bbtools_bbnorm: bbnorm.xml annotate

annotate bbnorm.xml @ 0:ac326f8788a2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce

author	iuc
date	Tue, 30 May 2023 09:00:12 +0000
parents
children	aa7b97bc2f3f

rev	line source
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	1 <tool id="bbtools_bbnorm" name="BBTools: BBNorm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	2 <description>Normalise sequencing coverage</description>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	3 <macros>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	4 <import>macros.xml</import>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	5 </macros>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	6 <expand macro="edam_ontology"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	7 <expand macro="requirements"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	8 <stdio>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	9 <regex match="This table is (very\|crazy\|totally) full, which may reduce accuracy. Ideal load is under" source="stderr" level="fatal_oom" description="Too low memory - generated results might be inaccurate."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	10 </stdio>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	11 <command detect_errors="exit_code"><![CDATA[
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	12 ## bbtools recommends keeping a proper file extension to determine the input format
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	13 ## so we hardcode them in the below block.
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	14 #if str($input_type_cond.input_type) == 'paired':
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	15 #set read1 = $input_type_cond.reads_collection['forward']
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	16 #set read2 = $input_type_cond.reads_collection['reverse']
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	17 #else:
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	18 #set read1 = $input_type_cond.read1
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	19 #if str($input_type_cond.input_type) == 'PE_2files':
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	20 #set read2 = $input_type_cond.read2
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	21 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	22 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	23
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	24 #if $read1.ext.endswith('.gz'):
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	25 #set read1_file = 'forward.fastq.gz'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	26 #else
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	27 #set read1_file = 'forward.fastq'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	28 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	29 ln -s '${read1}' '${read1_file}' &&
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	30
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	31 #if $str($input_type_cond.input_type) in ['PE_2files', 'paired']:
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	32 #if $read2.ext.endswith('.gz'):
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	33 #set read2_file = 'reverse.fastq.gz'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	34 #else
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	35 #set read2_file = 'reverse.fastq'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	36 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	37 ln -s '${read2}' '${read2_file}' &&
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	38 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	39
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	40
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	41 ## As the program relies on a count-min-sketch algorithm, the potential hash collisions
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	42 ## are ignored and translates to a decreased accuracy of the results. Therefore the allocated
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	43 ## memory amount effects the numerical output: the more RAM the more accurate the results.
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	44 ## Check if a memory cap was set.
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	45 if [[ "\${_JAVA_OPTIONS}" != -Xmx && "\${JAVA_TOOL_OPTIONS}" != -Xmx ]]; then
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	46 export _JAVA_OPTIONS="\${_JAVA_OPTIONS} -Xmx\${GALAXY_MEMORY_MB:-4096}m -Xms256m";
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	47 fi &&
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	48
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	49 bbnorm.sh tmpdir="\$TMPDIR" t="\${GALAXY_SLOTS:-2}"
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	50
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	51 #### Input parameters
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	52 #if str($input_type_cond.input_type) == 'single_end':
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	53 in='${read1_file}'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	54 interleaved=f
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	55 #else:
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	56 #if str($input_type_cond.input_type) == 'PE_1file':
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	57 in='${read1_file}'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	58 interleaved=t
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	59 #else:
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	60 in1='${read1_file}'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	61 in2='${read2_file}'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	62 interleaved=f
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	63 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	64 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	65
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	66 #### Output options
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	67 out=normalised_R1.fastq
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	68 #if $str($input_type_cond.input_type) in ['PE_2files', 'paired']:
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	69 out2=normalised_R2.fastq
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	70 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	71 #if $output_options.save_discarded_reads:
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	72 outt=discarded.fastq
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	73 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	74 touppercase=t
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	75 #if $output_options.save_kmer_hists:
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	76 hist=kmer_hist_input.tabular
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	77 histout=kmer_hist_output.tabular
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	78 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	79
