Mercurial > repos > florianbegusch > qiime2_suite
changeset 9:f190567fe3f6 draft
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--- a/qiime2/merge_feature_table_and_taxonomy.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/merge_feature_table_and_taxonomy.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="merge_feature_table_and_taxonomy" name="merge feature table and taxonomy" version="2019.4"> +<tool id="merge_feature_table_and_taxonomy" name="merge feature table and taxonomy" version="2019.7"> <description>- Merge features and taxonomy into a single biom file.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command> mkdir out;
--- a/qiime2/qiime_alignment_mafft.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_alignment_mafft.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_alignment_mafft" name="qiime alignment mafft" version="2019.4"> +<tool id="qiime_alignment_mafft" name="qiime alignment mafft" version="2019.7"> <description> - De novo multiple sequence alignment with MAFFT</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime alignment mafft
--- a/qiime2/qiime_alignment_mask.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_alignment_mask.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_alignment_mask" name="qiime alignment mask" version="2019.4"> +<tool id="qiime_alignment_mask" name="qiime alignment mask" version="2019.7"> <description> - Positional conservation and gap filtering.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime alignment mask
--- a/qiime2/qiime_composition_add-pseudocount.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_composition_add-pseudocount.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_composition_add-pseudocount" name="qiime composition add-pseudocount" version="2019.4"> +<tool id="qiime_composition_add-pseudocount" name="qiime composition add-pseudocount" version="2019.7"> <description> - Add pseudocount to table</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime composition add-pseudocount
--- a/qiime2/qiime_composition_ancom.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_composition_ancom.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_composition_ancom" name="qiime composition ancom" version="2019.4"> +<tool id="qiime_composition_ancom" name="qiime composition ancom" version="2019.7"> <description> - Apply ANCOM to identify features that differ in abundance.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime composition ancom
--- a/qiime2/qiime_cutadapt_demux-paired.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_cutadapt_demux-paired.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_cutadapt_demux-paired" name="qiime cutadapt demux-paired" version="2019.4"> +<tool id="qiime_cutadapt_demux-paired" name="qiime cutadapt demux-paired" version="2019.7"> <description> - Demultiplex paired-end sequence data with barcodes in- sequence.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime cutadapt demux-paired @@ -13,7 +13,7 @@ #def list_dict_to_string_forward(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: - #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') + #set $file_list = $file_list + ' --m-forward-barcodes-file=' + d['additional_input'].__getattr__('file_name') #end for #return $file_list #end def @@ -24,7 +24,7 @@ #def list_dict_to_string_reverse(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: - #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') + #set $file_list = $file_list + ' --m-reverse-barcodes-file=' + d['additional_input'].__getattr__('file_name') #end for #return $file_list #end def @@ -33,6 +33,16 @@ +#if str($pbatchsize): + --p-batch-size $pbatchsize +#end if + +#if str($pminimumlength): + --p-minimum-length $pminimumlength +#end if + + + #if '__sq__' in str($mforwardbarcodescolumn): #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__sq__', "'") @@ -44,10 +54,6 @@ #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp #end if -#if str($mforwardbarcodescolumn): ---m-forward-barcodes-column="$mforwardbarcodescolumn" -#end if - @@ -61,13 +67,19 @@ #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp #end if + + +#if str($mforwardbarcodescolumn): +--m-forward-barcodes-column="$mforwardbarcodescolumn" +#end if + #if str($mreversebarcodescolumn): --m-reverse-barcodes-column="$mreversebarcodescolumn" #end if -#if $perrorrate: +#if str($perrorrate): --p-error-rate=$perrorrate #end if @@ -81,6 +93,12 @@ cp ountrimmedsequences.qza $ountrimmedsequences ]]></command> <inputs> + + <param label="--p-batch-size: INTEGER The number of samples cutadapt demultiplexes Range(0, None) concurrently. Demultiplexing in smaller batches will yield the same result with marginal speed loss, and may solve 'too many files' errors related to sample quantity. Set to '0' to process all samples at once. [default: 0]" name="pbatchsize" optional="True" type="integer" value="0" min="0"/> + <param label="--p-minimum-length: INTEGER Range(1, None) Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" name="pminimumlength" optional="True" type="integer" value="1" min="1"/> + + + <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedPairedEndBarcodeInSequence The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/> <param label="--m-forward-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes for the forward reads. [required]" name="mforwardbarcodescolumn" optional="False" type="text"/> <param label="--m-reverse-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes for the reverse reads. [optional]" name="mreversebarcodescolumn" optional="True" type="text"/> @@ -101,7 +119,7 @@ </outputs> <help><![CDATA[ Demultiplex paired-end sequence data with barcodes in-sequence. -############################################################### +################################################################ Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes are expected to be located within the sequence data (versus the header, or @@ -120,6 +138,15 @@ error_rate : Float % Range(0, 1, inclusive_end=True), optional The level of error tolerance, specified as the maximum allowable error rate. +batch_size : Int % Range(0, None), optional + The number of samples cutadapt demultiplexes concurrently. + Demultiplexing in smaller batches will yield the same result with + marginal speed loss, and may solve "too many files" errors related to + sample quantity. Set to "0" to process all samples at once. +minimum_length : Int % Range(1, None), optional + Discard reads shorter than specified value. Note, the cutadapt default + of 0 has been overridden, because that value produces empty sequence + records. Returns -------
--- a/qiime2/qiime_cutadapt_demux-single.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_cutadapt_demux-single.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_cutadapt_demux-single" name="qiime cutadapt demux-single" version="2019.4"> +<tool id="qiime_cutadapt_demux-single" name="qiime cutadapt demux-single" version="2019.7"> <description> - Demultiplex single-end sequence data with barcodes in- sequence.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime cutadapt demux-single @@ -10,6 +10,30 @@ --i-seqs=$iseqs +#if str($pbatchsize): + --p-batch-size $pbatchsize +#end if + +#if str($pminimumlength): + --p-minimum-length $pminimumlength +#end if + + + + + +#if $input_files_mbarcodesfile: +#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-barcodes-file=' + d['additional_input'].__getattr__('file_name') +#end for +#return $file_list +#end def +--m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile) +#end if + + #if '__sq__' in str($mbarcodescolumn): #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'") @@ -19,36 +43,25 @@ --m-barcodes-column="$mbarcodescolumn" ---o-per-sample-sequences=opersamplesequences ---o-untrimmed-sequences=ountrimmedsequences - - - - - -#if $input_files_mbarcodesfile: -#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 + ',' + d['additional_input'].__getattr__('file_name') -#end for -#return $file_list -#end def ---m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile) +#if str($perrorrate): + --p-error-rate=$perrorrate #end if -#if $perrorrate: - --p-error-rate=$perrorrate -#end if - +--o-per-sample-sequences=opersamplesequences +--o-untrimmed-sequences=ountrimmedsequences ; cp opersamplesequences.qza $opersamplesequences; cp ountrimmedsequences.qza $ountrimmedsequences ]]></command> <inputs> + + <param label="--p-batch-size: INTEGER The number of samples cutadapt demultiplexes Range(0, None) concurrently. Demultiplexing in smaller batches will yield the same result with marginal speed loss, and may solve 'too many files' errors related to sample quantity. Set to '0' to process all samples at once. [default: 0]" name="pbatchsize" optional="True" type="integer" value="0" min="0"/> + <param label="--p-minimum-length: INTEGER Range(1, None) Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" name="pminimumlength" optional="True" type="integer" value="1" min="1"/> + + <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedSingleEndBarcodeInSequence The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/> <repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file"> <param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> @@ -78,6 +91,15 @@ The level of error tolerance, specified as the maximum allowable error rate. The default value specified by cutadapt is 0.1 (=10%), which is greater than `demux emp-*`, which is 0.0 (=0%). +batch_size : Int % Range(0, None), optional + The number of samples cutadapt demultiplexes concurrently. + Demultiplexing in smaller batches will yield the same result with + marginal speed loss, and may solve "too many files" errors related to + sample quantity. Set to "0" to process all samples at once. +minimum_length : Int % Range(1, None), optional + Discard reads shorter than specified value. Note, the cutadapt default + of 0 has been overridden, because that value produces empty sequence + records. Returns -------
--- a/qiime2/qiime_cutadapt_trim-paired.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_cutadapt_trim-paired.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_cutadapt_trim-paired" name="qiime cutadapt trim-paired" version="2019.4"> +<tool id="qiime_cutadapt_trim-paired" name="qiime cutadapt trim-paired" version="2019.7"> <description> - Find and remove adapters in demultiplexed paired-end sequences.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime cutadapt trim-paired
--- a/qiime2/qiime_cutadapt_trim-single.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_cutadapt_trim-single.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_cutadapt_trim-single" name="qiime cutadapt trim-single" version="2019.4"> +<tool id="qiime_cutadapt_trim-single" name="qiime cutadapt trim-single" version="2019.7"> <description> - Find and remove adapters in demultiplexed single-end sequences.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime cutadapt trim-single
