krakentools: extract_kraken_reads.xml annotate

annotate extract_kraken_reads.xml @ 0:97270150a938 draft

"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty"

author	jdv
date	Thu, 01 Apr 2021 04:31:48 +0000
parents
children	92b1c7935d72

rev	line source
0 97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	1 <tool id="krakentools_extract_kraken_reads" name="Extract Kraken Reads By ID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	2 <description>Extract reads that were classified by the Kraken family at specified taxonomic IDs</description>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	3 <macros>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	4 <import>macros.xml</import>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	5 </macros>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	6 <expand macro="requirements" />
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	7 <expand macro="stdio" />
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	8 <version_command>echo -n @TOOL_VERSION@</version_command>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	9
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	10 <command detect_errors="exit_code"><![CDATA[
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	11
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	12 #if $library.type == 'paired':
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	13 #set input_1 = $library.input_1
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	14 #set input_2 = $library.input_2
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	15 #else if $library.type == 'paired_collection'
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	16 #set input_1 = $library.input_1.forward
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	17 #set input_2 = $library.input_1.reverse
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	18 #else
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	19 #set input_1 = $library.input_1
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	20 #end if
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	21
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	22 ## do not quote $taxid
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	23 extract_kraken_reads.py
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	24
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	25 -k '$results'
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	26 -s '$input_1'
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	27 -o '$output_1'
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	28 --taxid $taxid
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	29 --max '$max'
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	30 $include_parents
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	31 $include_children
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	32 $exclude
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	33 $fastq_output
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	34 #if str( $library.type ) != "single":
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	35 -s2 '$input_2'
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	36 -o2 '$output_2'
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	37 #end if
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	38 #if $include_parents or $include_children:
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	39 --report $report
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	40 #end if
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	41
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	42 ]]></command>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	43 <inputs>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	44
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	45 <!-- Reads -->
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	46 <conditional name="library">
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	47 <param name="type" type="select" label="Single or paired reads?">
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	48 <option value="single">Single</option>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	49 <option value="paired">Paired</option>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	50 <option value="paired_collection">Paired Collection</option>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	51 </param>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	52
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	53 <when value="single">
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	54 <param name="input_1" format="fastq,fastqsanger,fasta" type="data" label="FASTQ/A file" help="FASTQ or FASTQ input reads" />
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	55 </when>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	56
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	57 <when value="paired">
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	58 <param name="input_1" format="fastq,fastqsanger,fasta" type="data" label="FASTQ/A forward file" help="FASTQ or FASTQ input reads" />
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	59 <param name="input_2" format="fastq,fastqsanger,fasta" type="data" label="FASTQ/A reverse file" help="FASTQ or FASTQ input reads" />
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	60 </when>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	61
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	62 <when value="paired_collection">
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	63 <param name="input_1" format="fastq,fastqsanger,fasta" type="data_collection" collection_type="paired" label="Paired Collection" help="FASTQ or FASTA read pair collection" />
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	64 </when>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	65
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	66 </conditional>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	67 <param argument="results" format="tabular" type="data" label="Results" help="Results (classification) file from Kraken/KrakenUniq/Kraken2" />
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	68 <param argument="report" format="tabular" type="data" label="Report" optional="True" help="Report file from Kraken/KrakenUniq/Kraken2" />
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	69
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	70 <param argument="--taxid" type="text" value="" label="Taxonomic ID(s) to match" help="Space-delimited list of taxonomic IDs for which to extract matching reads">
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	71 <validator type="regex" message="Enter a space-separated list of numeric tax IDs">^\d+[\d ]*$</validator>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	72 </param>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	73 <param argument="--max" type="integer" value="100000000" min="1" label="Maximum reads to save" help="Maximum number of reads to save for each ID" />
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	74 <param argument="--exclude" type="boolean" value="False" truevalue="--exclude" falsevalue="" label="Invert output" help="Instead of finding reads that match given taxonomic IDs, find all reads that DO NOT match given IDs" />
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	75 <param argument="--fastq-output" type="boolean" value="False" truevalue="--fastq-output" falsevalue="" label="Output as FASTQ" help="Write output as FASTQ instead of the default FASTA" />
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	76 <param argument="--include-parents" type="boolean" value="False" truevalue="--include-parents" falsevalue="" label="Include parents" help="Include reads classified at parent levels of the specified tax IDs" />
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	77 <param argument="--include-children" type="boolean" value="False" truevalue="--include-children" falsevalue="" label="Include children" help="Include reads classified more specifically than the specified tax IDs" />
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	78
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	79 </inputs>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	80
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	81 <outputs>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	82 <data name="output_1" format="fasta" metadata_source="input_1" label="${tool.name} on ${on_string}: forward reads">
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	83 <change_format>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	84 <when input="fastq_output" value="True" format="fastq" />
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	85 </change_format>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	86 </data>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	87 <data name="output_2" format="fasta" metadata_source="input_2" label="${tool.name} on ${on_string}: reverse reads" >
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	88 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	89 <change_format>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	90 <when input="fastq_output" value="True" format="fastq" />
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	91 </change_format>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	92 </data>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	93 </outputs>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	94
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	95 <tests>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	96 <!-- test Kraken2 input, single input -->
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	97 <test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	98 <param name="input_1" value="R1.fq.gz" ftype="fastqsanger"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	99 <param name="library\|type" value="single"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	100 <param name="results" value="kraken2.results" ftype="tabular"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	101 <param name="taxid" value="11176"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	102 <output name="output_1" file="out1.k2.11176.fa"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	103 </test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	104 <!-- test paired input -->