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	80 #### Hashing parameters
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	81 k=$hashing_params.k
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	82 bits=$hashing_params.bits
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	83 hashes=$hashing_params.hashes
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	84 #if str($hashing_params.prefilter) == "true":
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	85 prefilter=t
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	86 prehashes=$hashing_params.prehashes
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	87 prefilterbits=$hashing_params.prefilterbits
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	88 prefiltersize=$hashing_params.prefiltersize
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	89 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	90 buildpasses=$hashing_params.buildpasses
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	91 minq=$hashing_params.minq
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	92 minprob=$hashing_params.minprob
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	93 rdk=$hashing_params.rdk
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	94
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	95 ### Normalization parameters
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	96 fixspikes=$norm_params.fixspikes
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	97 target=$target
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	98 maxdepth=$norm_params.maxdepth
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	99 mindepth=$norm_params.mindepth
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	100 minkmers=$norm_params.minkmers
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	101 percentile=$norm_params.percentile
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	102 uselowerdepth=$norm_params.uselowerdepth
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	103 deterministic=$norm_params.deterministic
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	104 passes=$norm_params.passes
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	105
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	106 ### Error detection parameters
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	107 hdp=$error_det_params.hdp
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	108 ldp=$error_det_params.ldp
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	109 tossbadreads=$error_det_params.tossbadreads
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	110 requirebothbad=$error_det_params.requirebothbad
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	111 errordetectratio=$error_det_params.errordetectratio
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	112 highthresh=$error_det_params.highthresh
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	113 lowthresh=$error_det_params.lowthresh
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	114
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	115 ### Error correction parameters
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	116 #if str($error_corr_params.ecc.ecc) == "true":
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	117 ecc=t
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	118 ecclimit=$error_corr_params.ecclimit
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	119 errorcorrectratio=$error_corr_params.errorcorrectratio
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	120 echighthresh=$error_corr_params.echighthresh
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	121 eclowthresh=$error_corr_params.eclowthresh
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	122 eccmaxqual=$error_corr_params.eccmaxqual
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	123 meo=$error_corr_params.meo
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	124 mue=$error_corr_params.mue
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	125 overlap=$error_corr_params.overlap
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	126 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	127 ]]></command>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	128 <inputs>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	129 <conditional name="input_type_cond">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	130 <param name="input_type" type="select" label="Choose the category of inputs to be analyzed">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	131 <option value="single_end">Single-end reads</option>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	132 <option value="PE_1file">Paired-end reads as a single, interleaved dataset</option>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	133 <option value="PE_2files" selected="true">Paired-end reads as two separate datasets</option>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	134 <option value="paired">Paired-end reads as a collection</option>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	135 </param>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	136 <when value="single_end">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	137 <param name="read1" type="data" format="fastqsanger,fastqsanger.gz" label="Single-end data"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	138 </when>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	139 <when value="PE_1file">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	140 <param name="read1" type="data" format="fastqsanger,fastqsanger.gz" label="Interleaved paired-end data"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	141 </when>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	142 <when value="PE_2files">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	143 <param name="read1" type="data" format="fastqsanger,fastqsanger.gz" label="Forward reads"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	144 <param name="read2" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse reads"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	145 </when>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	146 <when value="paired">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	147 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of forward and reverse reads"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	148 </when>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	149 </conditional>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	150 <param argument="target" type="integer" value="100" min="1" label="Target normalization depth" help="All depth parameters control kmer depth, not read depth. For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1))"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	151 <section name="norm_params" title="Normalization parameters">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	152 <param argument="maxdepth" type="integer" value="-1" min="-1" label="Reads will not be downsampled when below this depth, even if they are above the target depth." help="All depth parameters control kmer depth, not read depth. For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1))"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	153 <param argument="mindepth" type="integer" value="5" min="0" label="kmers with depth below this number will not be included when calculating the depth of a read." help="All depth parameters control kmer depth, not read depth. For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1))"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	154 <param argument="minkmers" type="integer" value="15" min="0" label="Reads must have at least this many kmers over min depth to be retained."