--- a/qiime2/qiime_dada2_denoise-paired.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_dada2_denoise-paired.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_dada2_denoise-paired" name="qiime dada2 denoise-paired" version="2019.4"> +<tool id="qiime_dada2_denoise-paired" name="qiime dada2 denoise-paired" version="2019.7"> <description> - Denoise and dereplicate paired-end sequences</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ @@ -82,10 +82,20 @@ --p-trim-left-r=$ptrimleftr #end if -#if str($pmaxee): - --p-max-ee=$pmaxee + + + +#if str($pmaxeef): + --p-max-ee-f=$pmaxeef #end if +#if str($pmaxeer): + --p-max-ee-r=$pmaxeer +#end if + + + + #if str($ptruncq): --p-trunc-q=$ptruncq #end if @@ -130,7 +140,14 @@ <param label="--p-trunc-len-r: INTEGER Position at which reverse read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 20 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]" name="ptrunclenr" optional="False" value="" type="integer"/> <param label="--p-trim-left-f: INTEGER Position at which forward read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]" name="ptrimleftf" optional="True" type="integer" value="0"/> <param label="--p-trim-left-r: INTEGER Position at which reverse read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]" name="ptrimleftr" optional="True" type="integer" value="0"/> - <param label="--p-max-ee: NUMBER Reads with number of expected errors higher than this value will be discarded. [default: 2.0]" name="pmaxee" optional="True" type="float" value="2.0"/> + + + + <param label="--p-max-ee-f: NUMBER Forward reads with number of expected errors higher than this value will be discarded. [default: 2.0]" name="pmaxeef" optional="True" type="float" value="2.0"/> + <param label="--p-max-ee-r: NUMBER Reverse reads with number of expected errors higher than this value will be discarded. [default: 2.0]" name="pmaxeer" optional="True" type="float" value="2.0"/> + + + <param label="--p-trunc-q: INTEGER Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len-f` or `trunc-len-r` (depending on the direction of the read) it is discarded. [default: 2]" name="ptruncq" optional="True" type="integer" value="2"/> <param label="--p-chimera-method: " name="pchimeramethod" optional="True" type="select"> <option selected="True" value="None">Selection is Optional</option> @@ -149,7 +166,7 @@ </outputs> <help><![CDATA[ Denoise and dereplicate paired-end sequences -############################################ +############################################# This method denoises paired-end sequences, dereplicates them, and filters chimeras. @@ -182,15 +199,18 @@ Position at which reverse read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences, which will be the bases that were sequenced in the first cycles. -max_ee : Float, optional - Reads with number of expected errors higher than this value will be - discarded. +max_ee_f : Float, optional + Forward reads with number of expected errors higher than this value + will be discarded. +max_ee_r : Float, optional + Reverse reads with number of expected errors higher than this value + will be discarded. trunc_q : Int, optional Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc_len_f` or `trunc_len_r` (depending on the direction of the read) it is discarded. -chimera_method : Str % Choices('consensus', 'pooled', 'none'), optional +chimera_method : Str % Choices('consensus', 'none', 'pooled'), optional The method used to remove chimeras. "none": No chimera removal is performed. "pooled": All reads are pooled prior to chimera detection. "consensus": Chimeras are detected in samples individually, and @@ -202,7 +222,6 @@ sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera_method is "none". - provided, all available cores will be used. n_reads_learn : Int, optional The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error
--- a/qiime2/qiime_dada2_denoise-pyro.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_dada2_denoise-pyro.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_dada2_denoise-pyro" name="qiime dada2 denoise-pyro" version="2019.4"> +<tool id="qiime_dada2_denoise-pyro" name="qiime dada2 denoise-pyro" version="2019.7"> <description> - Denoise and dereplicate single-end pyrosequences</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime dada2 denoise-pyro
--- a/qiime2/qiime_dada2_denoise-single.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_dada2_denoise-single.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_dada2_denoise-single" name="qiime dada2 denoise-single" version="2019.4"> +<tool id="qiime_dada2_denoise-single" name="qiime dada2 denoise-single" version="2019.7"> <description> - Denoise and dereplicate single-end sequences</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime dada2 denoise-single
--- a/qiime2/qiime_deblur_denoise-16S.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_deblur_denoise-16S.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_deblur_denoise-16S" name="qiime deblur denoise-16S" version="2019.4"> +<tool id="qiime_deblur_denoise-16S" name="qiime deblur denoise-16S" version="2019.7"> <description> - Deblur sequences using a 16S positive filter.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime deblur denoise-16S
--- a/qiime2/qiime_deblur_denoise-other.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_deblur_denoise-other.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_deblur_denoise-other" name="qiime deblur denoise-other" version="2019.4"> +<tool id="qiime_deblur_denoise-other" name="qiime deblur denoise-other" version="2019.7"> <description> - Deblur sequences using a user-specified positive filter.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime deblur denoise-other
--- a/qiime2/qiime_deblur_visualize-stats.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_deblur_visualize-stats.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_deblur_visualize-stats" name="qiime deblur visualize-stats" version="2019.4"> +<tool id="qiime_deblur_visualize-stats" name="qiime deblur visualize-stats" version="2019.7"> <description> - Visualize Deblur stats per sample.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime deblur visualize-stats
--- a/qiime2/qiime_demux_emp-paired.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_demux_emp-paired.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_demux_emp-paired" name="qiime demux emp-paired" version="2019.4"> +<tool id="qiime_demux_emp-paired" name="qiime demux emp-paired" version="2019.7"> <description> - Demultiplex paired-end sequence data generated with the EMP protocol.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime demux emp-paired @@ -15,7 +15,7 @@ #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 + ',' + d['additional_input'].__getattr__('file_name') + #set $file_list = $file_list + ' --m-barcodes-file=' + d['additional_input'].__getattr__('file_name') #end for #return $file_list #end def
--- a/qiime2/qiime_demux_emp-single.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_demux_emp-single.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_demux_emp-single" name="qiime demux emp-single" version="2019.4"> +<tool id="qiime_demux_emp-single" name="qiime demux emp-single" version="2019.7"> <description> - Demultiplex sequence data generated with the EMP protocol.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime demux emp-single @@ -15,7 +15,7 @@ #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 + ',' + d['additional_input'].__getattr__('file_name') + #set $file_list = $file_list + ' --m-barcodes-file=' + d['additional_input'].__getattr__('file_name') #end for #return $file_list #end def
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_demux_filter-samples.xml Wed Aug 14 15:12:48 2019 -0400 @@ -0,0 +1,95 @@ +<?xml version="1.0" ?> +<tool id="qiime_demux_filter-samples" name="qiime demux filter-samples" version="2019.7"> + <description> - Filter samples out of demultiplexed data.</description> + <requirements> + <requirement type="package" version="2019.7">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime demux filter-samples + +--i-demux=$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 + + +--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[ +Filter samples out of demultiplexed data. +######################################### + +Filter samples indicated in given metadata out of demultiplexed data. +Specific samples can be further selected with the WHERE clause, and the +`exclude_ids` parameter allows for filtering of all samples not specified. + +Parameters +---------- +demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] + The demultiplexed data from which samples should be filtered. +metadata : Metadata + Sample metadata indicating which sample ids to filter. The optional + `where` parameter may be used to filter ids based on specified + conditions in the metadata. The optional `exclude_ids` parameter may be + used to exclude the ids specified in the metadata from the filter. +where : Str, optional + 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. +exclude_ids : Bool, optional + Defaults to False. If True, the samples selected by the `metadata` and + optional `where` parameter will be excluded from the filtered data. + +Returns +------- +filtered_demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³] + Filtered demultiplexed data. + ]]></help> +<macros> + <import>qiime_citation.xml</import> +</macros> +<expand macro="qiime_citation"/> +</tool>
--- a/qiime2/qiime_demux_subsample-paired.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_demux_subsample-paired.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_demux_subsample-paired" name="qiime demux subsample-paired" version="2019.4"> +<tool id="qiime_demux_subsample-paired" name="qiime demux subsample-paired" version="2019.7"> <description> - Subsample paired-end sequences without replacement.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime demux subsample-paired
--- a/qiime2/qiime_demux_subsample-single.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_demux_subsample-single.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_demux_subsample-single" name="qiime demux subsample-single" version="2019.4"> +<tool id="qiime_demux_subsample-single" name="qiime demux subsample-single" version="2019.7"> <description> - Subsample single-end sequences without replacement.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime demux subsample-single
--- a/qiime2/qiime_demux_summarize.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_demux_summarize.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_demux_summarize" name="qiime demux summarize" version="2019.4"> +<tool id="qiime_demux_summarize" name="qiime demux summarize" version="2019.7"> <description> - Summarize counts per sample.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime demux summarize
--- a/qiime2/qiime_diversity_adonis.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_adonis.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_adonis" name="qiime diversity adonis" version="2019.4"> +<tool id="qiime_diversity_adonis" name="qiime diversity adonis" version="2019.7"> <description> - adonis PERMANOVA test for beta group significance</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity adonis @@ -61,15 +61,15 @@ </outputs> <help><![CDATA[ adonis PERMANOVA test for beta group significance -################################################# +################################################## Determine whether groups of samples are significantly different from one another using the ADONIS permutation-based statistical test in vegan-R. The function partitions sums of squares of a multivariate data set, and is directly analogous to MANOVA (multivariate analysis of variance). This -action differs from beta_group_signficance in that it accepts R formulae to -perform multi-way ADONIS tests; beta_group_signficance only performs one- -way tests. For more details see +action differs from beta_group_significance in that it accepts R formulae +to perform multi-way ADONIS tests; beta_group_signficance only performs +one-way tests. For more details see http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/adonis.html Parameters
--- a/qiime2/qiime_diversity_alpha-correlation.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_alpha-correlation.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_alpha-correlation" name="qiime diversity alpha-correlation" version="2019.4"> +<tool id="qiime_diversity_alpha-correlation" name="qiime diversity alpha-correlation" version="2019.7"> <description> - Alpha diversity correlation</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity alpha-correlation
