qiime_split_libraries_fastq: split_libraries

annotate split_libraries_fastq.xml @ 6:f3f3afb3b221 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"

author	iuc
date	Thu, 05 Dec 2019 12:22:51 +0000
parents	3bc4d476fc29
children

rev	line source
6 f3f3afb3b221 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c" iuc parents: 4 diff changeset	1 <tool id="qiime_split_libraries_fastq" name="Split fastq libraries" version="@WRAPPER_VERSION@.0" profile="@PROFILE@">
4 3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	2 <description> to performs demultiplexing of Fastq sequence data (split_libraries_fastq)</description>
0 c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	3 <macros>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	4 <import>macros.xml</import>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	5 </macros>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	6 <expand macro="requirements"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	7 <version_command>split_libraries_fastq.py --version</version_command>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	8 <command detect_errors="aggressive"><![CDATA[
6 f3f3afb3b221 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c" iuc parents: 4 diff changeset	9 @MPLBACKEND@
4 3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	10 split_libraries_fastq.py
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	11 #set $seq_files = ''
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	12 #set $sep = ''
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	13 #for $file in $sequence_read_fps
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	14 #set $seq_files += $sep + str($file)
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	15 #set $sep = ','
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	16 #end for
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	17 --sequence_read_fps '$seq_files'
0 c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	18
4 3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	19 -o split_libraries
0 c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	20
4 3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	21 #set $mapping_files = ''
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	22 #set $sep = ''
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	23 #for $file in $mapping_fps
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	24 #set $mapping_files += $sep + str($file)
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	25 #set $sep = ','
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	26 #end for
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	27 #if $mapping_files != 'None'
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	28 --mapping_fps '$mapping_files'
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	29 #end if
0 c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	30
4 3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	31 #set $barcode_files = ''
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	32 #set $sep = ''
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	33 #for $file in $barcode_read_fps
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	34 #set $barcode_files += $sep + str($file)
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	35 #set $sep = ','
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	36 #end for
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	37 #if $barcode_files != 'None'
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	38 --barcode_read_fps '$barcode_files'
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	39 #end if
0 c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	40
4 3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	41 $store_qual_scores
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	42 #if str($sample_ids) != ''
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	43 --sample_ids '$sample_ids'
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	44 #end if
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	45 $store_demultiplexed_fastq
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	46 $retain_unassigned_reads
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	47
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	48 --max_bad_run_length '$max_bad_run_length'
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	49 --min_per_read_length_fraction '$min_per_read_length_fraction'
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	50 --sequence_max_n '$sequence_max_n'
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	51 --start_seq_id '$start_seq_id'
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	52 $rev_comp_barcode
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	53 $rev_comp_mapping_barcodes
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	54 $rev_comp
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	55 --phred_quality_threshold '$phred_quality_threshold'
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	56 #if str( $barcode.barcode_type ) != "custom_length"
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	57 --barcode_type '$barcode.barcode_type'
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	58 #else
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	59 --barcode_type '$barcode.barcode_length'
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	60 #end if
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	61 --max_barcode_errors '$max_barcode_errors'
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	62 $phred_offset
0 c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	63 ]]></command>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	64 <inputs>
4 3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	65 <param argument="--sequence_read_fps" type="data" format="fastq,fastqsanger,fastqsolexa" multiple="true" label="Input fastq files"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	66 <param argument="--mapping_fps" type="data" format="txt,tabular,tsv,csv" multiple="true" optional="true" label="Metadata mapping files"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	67 <param argument="--barcode_read_fps" type="data" format="fastq,fastqsanger,fastqsolexa" multiple="true" optional="true" label="Barcode read files"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	68 <param argument="--store_qual_scores" type="boolean" truevalue="--store_qual_scores" falsevalue="" checked="false" label="Store quality strings in files?"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	69 <param argument="--sample_ids" type="text" optional="true" label="Comma-separated list of samples ids to be applied to all sequences" help="It must be one per input file path (used when data is not multiplexed)"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	70 <param argument="--store_demultiplexed_fastq" type="boolean" truevalue="--store_demultiplexed_fastq" falsevalue="" checked="false" label="Write demultiplexed fastq files?"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	71 <param argument="--retain_unassigned_reads" type="boolean" truevalue="--retain_unassigned_reads" falsevalue="" checked="false" label="Retain sequences which don’t map to a barcode in the mapping file?" help="Sample ID will be 'Unassigned'"/>