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	105 <test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	106 <param name="input_1" value="R1.fq.gz" ftype="fastqsanger"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	107 <param name="input_2" value="R2.fq.gz" ftype="fastqsanger"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	108 <param name="library\|type" value="paired"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	109 <param name="results" value="kraken2.results" ftype="tabular"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	110 <param name="taxid" value="11176"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	111 <output name="output_1" file="out1.k2.11176.fa"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	112 <output name="output_2" file="out2.k2.11176.fa"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	113 </test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	114 <!-- test paired collection input -->
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	115 <test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	116 <param name="input_1">
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	117 <collection type="paired">
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	118 <element name="forward" value="R1.fq.gz" ftype="fastqsanger"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	119 <element name="reverse" value="R2.fq.gz" ftype="fastqsanger"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	120 </collection>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	121 </param>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	122 <param name="library\|type" value="paired_collection"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	123 <param name="results" value="kraken2.results" ftype="tabular"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	124 <param name="taxid" value="11176"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	125 <output name="output_1" file="out1.k2.11176.fa"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	126 <output name="output_2" file="out2.k2.11176.fa"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	127 </test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	128 <!-- test Kraken1 input, include children -->
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	129 <test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	130 <param name="input_1" value="R1.fq.gz" ftype="fastqsanger"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	131 <param name="library\|type" value="single"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	132 <param name="results" value="kraken1.results" ftype="tabular"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	133 <param name="report" value="kraken1.report" ftype="tabular"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	134 <param name="taxid" value="11176"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	135 <param name="include_children" value="True"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	136 <output name="output_1" file="out1.k1.11176.children.fa"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	137 </test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	138 <!-- test exclude -->
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	139 <test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	140 <param name="input_1" value="R1.fq.gz" ftype="fastqsanger"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	141 <param name="library\|type" value="single"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	142 <param name="results" value="kraken1.results" ftype="tabular"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	143 <param name="report" value="kraken1.report" ftype="tabular"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	144 <param name="taxid" value="10386"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	145 <param name="include_children" value="True"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	146 <param name="exclude" value="True"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	147 <output name="output_1" file="out1.k1.e10386.children.fa"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	148 </test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	149 <!-- test max -->
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	150 <test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	151 <param name="input_1" value="R1.fq.gz" ftype="fastqsanger"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	152 <param name="library\|type" value="single"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	153 <param name="results" value="kraken2.results" ftype="tabular"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	154 <param name="taxid" value="11176"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	155 <param name="max" value="2"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	156 <output name="output_1" file="out1.k2.11176.max2.fa"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	157 </test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	158 <!-- test include parents -->
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	159 <test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	160 <param name="input_1" value="R1.fq.gz" ftype="fastqsanger"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	161 <param name="library\|type" value="single"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	162 <param name="results" value="kraken2.results" ftype="tabular"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	163 <param name="taxid" value="11176"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	164 <param name="include_parents" value="True"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	165 <param name="report" value="kraken2.report" ftype="tabular"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	166 <output name="output_1" file="out1.k2.11176.parents.fa"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	167 </test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	168 <!-- test multiple tax IDs-->
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	169 <test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	170 <param name="input_1" value="R1.fq.gz" ftype="fastqsanger"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	171 <param name="library\|type" value="single"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	172 <param name="results" value="kraken2.results" ftype="tabular"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	173 <param name="taxid" value="10386 11176"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	174 <param name="exclude" value="True"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	175 <param name="include_parents" value="True"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	176 <param name="report" value="kraken2.report" ftype="tabular"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	177 <output name="output_1" file="out1.k2.exclude_both.fa"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	178 </test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	179 <!-- test multiple tax IDs-->
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	180 <test expect_failure="True">
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	181 <param name="input_1" value="R1.fq.gz" ftype="fastqsanger"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	182 <param name="library\|type" value="single"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	183 <param name="results" value="kraken2.results" ftype="tabular"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	184 <param name="taxid" value="10386 f5"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	185 </test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	186 <!-- test FASTQ output -->
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	187 <test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	188 <param name="input_1" value="R1.fq.gz" ftype="fastqsanger"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	189 <param name="library\|type" value="single"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	190 <param name="results" value="kraken2.results" ftype="tabular"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	191 <param name="taxid" value="11176"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	192 <param name="fastq_output" value="True"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	193 <output name="output_1" file="out1.k2.11176.fq"/>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	194 </test>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	195
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	196 </tests>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	197
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	198 <help><![CDATA[
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	199
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	200 .. class:: infomark
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	201
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	202 What it does
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	203
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	204 -------------------
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	205
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	206 Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	207
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	208 Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’ sequencing adapter because the read is longer than the molecule that is sequenced, such as in microRNA, or CRISPR data, or Poly-A tails that are useful for pulling out RNA from your sample but often you don’t want them to be in your reads.