--- a/qiime2/qiime_diversity_alpha-group-significance.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_alpha-group-significance.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_alpha-group-significance" name="qiime diversity alpha-group-significance" version="2019.4"> +<tool id="qiime_diversity_alpha-group-significance" name="qiime diversity alpha-group-significance" version="2019.7"> <description> - Alpha diversity comparisons</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity alpha-group-significance
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity_alpha-phylogenetic-alt.xml Wed Aug 14 15:12:48 2019 -0400 @@ -0,0 +1,62 @@ +<?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[ +Alpha diversity (phylogenetic) - alternative implementation +############################################################ + +Computes a user-specified phylogenetic alpha diversity metric for all +samples in a feature table. This implementation is recommended for large +datasets, otherwise the results are identical to alpha_phylogenetic. This +method is an implementation of the Stacked Faith Algorithm (manuscript in +preparation). + +Parameters +---------- +table : FeatureTable[Frequency] + The feature table containing the samples for which alpha diversity + should be computed. +phylogeny : Phylogeny[Rooted] + Phylogenetic tree containing tip identifiers that 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. +metric : Str % Choices('faith_pd') + The alpha diversity metric to be computed. + +Returns +------- +alpha_diversity : SampleData[AlphaDiversity] % Properties('phylogenetic') + Vector containing per-sample alpha diversities. + ]]></help> +<macros> + <import>qiime_citation.xml</import> +</macros> +<expand macro="qiime_citation"/> +</tool>
--- a/qiime2/qiime_diversity_alpha-phylogenetic.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_alpha-phylogenetic.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_alpha-phylogenetic" name="qiime diversity alpha-phylogenetic" version="2019.4"> +<tool id="qiime_diversity_alpha-phylogenetic" name="qiime diversity alpha-phylogenetic" version="2019.7"> <description> - Alpha diversity (phylogenetic)</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity alpha-phylogenetic
--- a/qiime2/qiime_diversity_alpha-rarefaction.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_alpha-rarefaction.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_alpha-rarefaction" name="qiime diversity alpha-rarefaction" version="2019.4"> +<tool id="qiime_diversity_alpha-rarefaction" name="qiime diversity alpha-rarefaction" version="2019.7"> <description> - Alpha rarefaction curves</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity alpha-rarefaction
--- a/qiime2/qiime_diversity_alpha.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_alpha.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_alpha" name="qiime diversity alpha" version="2019.4"> +<tool id="qiime_diversity_alpha" name="qiime diversity alpha" version="2019.7"> <description> - Alpha diversity</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity alpha
--- a/qiime2/qiime_diversity_beta-correlation.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_beta-correlation.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_beta-correlation" name="qiime diversity beta-correlation" version="2019.4"> +<tool id="qiime_diversity_beta-correlation" name="qiime diversity beta-correlation" version="2019.7"> <description> - Beta diversity correlation</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity beta-correlation
--- a/qiime2/qiime_diversity_beta-group-significance.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_beta-group-significance.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_beta-group-significance" name="qiime diversity beta-group-significance" version="2019.4"> +<tool id="qiime_diversity_beta-group-significance" name="qiime diversity beta-group-significance" version="2019.7"> <description> - Beta diversity group significance</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity beta-group-significance
--- a/qiime2/qiime_diversity_beta-phylogenetic.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_beta-phylogenetic.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_beta-phylogenetic" name="qiime diversity beta-phylogenetic" version="2019.4"> +<tool id="qiime_diversity_beta-phylogenetic" name="qiime diversity beta-phylogenetic" version="2019.7"> <description> - Beta diversity (phylogenetic)</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity beta-phylogenetic
--- a/qiime2/qiime_diversity_beta-rarefaction.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_beta-rarefaction.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_beta-rarefaction" name="qiime diversity beta-rarefaction" version="2019.4"> +<tool id="qiime_diversity_beta-rarefaction" name="qiime diversity beta-rarefaction" version="2019.7"> <description> - Beta diversity rarefaction</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity beta-rarefaction
--- a/qiime2/qiime_diversity_beta.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_beta.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_beta" name="qiime diversity beta" version="2019.4"> +<tool id="qiime_diversity_beta" name="qiime diversity beta" version="2019.7"> <description> - Beta diversity</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity beta
--- a/qiime2/qiime_diversity_bioenv.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_bioenv.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_bioenv" name="qiime diversity bioenv" version="2019.4"> +<tool id="qiime_diversity_bioenv" name="qiime diversity bioenv" version="2019.7"> <description> - bioenv</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity bioenv
--- a/qiime2/qiime_diversity_core-metrics-phylogenetic.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_core-metrics-phylogenetic.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_core-metrics-phylogenetic" name="qiime diversity core-metrics-phylogenetic" version="2019.4"> +<tool id="qiime_diversity_core-metrics-phylogenetic" name="qiime diversity core-metrics-phylogenetic" version="2019.7"> <description> - Core diversity metrics (phylogenetic and non- phylogenetic)</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity core-metrics-phylogenetic
--- a/qiime2/qiime_diversity_core-metrics.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_core-metrics.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_core-metrics" name="qiime diversity core-metrics" version="2019.4"> +<tool id="qiime_diversity_core-metrics" name="qiime diversity core-metrics" version="2019.7"> <description> - Core diversity metrics (non-phylogenetic)</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity core-metrics
--- a/qiime2/qiime_diversity_filter-distance-matrix.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_filter-distance-matrix.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_filter-distance-matrix" name="qiime diversity filter-distance-matrix" version="2019.4"> +<tool id="qiime_diversity_filter-distance-matrix" name="qiime diversity filter-distance-matrix" version="2019.7"> <description> - Filter samples from a distance matrix.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity filter-distance-matrix
--- a/qiime2/qiime_diversity_mantel.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_mantel.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_mantel" name="qiime diversity mantel" version="2019.4"> +<tool id="qiime_diversity_mantel" name="qiime diversity mantel" version="2019.7"> <description> - Apply the Mantel test to two distance matrices</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity mantel
--- a/qiime2/qiime_diversity_pcoa-biplot.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_pcoa-biplot.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_pcoa-biplot" name="qiime diversity pcoa-biplot" version="2019.4"> +<tool id="qiime_diversity_pcoa-biplot" name="qiime diversity pcoa-biplot" version="2019.7"> <description> - Principal Coordinate Analysis Biplot</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity pcoa-biplot
--- a/qiime2/qiime_diversity_pcoa.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_pcoa.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_pcoa" name="qiime diversity pcoa" version="2019.4"> +<tool id="qiime_diversity_pcoa" name="qiime diversity pcoa" version="2019.7"> <description> - Principal Coordinate Analysis</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity pcoa
--- a/qiime2/qiime_diversity_procrustes-analysis.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_diversity_procrustes-analysis.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_procrustes-analysis" name="qiime diversity procrustes-analysis" version="2019.4"> +<tool id="qiime_diversity_procrustes-analysis" name="qiime diversity procrustes-analysis" version="2019.7"> <description> - Procrustes Analysis</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity procrustes-analysis
--- a/qiime2/qiime_emperor_biplot.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_emperor_biplot.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_emperor_biplot" name="qiime emperor biplot" version="2019.4"> +<tool id="qiime_emperor_biplot" name="qiime emperor biplot" version="2019.7"> <description> - Visualize and Interact with Principal Coordinates Analysis Biplot</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime emperor biplot
--- a/qiime2/qiime_emperor_plot.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_emperor_plot.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_emperor_plot" name="qiime emperor plot" version="2019.4"> +<tool id="qiime_emperor_plot" name="qiime emperor plot" version="2019.7"> <description> - Visualize and Interact with Principal Coordinates Analysis Plots</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime emperor plot
--- a/qiime2/qiime_emperor_procrustes-plot.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_emperor_procrustes-plot.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_emperor_procrustes-plot" name="qiime emperor procrustes-plot" version="2019.4"> +<tool id="qiime_emperor_procrustes-plot" name="qiime emperor procrustes-plot" version="2019.7"> <description> - Visualize and Interact with a procrustes plot</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime emperor procrustes-plot
--- a/qiime2/qiime_feature-classifier_classify-consensus-blast.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-classifier_classify-consensus-blast.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-classifier_classify-consensus-blast" name="qiime feature-classifier classify-consensus-blast" version="2019.4"> +<tool id="qiime_feature-classifier_classify-consensus-blast" name="qiime feature-classifier classify-consensus-blast" version="2019.7"> <description> - BLAST+ consensus taxonomy classifier</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-classifier classify-consensus-blast