0 c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	72 <param argument="--max_bad_run_length" type="integer" value="3" label="Maximum number of consecutive low quality base calls allowed before truncating a read"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	73 <param argument="--min_per_read_length_fraction" type="float" value="0.75" label="Minimum number of consecutive high quality base calls to include a read (per single end read) as a fraction of the input read length"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	74 <param argument="--sequence_max_n" type="integer" value="0" label="Maximum number of N characters allowed in a sequence to retain it" help="This is applied after quality trimming, and is total over combined paired end reads if applicable"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	75 <param argument="--start_seq_id" type="integer" value="0" label="Start seq_ids as ascending integers beginning with start_seq_id"/>
4 3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	76 <param argument="--rev_comp_barcode" type="boolean" truevalue="--rev_comp_barcode" falsevalue="" checked="false" label="Reverse complement barcode reads before lookup?"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	77 <param argument="--rev_comp_mapping_barcodes" type="boolean" truevalue="--rev_comp_mapping_barcodes" falsevalue="" checked="false" label="Reverse complement barcode in mapping before lookup?" help="It is useful if barcodes in mapping file are reverse complements of golay codes"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	78 <param argument="--rev_comp" type="boolean" truevalue="--rev_comp" falsevalue="" checked="false" label="Reverse complement sequence before writing to output file?"/>
0 c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	79 <param argument="--phred_quality_threshold" type="integer" value="3" label="Maximum unacceptable Phred quality score" help="E.g., for Q20 and better, 19 must be specified"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	80 <conditional name="barcode">
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	81 <param argument="--barcode_type" type="select" label="Type of barcode">
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	82 <option value="hamming_8">hamming_8</option>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	83 <option value="golay_12" selected="true">golay_12</option>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	84 <option value="variable_length">variable_length (disable any barcode correction)</option>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	85 <option value="custom_length">Custom length</option>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	86 <option value="not-barcoded">Data not barcoded</option>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	87 </param>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	88 <when value="hamming_8"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	89 <when value="golay_12"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	90 <when value="variable_length"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	91 <when value="custom_length">
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	92 <param name="barcode_length" type="integer" value="4" label="Barcode length"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	93 </when>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	94 <when value="not-barcoded"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	95 </conditional>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	96 <param argument="--max_barcode_errors" type="float" value="1.5" label="Maximum number of errors in barcode"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	97 <param argument="--phred_offset" type="select" label="Ascii offset to use when decoding phred scores">
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	98 <option value="--phred_offset 33">33</option>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	99 <option value="--phred_offset 64">64</option>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	100 <option value="" selected="true">Automatically determined</option>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	101 </param>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	102 </inputs>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	103 <outputs>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	104 <data name="log" format="txt" from_work_dir="split_libraries/split_library_log.txt" label="${tool.name} on ${on_string}: log"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	105 <data name="histograms" format="tabular" from_work_dir="split_libraries/histograms.txt" label="${tool.name} on ${on_string}: histograms"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	106 <data name="seqs" format="fasta" from_work_dir="split_libraries/seqs.fna" label="${tool.name} on ${on_string}: sequences"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	107 <data name="seqs_qual" format="qual" from_work_dir="split_libraries/seqs.qual" label="${tool.name} on ${on_string}: sequence qualities">
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	108 <filter>store_qual_scores is True</filter>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	109 </data>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	110 <data name="seqs_fastq" format="fastq" from_work_dir="split_libraries/seqs.fastq" label="${tool.name} on ${on_string}: demultiplexed sequences (fastq)">
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	111 <filter>store_demultiplexed_fastq is True</filter>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	112 </data>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	113 </outputs>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	114 <tests>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	115 <test>