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	155 <param argument="percentile" type="integer" value="54" min="1" max="100" label="Percentile to infer read depth" help="Read depth is by default inferred from the 54th percentile of kmer depth, but this may be changed to any number 1-100."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	156 <param argument="uselowerdepth" type="boolean" checked="true" label="For pairs, use the depth of the lower read as the depth proxy."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	157 <param argument="deterministic" type="boolean" checked="true" label="Generate random numbers deterministically" help="This would ensure identical output between multiple runs. May decrease speed with a huge number of threads."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	158 <param argument="fixspikes" type="boolean" checked="false" label="Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	159 <param argument="passes" type="integer" value="2" label="Number of passes to perform" help=" pass is the basic mode. 2 passes allows greater accuracy, error detection, better contol of output depth."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	160 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	161 <section name="hashing_params" title="Hashing parameters">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	162 <param argument="k" type="integer" value="31" min="1" label="kmer length" help="Values under 32 are most efficient, but arbitrarily high values are supported."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	163 <param argument="bits" type="select" label="Bits per cell in bloom filter" help="Maximum kmer depth recorded is 2^c bits. Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers.">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	164 <option value="2">2</option>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	165 <option value="4">4</option>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	166 <option value="8">8</option>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	167 <option value="16" selected="true">16</option>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	168 <option value="32">32</option>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	169 </param>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	170 <param argument="hashes" type="integer" value="3" min="1" label="Number of times each kmer is hashed and stored." help="Higher is slower. Higher is more accurate if there is enough memory, but less accurate if there is not enough memory."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	171 <conditional name="prefilter">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	172 <param argument="prefilter" type="select" label="Use a prefilter to eliminate low-depth kmers" help="True is slower, but generally more accurate; filters out low-depth kmers from the main hashtable. The prefilter is more memory-efficient because it uses 2-bit cells.">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	173 <option value="true">Yes</option>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	174 <option value="false" selected="true">No</option>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	175 </param>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	176 <when value="false"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	177 <when value="true">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	178 <param argument="prehashes" type="integer" value="2" min="1" label="Number of hashes for the prefilter"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	179 <param argument="prefilterbits" type="integer" value="2" min="1" label="Bits per cell in prefilter"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	180 <param argument="prefiltersize" type="float" value="0.35" min="0" max="1" label="Fraction of memory to allocate for the prefilter."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	181 </when>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	182 </conditional>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	183 <param argument="buildpasses" type="integer" value="1" min="1" label="Number of passes" help="More passes can sometimes increase accuracy by iteratively removing low-depth kmers"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	184 <param argument="minq" type="integer" value="6" min="0" label="Ignore kmers containing bases with quality below this threshold"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	185 <param argument="minprob" type="float" value="0.5" min="0" max="1" label="Ignore kmers with overall probability of correctness below this threshold"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	186 <param argument="rdk" type="boolean" checked="true" label="Remove duplicate kmers" help="When true, a kmer's count will only be incremented once per read pair, even if that kmer occurs more than once."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	187 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	188 <section name="error_det_params" title="Error detection parameters">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	189 <param argument="hdp" type="integer" value="90" min="0" max="100" label="highdepthpercentile" help="Position in sorted kmer depth array used as proxy of a read's high kmer depth."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	190 <param argument="ldp" type="integer" value="25" min="0" max="100" label="lowdepthpercentile" help="Position in sorted kmer depth array used as proxy of a read's low kmer depth."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	191 <param argument="tossbadreads" type="boolean" checked="false" label="Throw away reads detected as containing errors."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	192 <param argument="requirebothbad" type="boolean" checked="false" label="Only toss bad pairs if both reads are bad."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	193 <param argument="errordetectratio" type="integer" value="125" min="0" label="Error detection ratio" help="Reads with a ratio of at least this much between their high and low depth kmers will be classified as error reads."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	194 <param argument="highthresh" type="integer" value="12" min="0" label="Threshold for high kmer" help="A high kmer at this or above are considered non-error."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	195 <param argument="lowthresh" type="integer" value="3" min="0" label="Threshold for low kmer" help="Kmers at this and below are always considered errors."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	196 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	197