--- a/qiime2/qiime_feature-classifier_classify-consensus-vsearch.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-classifier_classify-consensus-vsearch.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-classifier_classify-consensus-vsearch" name="qiime feature-classifier classify-consensus-vsearch" version="2019.4"> +<tool id="qiime_feature-classifier_classify-consensus-vsearch" name="qiime feature-classifier classify-consensus-vsearch" version="2019.7"> <description> - VSEARCH consensus taxonomy classifier</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-classifier classify-consensus-vsearch @@ -20,6 +20,16 @@ #end if +#if $psearchexact: + --p-search-exact +#end if + + +#if $ptophitsonly: + --p-top-hits-only +#end if + + #if str($pmaxaccepts): --p-maxaccepts=$pmaxaccepts @@ -63,6 +73,7 @@ #end if --o-classification=oclassification + ; cp oclassification.qza $oclassification ]]></command> @@ -95,13 +106,17 @@ </param> <param label="--p-min-consensus: NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. Must be in range (0.5, 1.0]. [default: 0.51]" name="pminconsensus" optional="True" type="float" min="0.5" max="1" exclude_min="True" exclude_max="False" value="0.51"/> <param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="Unassigned"/> + + + <param label="--p-search-exact: Search for exact full-length matches to the query sequences. Only 100% exact matches are reported and this command is much faster than the default. If True, the perc-identity and query-cov settings are ignored. Note: query and reference reads must be trimmed to the exact same DNA locus (e.g., primer site) because only exact matches will be reported. [default: False]" name="psearchexact" selected="False" type="boolean"/> + <param label="--p-top-hits-only: Only the top hits between the query and reference sequence sets are reported. For each query, the top hit is the one presenting the highest percentage of identity. Multiple equally scored top hits will be used for consensus taxonomic assignment if maxaccepts is greater than 1. [default: False]" name="ptophitsonly" selected="False" type="boolean"/> + </inputs> <outputs> <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/> </outputs> <help><![CDATA[ -VSEARCH consensus taxonomy classifier -##################################### +VSEARCH-based consensus taxonomy classifier Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global alignment between query and reference_reads, then assigns consensus @@ -118,23 +133,34 @@ reference sequences. reference_taxonomy : FeatureData[Taxonomy] reference taxonomy labels. -maxaccepts : Int % Range(0, None), optional - Maximum number of hits to keep for each query. Set to 0 to keep all - hits > perc_identity similarity. Must be in range [0, infinity]. +maxaccepts : Int % Range(1, None) | Str % Choices('all'), optional + Maximum number of hits to keep for each query. Set to "all" to keep all + hits > perc_identity similarity. perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional - Reject match if percent identity to query is lower. Must be in range - [0.0, 1.0]. + Reject match if percent identity to query is lower. query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional Reject match if query alignment coverage per high-scoring pair is - lower. Must be in range [0.0, 1.0]. + lower. strand : Str % Choices('both', 'plus'), optional Align against reference sequences in forward ("plus") or both directions ("both"). min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional Minimum fraction of assignments must match top hit to be accepted as - consensus assignment. Must be in range (0.5, 1.0]. + consensus assignment. unassignable_label : Str, optional - \ +search_exact : Bool, optional + Search for exact full-length matches to the query sequences. Only 100% + exact matches are reported and this command is much faster than the + default. If True, the perc_identity and query_cov settings are ignored. + Note: query and reference reads must be trimmed to the exact same DNA + locus (e.g., primer site) because only exact matches will be reported. +top_hits_only : Bool, optional + Only the top hits between the query and reference sequence sets are + reported. For each query, the top hit is the one presenting the highest + percentage of identity. Multiple equally scored top hits will be used + for consensus taxonomic assignment if maxaccepts is greater than 1. +threads : Int % Range(1, None), optional + Number of threads to use for job parallelization. Returns -------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-classifier_classify-hybrid-vsearch-sklearn.xml Wed Aug 14 15:12:48 2019 -0400 @@ -0,0 +1,241 @@ +<?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 + + + + +#if str( $id_to_taxonomy_fp.selector ) == 'history' +#set $tax = $id_to_taxonomy_fp.taxonomy_fp +--i-reference-taxonomy '$tax' +#else: +#set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path +--i-reference-taxonomy '$tax' +#end if + + + + + +#if str( $id_to_classifier_fp.selector ) == 'history' +#set $classifier = $id_to_classifier_fp.classifier_fp +--i-classifier '$classifier' +#else: +#set $classifier = $id_to_classifier_fp.classifier_fp.fields.path +--i-classifier '$classifier' +#end if + + + + + +#if str($pmaxaccepts): + --p-maxaccepts=$pmaxaccepts +#end if + +#if str($pconfidence): + --p-confidence=$pconfidence +#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($preadorientation) != 'None': + --p-read-orientation=$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"/> + + + <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> + + + <conditional name="id_to_classifier_fp" optional="True"> + <param name="selector" type="select" label="Reference classifier to query"> + <option value="cached">Public classifiers</option> + <option value="history">Classifiers from your history</option> + </param> + <when value="cached"> + <param name="classifier_fp" label="Reference classifier" type="select" optional="True"> + <options from_data_table="qiime_rep_set" /> + </param> + </when> + <when value="history"> + <param name="classifier_fp" type="data" format="qza,no_unzip.zip" label="Reference classifier" optional="True" /> + </when> + </conditional> + + + <param label="--p-maxaccepts: VALUE Int % Range(1, None) | Str % Choices('all') Maximum number of hits to keep for each query. Set to 'all' to keep all hits > perc-identity similarity. [default: 10]" name="pmaxaccepts" optional="True" type="text" value="10" /> + <param label="--p-confidence: VALUE Float % Range(0, 1, inclusive_end=True) | Str % Choices('disable') Confidence threshold for limiting taxonomic depth. Set to 'disable' to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments. [default: 0.7]" name="pconfidence" optional="True" type="text" value="0.7" /> + + + <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" min="0" max="1" exclusive_end="False" /> + <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" min="0" max="1" exclusive_end="False" /> + <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" min="0.5" max="1" exclusive_end="True" /> + <param label="--p-read-orientation: TEXT Choices('same', 'reverse-complement', 'auto') Direction of reads with respect to reference sequences in pre-trained sklearn classifier. same will cause reads to be classified unchanged; reverse-complement will cause reads to be reversed and complemented prior to classification. 'auto' will autodetect orientation based on the confidence estimates for the first 100 reads. [default: 'auto'] " name="preadorientation" optional="True" type="select" > + <option value="None">Selection is Optional</option> + <option value="same">same</option> + <option value="reverse-complement">reverse-complement</option> + <option selected="True" 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" min="1"/> + <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" min="0"/> + </inputs> + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/> + </outputs> + <help><![CDATA[ +ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier +################################################################## + +NOTE: THIS PIPELINE IS AN ALPHA RELEASE. Please report bugs to +https://forum.qiime2.org! Assign taxonomy to query sequences using hybrid +classifier. First performs rough positive filter to remove artifact and +low-coverage sequences (use "prefilter" parameter to toggle this step on or +off). Second, performs VSEARCH exact match between query and +reference_reads to find exact matches, followed by least common ancestor +consensus taxonomy assignment from among maxaccepts top hits, min_consensus +of which share that taxonomic assignment. Query sequences without an exact +match are then classified with a pre-trained sklearn taxonomy classifier to +predict the most likely taxonomic lineage. + +Parameters +---------- +query : FeatureData[Sequence] + Sequences to classify taxonomically. +reference_reads : FeatureData[Sequence] + reference sequences. +reference_taxonomy : FeatureData[Taxonomy] + reference taxonomy labels. +classifier : TaxonomicClassifier + Pre-trained sklearn taxonomic classifier for classifying the reads. +maxaccepts : Int % Range(1, None) | Str % Choices('all'), optional + Maximum number of hits to keep for each query. Set to "all" to keep all + hits > perc_identity similarity. +perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional + 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. +query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional + 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. +strand : Str % Choices('both', 'plus'), optional + Align against reference sequences in forward ("plus") or both + directions ("both"). +min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional + Minimum fraction of assignments must match top hit to be accepted as + consensus assignment. +reads_per_batch : Int % Range(0, None), optional + Number of reads to process in each batch for sklearn classification. If + "auto", this parameter is autoscaled to min(number of query sequences / + threads, 20000). +confidence : Float % Range(0, 1, inclusive_end=True) | Str % Choices('disable'), optional + Confidence threshold for limiting taxonomic depth. Set to "disable" to + disable confidence calculation, or 0 to calculate confidence but not + apply it to limit the taxonomic depth of the assignments. +read_orientation : Str % Choices('same', 'reverse-complement', 'auto'), optional + Direction of reads with respect to reference sequences in pre-trained + sklearn classifier. same will cause reads to be classified unchanged; + reverse-complement will cause reads to be reversed and complemented + prior to classification. "auto" will autodetect orientation based on + the confidence estimates for the first 100 reads. +prefilter : Bool, optional + Toggle positive filter of query sequences on or off. +sample_size : Int % Range(1, None), optional + Randomly extract the given number of sequences from the reference + database to use for prefiltering. This parameter is ignored if + `prefilter` is disabled. +randseed : Int % Range(0, None), optional + Use integer as a seed for the pseudo-random generator 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. + +Returns +------- +classification : FeatureData[Taxonomy] + The resulting taxonomy classifications. + ]]></help> +<macros> + <import>qiime_citation.xml</import> +</macros> +<expand macro="qiime_citation"/> +</tool>
--- a/qiime2/qiime_feature-classifier_classify-sklearn.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-classifier_classify-sklearn.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-classifier_classify-sklearn" name="qiime feature-classifier classify-sklearn" version="2019.4"> +<tool id="qiime_feature-classifier_classify-sklearn" name="qiime feature-classifier classify-sklearn" version="2019.7"> <description> - Pre-fitted sklearn-based taxonomy classifier</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-classifier classify-sklearn
--- a/qiime2/qiime_feature-classifier_extract-reads.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-classifier_extract-reads.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-classifier_extract-reads" name="qiime feature-classifier extract-reads" version="2019.4"> +<tool id="qiime_feature-classifier_extract-reads" name="qiime feature-classifier extract-reads" version="2019.7"> <description> - Extract reads from reference</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[
--- a/qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-classifier_fit-classifier-naive-bayes" name="qiime feature-classifier fit-classifier-naive-bayes" version="2019.4"> +<tool id="qiime_feature-classifier_fit-classifier-naive-bayes" name="qiime feature-classifier fit-classifier-naive-bayes" version="2019.7"> <description> - Train the naive_bayes classifier</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[