4 3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	116 <param name="sequence_read_fps" value="split_libraries_fastq/lane1_read1.fastq.gz"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	117 <param name="mapping_fps" value="split_libraries_fastq/map.txt"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	118 <param name="barcode_read_fps" value="split_libraries_fastq/lane1_barcode.fastq.gz"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	119 <param name="store_qual_scores" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	120 <param name="store_demultiplexed_fastq" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	121 <param name="retain_unassigned_reads" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	122 <param name="max_bad_run_length" value="3"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	123 <param name="min_per_read_length_fraction" value="0.75"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	124 <param name="sequence_max_n" value="0"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	125 <param name="start_seq_id" value="0"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	126 <param name="rev_comp_barcode" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	127 <param name="rev_comp_mapping_barcodes" value="--rev_comp_mapping_barcodes"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	128 <param name="rev_comp" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	129 <param name="phred_quality_threshold" value="19"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	130 <conditional name="barcode">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	131 <param name="barcode_type" value="golay_12"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	132 </conditional>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	133 <param name="max_barcode_errors" value="1.5"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	134 <param name="phred_offset" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	135 <output name="log">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	136 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	137 <has_text text="Median sequence length: 151.00"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	138 <has_text text="s41"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	139 <has_text text="s122"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	140 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	141 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	142 <output name="seqs" ftype="fasta">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	143 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	144 <has_text text="s161_0 M00176:17:000000000-A0CNA:1:1:16738:1773 1:N:0:0 orig_bc=CTCGCTTCACTT new_bc=CTCGCTTCACTT bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	145 <has_text text="s26_84 M00176:17:000000000-A0CNA:1:1:18075:1844 1:N:0:0 orig_bc=AGGGTTCCAGTT new_bc=AGGGTTCCAGTT bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	146 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	147 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	148 <output name="histograms">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	149 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	150 <has_text text="Length"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	151 <has_text text="127.0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	152 <has_text text="157.0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	153 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	154 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	155 </test>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	156 <test>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	157 <param name="sequence_read_fps" value="split_libraries_fastq/lane1_read1.fastq.gz"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	158 <param name="mapping_fps" value="split_libraries_fastq/map.txt"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	159 <param name="barcode_read_fps" value="split_libraries_fastq/lane1_barcode.fastq.gz"/>
0 c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	160 <param name="store_qual_scores" value="--store_qual_scores"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	161 <param name="store_demultiplexed_fastq" value="--store_demultiplexed_fastq"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	162 <param name="retain_unassigned_reads" value=""/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	163 <param name="max_bad_run_length" value="3"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	164 <param name="min_per_read_length_fraction" value="0.75"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	165 <param name="sequence_max_n" value="0"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	166 <param name="start_seq_id" value="0"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	167 <param name="rev_comp_barcode" value=""/>
4 3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	168 <param name="rev_comp_mapping_barcodes" value="--rev_comp_mapping_barcodes"/>
0 c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	169 <param name="rev_comp" value=""/>
4 3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	170 <param name="phred_quality_threshold" value="19"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	171 <conditional name="barcode">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	172 <param name="barcode_type" value="golay_12"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	173 </conditional>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	174 <param name="max_barcode_errors" value="1.5"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	175 <param name="phred_offset" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	176 <output name="log">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	177 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	178 <has_text text="Median sequence length: 151.00"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	179 <has_text text="s41"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	180 <has_text text="s122"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	181 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	182 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	183 <output name="seqs" ftype="fasta">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	184 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	185 <has_text text="s161_0 M00176:17:000000000-A0CNA:1:1:16738:1773 1:N:0:0 orig_bc=CTCGCTTCACTT new_bc=CTCGCTTCACTT bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	186 <has_text text="s107_6 M00176:17:000000000-A0CNA:1:1:15276:1779 1:N:0:0 orig_bc=ATCTCCTCTCCA new_bc=ATCTCCTCTCCA bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	187 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	188 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	189 <output name="seqs_fastq" ftype="fastq">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	190 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	191 <has_text text="@s161_0 M00176:17:000000000-A0CNA:1:1:16738:1773 1:N:0:0 orig_bc=CTCGCTTCACTT new_bc=CTCGCTTCACTT bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	192 <has_text text="@s107_6 M00176:17:000000000-A0CNA:1:1:15276:1779 1:N:0:0 orig_bc=ATCTCCTCTCCA new_bc=ATCTCCTCTCCA bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	193 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	194 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	195 <output name="seqs_qual" ftype="qual">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	196 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	197 <has_text text="s161_0 M00176:17:000000000-A0CNA:1:1:16738:1773 1:N:0:0 orig_bc=CTCGCTTCACTT new_bc=CTCGCTTCACTT bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	198 <has_text text="s107_6 M00176:17:000000000-A0CNA:1:1:15276:1779 1:N:0:0 orig_bc=ATCTCCTCTCCA new_bc=ATCTCCTCTCCA bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	199 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	200 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	201 <output name="histograms">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	202 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	203 <has_text text="Length"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	204 <has_text text="127.0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	205 <has_text text="157.0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	206 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	207 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	208 </test>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	209 <test>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	210 <param name="sequence_read_fps" value="split_libraries_fastq/lane1_read1.fastq.gz,split_libraries_fastq/lane2_read1.fastq.gz"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	211 <param name="mapping_fps" value="split_libraries_fastq/map.txt,split_libraries_fastq/map.txt"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	212 <param name="barcode_read_fps" value="split_libraries_fastq/lane1_barcode.fastq.gz,split_libraries_fastq/lane2_barcode.fastq.gz"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	213 <param name="store_qual_scores" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	214 <param name="store_demultiplexed_fastq" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	215 <param name="retain_unassigned_reads" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	216 <param name="max_bad_run_length" value="3"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	217 <param name="min_per_read_length_fraction" value="0.75"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	218 <param name="sequence_max_n" value="0"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	219 <param name="start_seq_id" value="0"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	220 <param name="rev_comp_barcode" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	221 <param name="rev_comp_mapping_barcodes" value="--rev_comp_mapping_barcodes"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	222 <param name="rev_comp" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	223 <param name="phred_quality_threshold" value="19"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	224 <conditional name="barcode">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	225 <param name="barcode_type" value="golay_12"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	226 </conditional>
0 c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	227 <param name="max_barcode_errors" value="1.5"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	228 <param name="phred_offset" value=""/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	229 <output name="log">
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	230 <assert_contents>
4 3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	231 <has_text text="Median sequence length: 151.00"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	232 <has_text text="s41"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	233 <has_text text="s122"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	234 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	235 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	236 <output name="seqs" ftype="fasta">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	237 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	238 <has_text text="s161_0 M00176:17:000000000-A0CNA:1:1:16738:1773 1:N:0:0 orig_bc=CTCGCTTCACTT new_bc=CTCGCTTCACTT bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	239 <has_text text="s26_84 M00176:17:000000000-A0CNA:1:1:18075:1844 1:N:0:0 orig_bc=AGGGTTCCAGTT new_bc=AGGGTTCCAGTT bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	240 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	241 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	242 <output name="histograms">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	243 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	244 <has_text text="Length"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	245 <has_text text="127.0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	246 <has_text text="157.0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	247 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	248 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	249 </test>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	250 <test>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	251 <param name="sequence_read_fps" value="split_libraries_fastq/lane1_read1.fastq.gz"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	252 <param name="store_qual_scores" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	253 <param name="sample_ids" value="my.sample.1"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	254 <param name="store_demultiplexed_fastq" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	255 <param name="retain_unassigned_reads" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	256 <param name="max_bad_run_length" value="3"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	257 <param name="min_per_read_length_fraction" value="0.75"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	258 <param name="sequence_max_n" value="0"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	259 <param name="start_seq_id" value="0"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	260 <param name="rev_comp_barcode" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	261 <param name="rev_comp_mapping_barcodes" value="--rev_comp_mapping_barcodes"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	262 <param name="rev_comp" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	263 <param name="phred_quality_threshold" value="19"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	264 <conditional name="barcode">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	265 <param name="barcode_type" value="not-barcoded"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	266 </conditional>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	267 <param name="phred_offset" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	268 <output name="log">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	269 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	270 <has_text text="Median sequence length: 151.00"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	271 <has_text text="my.sample.1"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	272 <has_text text="Total number seqs written"></has_text>
