diff qiime2-2020.8/qiime_demux_emp-paired.xml @ 20:d93d8888f0b0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2-2020.8/qiime_demux_emp-paired.xml	Fri Sep 04 12:44:24 2020 +0000
@@ -0,0 +1,125 @@
+<?xml version="1.0" ?>
+<tool id="qiime_demux_emp-paired" name="qiime demux emp-paired"
+      version="2020.8">
+  <description>Demultiplex paired-end sequence data generated with the EMP protocol.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime demux emp-paired
+
+--i-seqs=$iseqs
+# 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($input_files_mbarcodesfile)
+# end if
+
+#if '__ob__' in str($mbarcodescolumn):
+  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__ob__', '[')
+  #set $mbarcodescolumn = $mbarcodescolumn_temp
+#end if
+#if '__cb__' in str($mbarcodescolumn):
+  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__cb__', ']')
+  #set $mbarcodescolumn = $mbarcodescolumn_temp
+#end if
+#if 'X' in str($mbarcodescolumn):
+  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('X', '\\')
+  #set $mbarcodescolumn = $mbarcodescolumn_temp
+#end if
+#if '__sq__' in str($mbarcodescolumn):
+  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'")
+  #set $mbarcodescolumn = $mbarcodescolumn_temp
+#end if
+#if '__db__' in str($mbarcodescolumn):
+  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__db__', '"')
+  #set $mbarcodescolumn = $mbarcodescolumn_temp
+#end if
+
+--m-barcodes-column=$mbarcodescolumn
+
+
+#if $pnogolayerrorcorrection:
+ --p-no-golay-error-correction
+#end if
+
+#if $prevcompbarcodes:
+ --p-rev-comp-barcodes
+#end if
+
+#if $prevcompmappingbarcodes:
+ --p-rev-comp-mapping-barcodes
+#end if
+
+--o-per-sample-sequences=opersamplesequences
+
+--o-error-correction-details=oerrorcorrectiondetails
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT EMPPairedEndSequences The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data" />
+    <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
+    </repeat>
+    <param label="--m-barcodes-column: COLUMN  MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes.                                    [required]" name="mbarcodescolumn" optional="False" type="text" />
+    <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads.                                  [default: True]" name="pnogolayerrorcorrection" selected="False" type="boolean" />
+    <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-barcodes: --p-rev-comp-barcodes: / --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean" />
+    <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-mapping-barcodes: --p-rev-comp-mapping-barcodes: / --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing.                        [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" />
+    <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Demultiplex paired-end sequence data generated with the EMP protocol.
+###############################################################
+
+Demultiplex paired-end sequence data (i.e., map barcode reads to sample
+ids) for data generated with the Earth Microbiome Project (EMP) amplicon
+sequencing protocol. Details about this protocol can be found at
+http://www.earthmicrobiome.org/protocols-and-standards/
+
+Parameters
+----------
+seqs : EMPPairedEndSequences
+    The paired-end sequences to be demultiplexed.
+barcodes : MetadataColumn[Categorical]
+    The sample metadata column containing the per-sample barcodes.
+golay_error_correction : Bool, optional
+    Perform 12nt Golay error correction on the barcode reads.
+rev_comp_barcodes : Bool, optional
+    If provided, the barcode sequence reads will be reverse complemented
+    prior to demultiplexing.
+rev_comp_mapping_barcodes : Bool, optional
+    If provided, the barcode sequences in the sample metadata will be
+    reverse complemented prior to demultiplexing.
+
+Returns
+-------
+per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
+    The resulting demultiplexed sequences.
+error_correction_details : ErrorCorrectionDetails
+    Detail about the barcode error corrections.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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