--- a/qiime2/qiime_feature-classifier_fit-classifier-sklearn.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-classifier_fit-classifier-sklearn.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-classifier_fit-classifier-sklearn" name="qiime feature-classifier fit-classifier-sklearn" version="2019.4"> +<tool id="qiime_feature-classifier_fit-classifier-sklearn" name="qiime feature-classifier fit-classifier-sklearn" version="2019.7"> <description> - Train an almost arbitrary scikit-learn classifier</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-classifier fit-classifier-sklearn
--- a/qiime2/qiime_feature-table_core-features.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_core-features.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_core-features" name="qiime feature-table core-features" version="2019.4"> +<tool id="qiime_feature-table_core-features" name="qiime feature-table core-features" version="2019.7"> <description> - Identify core features in table</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table core-features
--- a/qiime2/qiime_feature-table_filter-features.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_filter-features.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_filter-features" name="qiime feature-table filter-features" version="2019.4"> +<tool id="qiime_feature-table_filter-features" name="qiime feature-table filter-features" version="2019.7"> <description> - Filter features from table</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table filter-features
--- a/qiime2/qiime_feature-table_filter-samples.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_filter-samples.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_filter-samples" name="qiime feature-table filter-samples" version="2019.4"> +<tool id="qiime_feature-table_filter-samples" name="qiime feature-table filter-samples" version="2019.7"> <description> - Filter samples from table</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table filter-samples
--- a/qiime2/qiime_feature-table_filter-seqs.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_filter-seqs.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_filter-seqs" name="qiime feature-table filter-seqs" version="2019.4"> +<tool id="qiime_feature-table_filter-seqs" name="qiime feature-table filter-seqs" version="2019.7"> <description> - Filter features from sequences</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table filter-seqs
--- a/qiime2/qiime_feature-table_group.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_group.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_group" name="qiime feature-table group" version="2019.4"> +<tool id="qiime_feature-table_group" name="qiime feature-table group" version="2019.7"> <description> - Group samples or features by a metadata column</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table group
--- a/qiime2/qiime_feature-table_heatmap.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_heatmap.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_heatmap" name="qiime feature-table heatmap" version="2019.4"> +<tool id="qiime_feature-table_heatmap" name="qiime feature-table heatmap" version="2019.7"> <description> - Generate a heatmap representation of a feature table</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table heatmap
--- a/qiime2/qiime_feature-table_merge-seqs.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_merge-seqs.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_merge-seqs" name="qiime feature-table merge-seqs" version="2019.4"> +<tool id="qiime_feature-table_merge-seqs" name="qiime feature-table merge-seqs" version="2019.7"> <description> - Combine collections of feature sequences</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table merge-seqs
--- a/qiime2/qiime_feature-table_merge-taxa.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_merge-taxa.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_merge-taxa" name="qiime feature-table merge-taxa" version="2019.4"> +<tool id="qiime_feature-table_merge-taxa" name="qiime feature-table merge-taxa" version="2019.7"> <description> - Combine collections of feature taxonomies</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table merge-taxa
--- a/qiime2/qiime_feature-table_merge.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_merge.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_merge" name="qiime feature-table merge" version="2019.4"> +<tool id="qiime_feature-table_merge" name="qiime feature-table merge" version="2019.7"> <description> - Combine multiple tables</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table merge
--- a/qiime2/qiime_feature-table_presence-absence.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_presence-absence.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_presence-absence" name="qiime feature-table presence-absence" version="2019.4"> +<tool id="qiime_feature-table_presence-absence" name="qiime feature-table presence-absence" version="2019.7"> <description> - Convert to presence/absence</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table presence-absence
--- a/qiime2/qiime_feature-table_rarefy.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_rarefy.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_rarefy" name="qiime feature-table rarefy" version="2019.4"> +<tool id="qiime_feature-table_rarefy" name="qiime feature-table rarefy" version="2019.7"> <description> - Rarefy table</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table rarefy
--- a/qiime2/qiime_feature-table_relative-frequency.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_relative-frequency.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_relative-frequency" name="qiime feature-table relative-frequency" version="2019.4"> +<tool id="qiime_feature-table_relative-frequency" name="qiime feature-table relative-frequency" version="2019.7"> <description> - Convert to relative frequencies</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table relative-frequency
--- a/qiime2/qiime_feature-table_subsample.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_subsample.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_subsample" name="qiime feature-table subsample" version="2019.4"> +<tool id="qiime_feature-table_subsample" name="qiime feature-table subsample" version="2019.7"> <description> - Subsample table</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table subsample
--- a/qiime2/qiime_feature-table_summarize.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_summarize.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_summarize" name="qiime feature-table summarize" version="2019.4"> +<tool id="qiime_feature-table_summarize" name="qiime feature-table summarize" version="2019.7"> <description> - Summarize table</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table summarize @@ -14,7 +14,7 @@ #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 + ',' + d['additional_input'].__getattr__('file_name') + #set $file_list = $file_list + ' --m-sample-metadata-file=' + d['additional_input'].__getattr__('file_name') #end for #return $file_list #end def
--- a/qiime2/qiime_feature-table_tabulate-seqs.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_tabulate-seqs.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_tabulate-seqs" name="qiime feature-table tabulate-seqs" version="2019.4"> +<tool id="qiime_feature-table_tabulate-seqs" name="qiime feature-table tabulate-seqs" version="2019.7"> <description> - View sequence associated with each feature</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table tabulate-seqs
--- a/qiime2/qiime_feature-table_transpose.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_feature-table_transpose.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-table_transpose" name="qiime feature-table transpose" version="2019.4"> +<tool id="qiime_feature-table_transpose" name="qiime feature-table transpose" version="2019.7"> <description> - Transpose a feature table.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime feature-table transpose
--- a/qiime2/qiime_fragment-insertion_classify-otus-experimental.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_fragment-insertion_classify-otus-experimental.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_fragment-insertion_classify-otus-experimental" name="qiime fragment-insertion classify-otus-experimental" version="2019.4"> +<tool id="qiime_fragment-insertion_classify-otus-experimental" name="qiime fragment-insertion classify-otus-experimental" version="2019.7"> <description> - Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime fragment-insertion classify-otus-experimental
--- a/qiime2/qiime_fragment-insertion_filter-features.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_fragment-insertion_filter-features.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_fragment-insertion_filter-features" name="qiime fragment-insertion filter-features" version="2019.4"> +<tool id="qiime_fragment-insertion_filter-features" name="qiime fragment-insertion filter-features" version="2019.7"> <description> - Filter fragments in tree from table.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime fragment-insertion filter-features
--- a/qiime2/qiime_fragment-insertion_sepp.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_fragment-insertion_sepp.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_fragment-insertion_sepp" name="qiime fragment-insertion sepp" version="2019.4"> +<tool id="qiime_fragment-insertion_sepp" name="qiime fragment-insertion sepp" version="2019.7"> <description> - Insert fragment sequences using SEPP into reference phylogenies like Greengenes 13_8</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime fragment-insertion sepp
--- a/qiime2/qiime_gneiss_assign-ids.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_gneiss_assign-ids.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids" version="2019.4"> +<tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids" version="2019.7"> <description> - Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime gneiss assign-ids
--- a/qiime2/qiime_gneiss_balance-taxonomy.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_gneiss_balance-taxonomy.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_gneiss_balance-taxonomy" name="qiime gneiss balance-taxonomy" version="2019.4"> +<tool id="qiime_gneiss_balance-taxonomy" name="qiime gneiss balance-taxonomy" version="2019.7"> <description> - Balance Summary</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime gneiss balance-taxonomy
--- a/qiime2/qiime_gneiss_correlation-clustering.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_gneiss_correlation-clustering.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_gneiss_correlation-clustering" name="qiime gneiss correlation-clustering" version="2019.4"> +<tool id="qiime_gneiss_correlation-clustering" name="qiime gneiss correlation-clustering" version="2019.7"> <description> - Hierarchical clustering using feature correlation.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime gneiss correlation-clustering
--- a/qiime2/qiime_gneiss_dendrogram-heatmap.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_gneiss_dendrogram-heatmap.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_gneiss_dendrogram-heatmap" name="qiime gneiss dendrogram-heatmap" version="2019.4"> +<tool id="qiime_gneiss_dendrogram-heatmap" name="qiime gneiss dendrogram-heatmap" version="2019.7"> <description> - Dendrogram heatmap.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime gneiss dendrogram-heatmap
