]" name="ptrunclen" optional="True" type="integer" value="0"/>
		<param label="--p-trim-left: INTEGER   trim-left nucleotides are removed from the 5' end if trim-left is positive. Applied after trunc-len. [default: 0]" name="ptrimleft" optional="True" type="integer" value="0"/>
		<param label="--p-identity: NUMBER     minimum combined primer match identity threshold. [default: 0.8]" name="pidentity" optional="True" type="float" value="0.8"/>