0 c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	273 </assert_contents>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	274 </output>
4 3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	275 <output name="seqs" ftype="fasta">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	276 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	277 <has_text text="my.sample.1_0 M00176:17:000000000-A0CNA:1:1:15487:1773 1:N:0:0 orig_bc=AAAAAAAAAAAA new_bc=AAAAAAAAAAAA bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	278 <has_text text="my.sample.1_12 M00176:17:000000000-A0CNA:1:1:14889:1778 1:N:0:0 orig_bc=AAAAAAAAAAAA new_bc=AAAAAAAAAAAA bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	279 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	280 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	281 <output name="histograms">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	282 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	283 <has_text text="Length"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	284 <has_text text="124.0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	285 <has_text text="154.0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	286 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	287 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	288 </test>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	289 <test>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	290 <param name="sequence_read_fps" value="split_libraries_fastq/lane1_read1.fastq.gz,split_libraries_fastq/lane2_read1.fastq.gz"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	291 <param name="store_qual_scores" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	292 <param name="sample_ids" value="my.sample.1,my.sample.2"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	293 <param name="store_demultiplexed_fastq" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	294 <param name="retain_unassigned_reads" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	295 <param name="max_bad_run_length" value="3"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	296 <param name="min_per_read_length_fraction" value="0.75"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	297 <param name="sequence_max_n" value="0"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	298 <param name="start_seq_id" value="0"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	299 <param name="rev_comp_barcode" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	300 <param name="rev_comp_mapping_barcodes" value="--rev_comp_mapping_barcodes"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	301 <param name="rev_comp" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	302 <param name="phred_quality_threshold" value="19"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	303 <conditional name="barcode">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	304 <param name="barcode_type" value="not-barcoded"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	305 </conditional>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	306 <param name="phred_offset" value=""/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	307 <output name="log">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	308 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	309 <has_text text="Median sequence length: 151.00"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	310 <has_text text="my.sample.1"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	311 <has_text text="Total number seqs written"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	312 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	313 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	314 <output name="seqs" ftype="fasta">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	315 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	316 <has_text text="my.sample.1_0 M00176:17:000000000-A0CNA:1:1:15487:1773 1:N:0:0 orig_bc=AAAAAAAAAAAA new_bc=AAAAAAAAAAAA bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	317 <has_text text="my.sample.1_12 M00176:17:000000000-A0CNA:1:1:14889:1778 1:N:0:0 orig_bc=AAAAAAAAAAAA new_bc=AAAAAAAAAAAA bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	318 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	319 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	320 <output name="histograms">
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	321 <assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	322 <has_text text="Length"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	323 <has_text text="124.0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	324 <has_text text="154.0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	325 </assert_contents>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b iuc parents: 0 diff changeset	326 </output>
0 c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	327 </test>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	328 </tests>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	329 <help><![CDATA[
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	330 What it does
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	331
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	332 This tool performs demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files (common on Illumina runs).
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	333
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	334 More information about this tool is available on
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	335 `QIIME documentation <http://qiime.org/scripts/split_libraries_fastq.html>`_.
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	336 ]]></help>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	337 <citations>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	338 <expand macro="citations"/>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	339 </citations>
c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d iuc parents: diff changeset	340 </tool>

Mercurial > repos > iuc > qiime_split_libraries_fastq

annotate split_libraries_fastq.xml @ 6:f3f3afb3b221 draft default tip