--- a/qiime2/qiime_gneiss_gradient-clustering.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_gneiss_gradient-clustering.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_gneiss_gradient-clustering" name="qiime gneiss gradient-clustering" version="2019.4"> +<tool id="qiime_gneiss_gradient-clustering" name="qiime gneiss gradient-clustering" version="2019.7"> <description> - Hierarchical clustering using gradient information.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime gneiss gradient-clustering @@ -11,15 +11,8 @@ --m-gradient-column="$mgradientcolumn" -#if $input_files_mgradientfile: -#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 + ',' + d['additional_input'].__getattr__('file_name') - #end for - #return $file_list -#end def ---m-gradient-file=$list_dict_to_string($input_files_mgradientfile) +#if $mgradientfile: +--m-gradient-file=$mgradientfile #end if #if $pnoweighted: @@ -35,9 +28,7 @@ <param label="--m-gradient-column: COLUMN MetadataColumn[Numeric] Contains gradient values to sort the features and samples. [required]" name="mgradientcolumn" optional="False" type="text"/> <param label="--p-no-weighted : Specifies if abundance or presence/absence information should be used to perform the clustering. [default: False]" name="pnoweighted" selected="False" type="boolean"/> - <repeat name="input_files_mgradientfile" optional="False" title="--m-gradient-file"> - <param label="--m-gradient-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> - </repeat> + <param label="--m-gradient-file: " name="mgradientfile" optional="True" type="data" format="tabular,qza,no_unzip.zip" /> </inputs> <outputs>
--- a/qiime2/qiime_gneiss_ilr-hierarchical.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_gneiss_ilr-hierarchical.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_gneiss_ilr-hierarchical" name="qiime gneiss ilr-hierarchical" version="2019.4"> +<tool id="qiime_gneiss_ilr-hierarchical" name="qiime gneiss ilr-hierarchical" version="2019.7"> <description> - Isometric Log-ratio Transform applied to a hierarchical clustering</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime gneiss ilr-hierarchical
--- a/qiime2/qiime_gneiss_ilr-phylogenetic.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_gneiss_ilr-phylogenetic.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_gneiss_ilr-phylogenetic" name="qiime gneiss ilr-phylogenetic" version="2019.4"> +<tool id="qiime_gneiss_ilr-phylogenetic" name="qiime gneiss ilr-phylogenetic" version="2019.7"> <description> - Isometric Log-ratio Transform applied to a phylogenetic tree</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime gneiss ilr-phylogenetic
--- a/qiime2/qiime_gneiss_lme-regression.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_gneiss_lme-regression.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_gneiss_lme-regression" name="qiime gneiss lme-regression" version="2019.4"> +<tool id="qiime_gneiss_lme-regression" name="qiime gneiss lme-regression" version="2019.7"> <description> - Simplicial Linear mixed effects regression</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime gneiss lme-regression
--- a/qiime2/qiime_gneiss_ols-regression.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_gneiss_ols-regression.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_gneiss_ols-regression" name="qiime gneiss ols-regression" version="2019.4"> +<tool id="qiime_gneiss_ols-regression" name="qiime gneiss ols-regression" version="2019.7"> <description> - Simplicial Ordinary Least Squares Regression</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime gneiss ols-regression
--- a/qiime2/qiime_longitudinal_anova.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_longitudinal_anova.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_longitudinal_anova" name="qiime longitudinal anova" version="2019.4"> +<tool id="qiime_longitudinal_anova" name="qiime longitudinal anova" version="2019.7"> <description> - ANOVA test</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime longitudinal anova
--- a/qiime2/qiime_longitudinal_feature-volatility.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_longitudinal_feature-volatility.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_longitudinal_feature-volatility" name="qiime longitudinal feature-volatility" version="2019.4"> +<tool id="qiime_longitudinal_feature-volatility" name="qiime longitudinal feature-volatility" version="2019.7"> <description> - Feature volatility analysis</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime longitudinal feature-volatility
--- a/qiime2/qiime_longitudinal_first-differences.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_longitudinal_first-differences.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_longitudinal_first-differences" name="qiime longitudinal first-differences" version="2019.4"> +<tool id="qiime_longitudinal_first-differences" name="qiime longitudinal first-differences" version="2019.7"> <description> - Compute first differences or difference from baseline between sequential states</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime longitudinal first-differences
--- a/qiime2/qiime_longitudinal_first-distances.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_longitudinal_first-distances.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_longitudinal_first-distances" name="qiime longitudinal first-distances" version="2019.4"> +<tool id="qiime_longitudinal_first-distances" name="qiime longitudinal first-distances" version="2019.7"> <description> - Compute first distances or distance from baseline between sequential states</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime longitudinal first-distances
--- a/qiime2/qiime_longitudinal_linear-mixed-effects.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_longitudinal_linear-mixed-effects.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_longitudinal_linear-mixed-effects" name="qiime longitudinal linear-mixed-effects" version="2019.4"> +<tool id="qiime_longitudinal_linear-mixed-effects" name="qiime longitudinal linear-mixed-effects" version="2019.7"> <description> - Linear mixed effects modeling</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime longitudinal linear-mixed-effects
--- a/qiime2/qiime_longitudinal_maturity-index.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_longitudinal_maturity-index.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_longitudinal_maturity-index" name="qiime longitudinal maturity-index" version="2019.4"> +<tool id="qiime_longitudinal_maturity-index" name="qiime longitudinal maturity-index" version="2019.7"> <description> - Microbial maturity index prediction.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime longitudinal maturity-index
--- a/qiime2/qiime_longitudinal_nmit.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_longitudinal_nmit.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_longitudinal_nmit" name="qiime longitudinal nmit" version="2019.4"> +<tool id="qiime_longitudinal_nmit" name="qiime longitudinal nmit" version="2019.7"> <description> - Nonparametric microbial interdependence test</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime longitudinal nmit
--- a/qiime2/qiime_longitudinal_pairwise-differences.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_longitudinal_pairwise-differences.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_longitudinal_pairwise-differences" name="qiime longitudinal pairwise-differences" version="2019.4"> +<tool id="qiime_longitudinal_pairwise-differences" name="qiime longitudinal pairwise-differences" version="2019.7"> <description> - Paired difference testing and boxplots</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime longitudinal pairwise-differences
--- a/qiime2/qiime_longitudinal_pairwise-distances.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_longitudinal_pairwise-distances.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_longitudinal_pairwise-distances" name="qiime longitudinal pairwise-distances" version="2019.4"> +<tool id="qiime_longitudinal_pairwise-distances" name="qiime longitudinal pairwise-distances" version="2019.7"> <description> - Paired pairwise distance testing and boxplots</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime longitudinal pairwise-distances
--- a/qiime2/qiime_longitudinal_plot-feature-volatility.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_longitudinal_plot-feature-volatility.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_longitudinal_plot-feature-volatility" name="qiime longitudinal plot-feature-volatility" version="2019.4"> +<tool id="qiime_longitudinal_plot-feature-volatility" name="qiime longitudinal plot-feature-volatility" version="2019.7"> <description> - Plot longitudinal feature volatility and importances</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime longitudinal plot-feature-volatility
--- a/qiime2/qiime_longitudinal_volatility.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_longitudinal_volatility.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_longitudinal_volatility" name="qiime longitudinal volatility" version="2019.4"> +<tool id="qiime_longitudinal_volatility" name="qiime longitudinal volatility" version="2019.7"> <description> - Generate interactive volatility plot</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime longitudinal volatility
--- a/qiime2/qiime_metadata_distance-matrix.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_metadata_distance-matrix.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_metadata_distance-matrix" name="qiime metadata distance-matrix" version="2019.4"> +<tool id="qiime_metadata_distance-matrix" name="qiime metadata distance-matrix" version="2019.7"> <description> - Create a distance matrix from a numeric Metadata column</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime metadata distance-matrix
--- a/qiime2/qiime_metadata_tabulate.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_metadata_tabulate.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_metadata_tabulate" name="qiime metadata tabulate" version="2019.4"> +<tool id="qiime_metadata_tabulate" name="qiime metadata tabulate" version="2019.7"> <description> - Interactively explore Metadata in an HTML table</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime metadata tabulate
--- a/qiime2/qiime_phylogeny_align-to-tree-mafft-fasttree.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_phylogeny_align-to-tree-mafft-fasttree.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_phylogeny_align-to-tree-mafft-fasttree" name="qiime phylogeny align-to-tree-mafft-fasttree" version="2019.4"> +<tool id="qiime_phylogeny_align-to-tree-mafft-fasttree" name="qiime phylogeny align-to-tree-mafft-fasttree" version="2019.7"> <description> - Build a phylogenetic tree using fasttree and mafft alignment</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime phylogeny align-to-tree-mafft-fasttree
--- a/qiime2/qiime_phylogeny_fasttree.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_phylogeny_fasttree.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_phylogeny_fasttree" name="qiime phylogeny fasttree" version="2019.4"> +<tool id="qiime_phylogeny_fasttree" name="qiime phylogeny fasttree" version="2019.7"> <description> - Construct a phylogenetic tree with FastTree.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime phylogeny fasttree
--- a/qiime2/qiime_phylogeny_filter-table.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_phylogeny_filter-table.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_phylogeny_filter-table" name="qiime phylogeny filter-table" version="2019.4"> +<tool id="qiime_phylogeny_filter-table" name="qiime phylogeny filter-table" version="2019.7"> <description> - Remove features from table if they're not present in tree.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime phylogeny filter-table
--- a/qiime2/qiime_phylogeny_iqtree-ultrafast-bootstrap.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_phylogeny_iqtree-ultrafast-bootstrap.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_phylogeny_iqtree-ultrafast-bootstrap" name="qiime phylogeny iqtree-ultrafast-bootstrap" version="2019.4"> +<tool id="qiime_phylogeny_iqtree-ultrafast-bootstrap" name="qiime phylogeny iqtree-ultrafast-bootstrap" version="2019.7"> <description> - Construct a phylogenetic tree with IQ-TREE with bootstrap supports.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime phylogeny iqtree-ultrafast-bootstrap