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	209
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	210 Cutadapt_ helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Cutadapt searches for the adapter in all reads and removes it when it finds it. Unless you use a filtering option, all reads that were present in the input file will also be present in the output file, some of them trimmed, some of them not. Even reads that were trimmed entirely (because the adapter was found in the very beginning) are output. All of this can be changed with options in the tool form above.
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	211
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	212 The tool is based on the Open Source Cutadapt_ tool. See the complete `Cutadapt documentation`_ for additional details. If you use Cutadapt, please cite Marcel, 2011 under Citations below.
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	213
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	214 -------------------
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	215
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	216 Inputs
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	217
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	218 -------------------
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	219
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	220 Input files for Cutadapt need to be:
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	221
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	222 - FASTQ.GZ, FASTQ.BZ2, FASTQ or FASTA
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	223
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	224 To trim an adapter, input the ADAPTER sequence in plain text or in a FASTA file e.g. AACCGGTT (with the characters: $, ^, ..., if anchored or linked).
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	225
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	226 ============================================= ===================
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	227 Option Sequence
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	228 --------------------------------------------- -------------------
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	229 3’ (End) Adapter ADAPTER
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	230 Anchored 3’ Adapter ADAPTER$
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	231
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	232 5’ (Front) Adapter ADAPTER
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	233 Anchored 5’ Adapter ^ADAPTER
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	234
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	235 5’ or 3’ (Both possible) ADAPTER
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	236
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	237 Linked Adapter - 3' (End) only ADAPTER1...ADAPTER2
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	238 Non-anchored Linked Adapter - 5' (Front) only ADAPTER1...ADAPTER2
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	239 ============================================= ===================
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	240
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	241 Below is an illustration of the allowed adapter locations relative to the read and depending on the adapter type:
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	242
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	243 .. image:: $PATH_TO_IMAGES/adapters.svg
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	244
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	245
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	246 -------------------
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	247
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	248 Example: Illumina TruSeq Adapters
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	249
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	250 -------------------
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	251
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	252 If you have reads containing Illumina TruSeq adapters, for example, follow these steps.
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	253
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	254
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	255 For Single-end reads as well as the first reads of Paired-end data:
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	256
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	257 Read 1
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	258
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	259 In the 3' (End) Adapters option above, insert A + the “TruSeq Indexed Adapter” prefix that is common to all Indexed Adapter sequences, e.g insert:
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	260
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	261 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	262
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	263
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	264 For the second reads of Paired-end data:
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	265
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	266 Read 2
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	267
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	268 In the 3' (End) Adapters option above, insert the reverse complement of the “TruSeq Universal Adapter”:
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	269
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	270 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	271
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	272 The adapter sequences can be found in the document `Illumina TruSeq Adapters De-Mystified`_.
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	273
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	274 -----------
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	275
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	276 Outputs
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	277
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	278 -----------
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	279
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	280 - Trimmed reads
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	281
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	282 Optionally, under Output Options you can choose to output
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	283
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	284 * Report
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	285 * Info file
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	286
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	287
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	288 Report
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	289
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	290 Cutadapt can output per-adapter statistics if you select to output the report above.
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	291
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	292 Example:
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	293
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	294 This is cutadapt 1.16 with Python 3.6.4
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	295
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	296 Command line parameters: -j 1 --format=fastq -a AGATCGGAAGAGC --info-file=/tmp/tmpX0DlY1/files/000/dataset_21.dat --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 input_f.fastq
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	297 Running on 1 core
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	298 Trimming 1 adapter with at most 10.0% errors in single-end mode ...