--- a/qiime2/qiime_phylogeny_iqtree.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_phylogeny_iqtree.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_phylogeny_iqtree" name="qiime phylogeny iqtree" version="2019.4"> +<tool id="qiime_phylogeny_iqtree" name="qiime phylogeny iqtree" version="2019.7"> <description> - Construct a phylogenetic tree with IQ-TREE.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime phylogeny iqtree
--- a/qiime2/qiime_phylogeny_midpoint-root.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_phylogeny_midpoint-root.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_phylogeny_midpoint-root" name="qiime phylogeny midpoint-root" version="2019.4"> +<tool id="qiime_phylogeny_midpoint-root" name="qiime phylogeny midpoint-root" version="2019.7"> <description> - Midpoint root an unrooted phylogenetic tree.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime phylogeny midpoint-root
--- a/qiime2/qiime_phylogeny_raxml-rapid-bootstrap.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_phylogeny_raxml-rapid-bootstrap.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_phylogeny_raxml-rapid-bootstrap" name="qiime phylogeny raxml-rapid-bootstrap" version="2019.4"> +<tool id="qiime_phylogeny_raxml-rapid-bootstrap" name="qiime phylogeny raxml-rapid-bootstrap" version="2019.7"> <description> - Construct a phylogenetic tree with bootstrap supports using RAxML.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime phylogeny raxml-rapid-bootstrap
--- a/qiime2/qiime_phylogeny_raxml.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_phylogeny_raxml.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_phylogeny_raxml" name="qiime phylogeny raxml" version="2019.4"> +<tool id="qiime_phylogeny_raxml" name="qiime phylogeny raxml" version="2019.7"> <description> - Construct a phylogenetic tree with RAxML.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime phylogeny raxml
--- a/qiime2/qiime_quality-control_evaluate-composition.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_quality-control_evaluate-composition.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_quality-control_evaluate-composition" name="qiime quality-control evaluate-composition" version="2019.4"> +<tool id="qiime_quality-control_evaluate-composition" name="qiime quality-control evaluate-composition" version="2019.7"> <description> - Evaluate expected vs. observed taxonomic composition of samples</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime quality-control evaluate-composition
--- a/qiime2/qiime_quality-control_evaluate-seqs.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_quality-control_evaluate-seqs.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_quality-control_evaluate-seqs" name="qiime quality-control evaluate-seqs" version="2019.4"> +<tool id="qiime_quality-control_evaluate-seqs" name="qiime quality-control evaluate-seqs" version="2019.7"> <description> - Compare query (observed) vs. reference (expected) sequences.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime quality-control evaluate-seqs
--- a/qiime2/qiime_quality-control_evaluate-taxonomy.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_quality-control_evaluate-taxonomy.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_quality-control_evaluate-taxonomy" name="qiime quality-control evaluate-taxonomy" version="2019.4"> +<tool id="qiime_quality-control_evaluate-taxonomy" name="qiime quality-control evaluate-taxonomy" version="2019.7"> <description> - Evaluate expected vs. observed taxonomic assignments</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime quality-control evaluate-taxonomy
--- a/qiime2/qiime_quality-control_exclude-seqs.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_quality-control_exclude-seqs.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_quality-control_exclude-seqs" name="qiime quality-control exclude-seqs" version="2019.4"> +<tool id="qiime_quality-control_exclude-seqs" name="qiime quality-control exclude-seqs" version="2019.7"> <description> - Exclude sequences by alignment</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime quality-control exclude-seqs
--- a/qiime2/qiime_quality-filter_q-score-joined.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_quality-filter_q-score-joined.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_quality-filter_q-score-joined" name="qiime quality-filter q-score-joined" version="2019.4"> +<tool id="qiime_quality-filter_q-score-joined" name="qiime quality-filter q-score-joined" version="2019.7"> <description> - Quality filter based on joined sequence quality scores.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime quality-filter q-score-joined
--- a/qiime2/qiime_quality-filter_q-score.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_quality-filter_q-score.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_quality-filter_q-score" name="qiime quality-filter q-score" version="2019.4"> +<tool id="qiime_quality-filter_q-score" name="qiime quality-filter q-score" version="2019.7"> <description> - Quality filter based on sequence quality scores.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime quality-filter q-score
--- a/qiime2/qiime_sample-classifier_classify-samples-from-dist.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_sample-classifier_classify-samples-from-dist.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_classify-samples-from-dist" name="qiime sample-classifier classify-samples-from-dist" version="2019.4"> +<tool id="qiime_sample-classifier_classify-samples-from-dist" name="qiime sample-classifier classify-samples-from-dist" version="2019.7"> <description> - Run k-nearest-neighbors on a labeled distance matrix.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier classify-samples-from-dist
--- a/qiime2/qiime_sample-classifier_classify-samples-ncv.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_sample-classifier_classify-samples-ncv.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_classify-samples-ncv" name="qiime sample-classifier classify-samples-ncv" version="2019.4"> +<tool id="qiime_sample-classifier_classify-samples-ncv" name="qiime sample-classifier classify-samples-ncv" version="2019.7"> <description> - Nested cross-validated supervised learning classifier.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier classify-samples-ncv @@ -48,9 +48,11 @@ --p-missing-samples=$pmissingsamples #end if +--o-probabilities=oprobabilities --o-predictions=opredictions --o-feature-importance=ofeatureimportance ; +cp oprobabilities.qza $oprobabilities; cp opredictions.qza $opredictions; cp ofeatureimportance.qza $ofeatureimportance ]]></command> @@ -81,6 +83,7 @@ </inputs> <outputs> + <data format="qza" label="${tool.name} on ${on_string}: probabilities.qza" name="oprobabilities"/> <data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions"/> <data format="qza" label="${tool.name} on ${on_string}: featureimportance.qza" name="ofeatureimportance"/> </outputs> @@ -127,6 +130,8 @@ Predicted target values for each input sample. feature_importance : FeatureData[Importance] Importance of each input feature to model accuracy. +probabilities : SampleData[Probabilities] + Predicted class probabilities for each input sample. ]]></help> <macros> <import>qiime_citation.xml</import>
--- a/qiime2/qiime_sample-classifier_classify-samples.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_sample-classifier_classify-samples.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_classify-samples" name="qiime sample-classifier classify-samples" version="2019.4"> +<tool id="qiime_sample-classifier_classify-samples" name="qiime sample-classifier classify-samples" version="2019.7"> <description> - Train and test a cross-validated supervised learning classifier.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier classify-samples @@ -64,12 +64,14 @@ +--o-probabilities=oprobabilities --o-sample-estimator=osampleestimator --o-feature-importance=ofeatureimportance --o-predictions=opredictions --o-model-summary=omodelsummary --o-accuracy-results=oaccuracyresults ; +cp oprobabilities.qza $oprobabilities; cp osampleestimator.qza $osampleestimator; cp ofeatureimportance.qza $ofeatureimportance; cp opredictions.qza $opredictions; @@ -143,6 +145,7 @@ </inputs> <outputs> + <data format="qza" label="${tool.name} on ${on_string}: probabilities.qza" name="oprobabilities"/> <data format="qza" label="${tool.name} on ${on_string}: sampleestimator.qza" name="osampleestimator"/> <data format="qza" label="${tool.name} on ${on_string}: featureimportance.qza" name="ofeatureimportance"/> <data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions"/> @@ -213,6 +216,8 @@ the trained estimator. accuracy_results : Visualization Accuracy results visualization. +probabilities : SampleData[Probabilities] + Predicted class probabilities for each input sample. ]]></help> <macros> <import>qiime_citation.xml</import>
--- a/qiime2/qiime_sample-classifier_confusion-matrix.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_sample-classifier_confusion-matrix.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_confusion-matrix" name="qiime sample-classifier confusion-matrix" version="2019.4"> +<tool id="qiime_sample-classifier_confusion-matrix" name="qiime sample-classifier confusion-matrix" version="2019.7"> <description> - Make a confusion matrix from sample classifier predictions.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier confusion-matrix
--- a/qiime2/qiime_sample-classifier_fit-classifier.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_sample-classifier_fit-classifier.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_fit-classifier" name="qiime sample-classifier fit-classifier" version="2019.4"> +<tool id="qiime_sample-classifier_fit-classifier" name="qiime sample-classifier fit-classifier" version="2019.7"> <description> - Fit a supervised learning classifier.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier fit-classifier
--- a/qiime2/qiime_sample-classifier_fit-regressor.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_sample-classifier_fit-regressor.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_fit-regressor" name="qiime sample-classifier fit-regressor" version="2019.4"> +<tool id="qiime_sample-classifier_fit-regressor" name="qiime sample-classifier fit-regressor" version="2019.7"> <description> - Fit a supervised learning regressor.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier fit-regressor
--- a/qiime2/qiime_sample-classifier_heatmap.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_sample-classifier_heatmap.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_heatmap" name="qiime sample-classifier heatmap" version="2019.4"> +<tool id="qiime_sample-classifier_heatmap" name="qiime sample-classifier heatmap" version="2019.7"> <description> - Generate heatmap of important features.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier heatmap
--- a/qiime2/qiime_sample-classifier_metatable.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_sample-classifier_metatable.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_metatable" name="qiime sample-classifier metatable" version="2019.4"> +<tool id="qiime_sample-classifier_metatable" name="qiime sample-classifier metatable" version="2019.7"> <description> - Convert (and merge) positive numeric metadata (in)to feature table.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier metatable
--- a/qiime2/qiime_sample-classifier_predict-classification.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_sample-classifier_predict-classification.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_predict-classification" name="qiime sample-classifier predict-classification" version="2019.4"> +<tool id="qiime_sample-classifier_predict-classification" name="qiime sample-classifier predict-classification" version="2019.7"> <description> - Use trained classifier to predict target values for new samples.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier predict-classification
--- a/qiime2/qiime_sample-classifier_predict-regression.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_sample-classifier_predict-regression.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_predict-regression" name="qiime sample-classifier predict-regression" version="2019.4"> +<tool id="qiime_sample-classifier_predict-regression" name="qiime sample-classifier predict-regression" version="2019.7"> <description> - Use trained regressor to predict target values for new samples.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier predict-regression
--- a/qiime2/qiime_sample-classifier_regress-samples-ncv.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_sample-classifier_regress-samples-ncv.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_regress-samples-ncv" name="qiime sample-classifier regress-samples-ncv" version="2019.4"> +<tool id="qiime_sample-classifier_regress-samples-ncv" name="qiime sample-classifier regress-samples-ncv" version="2019.7"> <description> - Nested cross-validated supervised learning regressor.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier regress-samples-ncv
--- a/qiime2/qiime_sample-classifier_regress-samples.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_sample-classifier_regress-samples.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_regress-samples" name="qiime sample-classifier regress-samples" version="2019.4"> +<tool id="qiime_sample-classifier_regress-samples" name="qiime sample-classifier regress-samples" version="2019.7"> <description> - Train and test a cross-validated supervised learning regressor.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier regress-samples
--- a/qiime2/qiime_sample-classifier_scatterplot.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_sample-classifier_scatterplot.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_scatterplot" name="qiime sample-classifier scatterplot" version="2019.4"> +<tool id="qiime_sample-classifier_scatterplot" name="qiime sample-classifier scatterplot" version="2019.7"> <description> - Make 2D scatterplot and linear regression of regressor predictions.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier scatterplot
--- a/qiime2/qiime_sample-classifier_split-table.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_sample-classifier_split-table.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_split-table" name="qiime sample-classifier split-table" version="2019.4"> +<tool id="qiime_sample-classifier_split-table" name="qiime sample-classifier split-table" version="2019.7"> <description> - Split a feature table into training and testing sets.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier split-table
--- a/qiime2/qiime_sample-classifier_summarize.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_sample-classifier_summarize.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_sample-classifier_summarize" name="qiime sample-classifier summarize" version="2019.4"> +<tool id="qiime_sample-classifier_summarize" name="qiime sample-classifier summarize" version="2019.7"> <description> - Summarize parameter and feature extraction information for a trained estimator.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime sample-classifier summarize
--- a/qiime2/qiime_taxa_barplot.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_taxa_barplot.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_taxa_barplot" name="qiime taxa barplot" version="2019.4"> +<tool id="qiime_taxa_barplot" name="qiime taxa barplot" version="2019.7"> <description> - Visualize taxonomy with an interactive bar plot</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime taxa barplot
--- a/qiime2/qiime_taxa_collapse.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_taxa_collapse.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_taxa_collapse" name="qiime taxa collapse" version="2019.4"> +<tool id="qiime_taxa_collapse" name="qiime taxa collapse" version="2019.7"> <description> - Collapse features by their taxonomy at the specified level</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime taxa collapse
--- a/qiime2/qiime_taxa_filter-seqs.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_taxa_filter-seqs.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_taxa_filter-seqs" name="qiime taxa filter-seqs" version="2019.4"> +<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="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime taxa filter-seqs
--- a/qiime2/qiime_taxa_filter-table.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_taxa_filter-table.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_taxa_filter-table" name="qiime taxa filter-table" version="2019.4"> +<tool id="qiime_taxa_filter-table" name="qiime taxa filter-table" version="2019.7"> <description> - Taxonomy-based feature table filter.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime taxa filter-table
--- a/qiime2/qiime_tools_export.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_tools_export.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_tools_export" name="qiime tools export --input-path" version="2019.4"> +<tool id="qiime_tools_export" name="qiime tools export --input-path" version="2019.7"> <description> - Export data from a QIIME 2 Artifact or Visualization.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[qiime tools export --input-path $isequences --output-path test ]]></command>
--- a/qiime2/qiime_tools_export_collection.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_tools_export_collection.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="qiime_tools_export_collection" name="qiime tools export --input-path collection" version="2019.4"> +<tool id="qiime_tools_export_collection" name="qiime tools export --input-path collection" version="2019.7"> <description>- Export data from a QIIME 2 Artifact or Visualization.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[qiime tools export --input-path $isequences --output-path test && cd test && gunzip *]]></command> <inputs>
--- a/qiime2/qiime_tools_export_paired_collection.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_tools_export_paired_collection.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="qiime_tools_export_paired_collection" name="qiime tools export --input-path to paired collection" version="2019.4"> +<tool id="qiime_tools_export_paired_collection" name="qiime tools export --input-path to paired collection" version="2019.7"> <description>- Export data from a QIIME 2 Artifact or Visualization.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[qiime tools export --input-path $isequences --output-path test && cd test && gunzip *]]></command> <inputs>
--- a/qiime2/qiime_tools_import.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_tools_import.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_tools_import" name="qiime tools import" version="2019.4"> +<tool id="qiime_tools_import" name="qiime tools import" version="2019.7"> <description> - Import data into a new QIIME 2 Artifact.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command> <![CDATA[
--- a/qiime2/qiime_vsearch_cluster-features-closed-reference.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_vsearch_cluster-features-closed-reference.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_vsearch_cluster-features-closed-reference" name="qiime vsearch cluster-features-closed-reference" version="2019.4"> +<tool id="qiime_vsearch_cluster-features-closed-reference" name="qiime vsearch cluster-features-closed-reference" version="2019.7"> <description> - Closed-reference clustering of features.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime vsearch cluster-features-closed-reference
--- a/qiime2/qiime_vsearch_cluster-features-de-novo.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_vsearch_cluster-features-de-novo.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_vsearch_cluster-features-de-novo" name="qiime vsearch cluster-features-de-novo" version="2019.4"> +<tool id="qiime_vsearch_cluster-features-de-novo" name="qiime vsearch cluster-features-de-novo" version="2019.7"> <description> - De novo clustering of features.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime vsearch cluster-features-de-novo
--- a/qiime2/qiime_vsearch_cluster-features-open-reference.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_vsearch_cluster-features-open-reference.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_vsearch_cluster-features-open-reference" name="qiime vsearch cluster-features-open-reference" version="2019.4"> +<tool id="qiime_vsearch_cluster-features-open-reference" name="qiime vsearch cluster-features-open-reference" version="2019.7"> <description> - Open-reference clustering of features.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime vsearch cluster-features-open-reference
--- a/qiime2/qiime_vsearch_dereplicate-sequences.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_vsearch_dereplicate-sequences.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_vsearch_dereplicate-sequences" name="qiime vsearch dereplicate-sequences" version="2019.4"> +<tool id="qiime_vsearch_dereplicate-sequences" name="qiime vsearch dereplicate-sequences" version="2019.7"> <description> - Dereplicate sequences.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime vsearch dereplicate-sequences
--- a/qiime2/qiime_vsearch_join-pairs.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_vsearch_join-pairs.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_vsearch_join-pairs" name="qiime vsearch join-pairs" version="2019.4"> +<tool id="qiime_vsearch_join-pairs" name="qiime vsearch join-pairs" version="2019.7"> <description> - Join paired-end reads.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime vsearch join-pairs
--- a/qiime2/qiime_vsearch_uchime-denovo.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_vsearch_uchime-denovo.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_vsearch_uchime-denovo" name="qiime vsearch uchime-denovo" version="2019.4"> +<tool id="qiime_vsearch_uchime-denovo" name="qiime vsearch uchime-denovo" version="2019.7"> <description> - De novo chimera filtering with vsearch.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime vsearch uchime-denovo
--- a/qiime2/qiime_vsearch_uchime-ref.xml Tue Aug 13 07:57:53 2019 -0400 +++ b/qiime2/qiime_vsearch_uchime-ref.xml Wed Aug 14 15:12:48 2019 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0" ?> -<tool id="qiime_vsearch_uchime-ref" name="qiime vsearch uchime-ref" version="2019.4"> +<tool id="qiime_vsearch_uchime-ref" name="qiime vsearch uchime-ref" version="2019.7"> <description> - Reference-based chimera filtering with vsearch.</description> <requirements> - <requirement type="package" version="2019.4">qiime2</requirement> + <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime vsearch uchime-ref
--- a/tool_data/ref_classifier.loc Tue Aug 13 07:57:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -#<unique_id> <name> <database_caption> <qza_file_path> -# -#For each reference database, you need to download the qza file in qiime path -# -
--- a/tool_data/ref_taxnonomy.loc Tue Aug 13 07:57:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -#<unique_id> <name> <database_caption> <qza_file_path> -# -#For each reference database, you need to download the qza file in qiime path -# -
--- a/tool_data_table_conf.xml.sample Tue Aug 13 07:57:53 2019 -0400 +++ b/tool_data_table_conf.xml.sample Wed Aug 14 15:12:48 2019 -0400 @@ -1,11 +1,12 @@ <tables> <table name="taxonomy_fp" comment_char="#"> <columns>value, name, dbkey, path</columns> - <file path="tool_data/ref_taxnonomy.loc" /> + <file path="tool_data/qiime_rep_set.loc" /> </table> <table name="classifier_fp" comment_char="#"> <columns>value, name, dbkey, path</columns> - <file path="tool-data/ref_classifier.loc" /> + <file path="tool-data/qiime_taxonomy.loc" /> </table> </tables> +