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	299 Finished in 0.00 s (1426 us/read; 0.04 M reads/minute).
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	300
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	301 === Summary ===
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	302
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	303 * Total reads processed: 3*
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	304 * Reads with adapters: 0 (0.0%)*
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	305 * Reads written (passing filters): 3 (100.0%)*
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	306
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	307 * Total basepairs processed: 102 bp*
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	308 * Total written (filtered): 102 bp (100.0%)*
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	309
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	310 === Adapter 1 ===
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	311
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	312 Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times.
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	313
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	314
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	315 Info file
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	316
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	317 The info file contains information about the found adapters. The output is a tab-separated text file. Each line corresponds to one read of the input file.
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	318
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	319 Columns contain the following data:
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	320
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	321 * 1st: Read name
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	322 * 2nd: Number of errors
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	323 * 3rd: 0-based start coordinate of the adapter match
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	324 * 4th: 0-based end coordinate of the adapter match
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	325 * 5th: Sequence of the read to the left of the adapter match (can be empty)
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	326 * 6th: Sequence of the read that was matched to the adapter
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	327 * 7th: Sequence of the read to the right of the adapter match (can be empty)
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	328 * 8th: Name of the found adapter
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	329 * 9th: Quality values corresponding to sequence left of the adapter match (can be empty)
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	330 * 10th: Quality values corresponding to sequence matched to the adapter (can be empty)
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	331 * 11th: Quality values corresponding to sequence to the right of the adapter (can be empty)
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	332
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	333 The concatenation of columns 5-7 yields the full read sequence. Column 8 identifies the found adapter. Adapters without a name are numbered starting from 1. Fields 9-11 are empty if quality values are not available. Concatenating them yields the full sequence of quality values.
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	334
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	335 If no adapter was found, the format is as follows:
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	336
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	337 #. Read name
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	338 #. The value -1
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	339 #. The read sequence
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	340 #. Quality values
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	341
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	342 When parsing the file, be aware that additional columns may be added in the future. Note also that some fields can be empty, resulting in consecutive tabs within a line.
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	343
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	344 If the --times option is used and greater than 1, each read can appear more than once in the info file. There will be one line for each found adapter, all with identical read names. Only for the first of those lines will the concatenation of columns 5-7 be identical to the original read sequence (and accordingly for columns 9-11). For subsequent lines, the shown sequence are the ones that were used in subsequent rounds of adapter trimming, that is, they get successively shorter.
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	345
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	346 --------------------
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	347
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	348 More Information
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	349
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	350 --------------------
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	351
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	352 See the excellent `Cutadapt documentation`_
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	353
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	354 .. _Cutadapt: https://cutadapt.readthedocs.io/en/stable/
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	355 .. _`Cutadapt documentation`: https://cutadapt.readthedocs.io/en/latest/index.html
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	356 .. _`Illumina TruSeq Adapters De-Mystified`: http://tucf-genomics.tufts.edu/documents/protocols/TUCF_Understanding_Illumina_TruSeq_Adapters.pdf
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	357
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	358
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	359 --------------------
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	360
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	361 Galaxy Wrapper Development
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	362
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	363 --------------------
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	364
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	365 Author: Lance Parsons <lparsons@princeton.edu>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	366
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	367 ]]></help>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	368
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	369 <citations>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	370 <citation type="bibtex">
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	371 @article{marcel_cutadapt_2011,
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	372 title = {Cutadapt removes adapter sequences from high-throughput sequencing reads},
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	373 volume = {17},
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	374 copyright = {Authors who publish with this journal agree to the following terms: Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access ).},
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	375 url = {http://journal.embnet.org/index.php/embnetjournal/article/view/200},
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	376 abstract = {When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3' adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	377
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	378 Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/},
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	379 number = {1},
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	380 urldate = {2011-08-02},
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	381 journal = {EMBnet.journal},
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	382 author = {Marcel, Martin},
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	383 year = {2011},
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	384 note = {When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3' adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features. Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/},
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	385 keywords = {Adapter removal;, fastq, MicroRNA, Sequencing, Small RNA, software},
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	386 file = {Cutadapt removes adapter sequences from high-throughput sequencing reads \| Martin \| EMBnet.journal:/Users/lparsons/Library/Application Support/Firefox/Profiles/thd2t4je.default/zotero/storage/ZXZT4PSE/200.html:text/html}
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	387 }
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	388 </citation>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	389 </citations>
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	390
97270150a938 "planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/krakentools commit cb7f128b9ab6b8fb780d246427ec6e9c32dd5fd6-dirty" jdv parents: diff changeset	391 </tool>

Mercurial > repos > jdv > krakentools

annotate extract_kraken_reads.xml @ 0:97270150a938 draft