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	198 <section name="error_corr_params" title="Error correction parameters">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	199 <conditional name="ecc">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	200 <param argument="ecc" type="select" label="What should be done with detected errors?" help="Tadpole is now preferred for error correction, as it does a better job.">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	201 <option value="true" >Correct errors when possible</option>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	202 <option value="false" selected="true">Do not attempt to correct errors</option>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	203 </param>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	204 <when value="false"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	205 <when value="true">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	206 <param argument="ecclimit" type="integer" value="3" min="1" label="Correct up to this many errors per read." help="If more are detected, the read will remain unchanged."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	207 <param argument="errorcorrectratio" type="integer" value="140" min="0" label="Depth ratio" help="Adjacent kmers with a depth ratio of at least this much between will be classified as an error."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	208 <param argument="echighthresh" type="integer" value="22" min="0" label="Threshold for high kmer" help="A kmer at this or above may be considered non-error."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	209 <param argument="eclowthresh" type="integer" value="2" min="0" label="Threshold for low kmer." help="kmers at this depth or below will be considered as errors."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	210 <param argument="eccmaxqual" type="integer" value="127" min="0" label="Do not correct bases with quality above this value."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	211 <param argument="meo" type="boolean" checked="false" label="Marks errors by reducing quality value of suspected errors; does not correct anything."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	212 <param argument="mue" type="boolean" checked="true" label="Mark errors only on uncorrectable reads."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	213 <param argument="overlap" type="boolean" checked="false" label="Correct errors by read overlap."/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	214 </when>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	215 </conditional>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	216 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	217
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	218 <section name="output_options" title="Output options">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	219 <param name="save_discarded_reads" type="boolean" checked="false" label="Save the reads that were eliminated from the input datasets to the history"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	220 <param name="save_kmer_hists" type="boolean" checked="false" label="Save the kmer histograms (in tabular format) for the input and output datasets to the history"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	221 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	222 </inputs>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	223 <outputs>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	224 <data name="output_normalised_R1" format_source="read1" from_work_dir="normalised_R1.fastq" label="${tool.name} on ${on_string} (normalised R1 reads)">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	225 <filter>input_type_cond['input_type'] != 'paired'</filter>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	226 </data>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	227 <data name="output_normalised_R2" format_source="read2" from_work_dir="normalised_R2.fastq" label="${tool.name} on ${on_string} (normalised R2 reads)">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	228 <filter>input_type_cond['input_type'] == 'PE_2files'</filter>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	229 </data>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	230 <collection name="output_pair" type="paired" format_source="reads_collection" label="${tool.name} on ${on_string} (normalised reads)">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	231 <filter>input_type_cond['input_type'] == 'paired'</filter>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	232 <data name="forward" from_work_dir="normalised_R1.fastq" label="${tool.name} on ${on_string} (normalised R1 reads)"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	233 <data name="reverse" from_work_dir="normalised_R2.fastq" label="${tool.name} on ${on_string} (normalised R2 reads)"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	234 </collection>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	235 <data name="output_discarded" format="fastqsanger" from_work_dir="discarded.fastq" label="${tool.name} on ${on_string} (discarded reads)">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	236 <filter>output_options['save_discarded_reads'] is True</filter>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	237 </data>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	238 <data name="kmer_hist_input" format="tabular" from_work_dir="kmer_hist_input.tabular" label="${tool.name} on ${on_string} (kmer histogram input)">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	239 <filter>output_options['save_kmer_hists'] is True</filter>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	240 </data>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	241 <data name="kmer_hist_output" format="tabular" from_work_dir="kmer_hist_output.tabular" label="${tool.name} on ${on_string} (kmer histogram output)">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	242 <filter>output_options['save_kmer_hists'] is True</filter>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	243 </data>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	244 </outputs>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	245 <tests>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	246 <!-- Single end sequencing -->
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	247 <test expect_num_outputs="1">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	248 <param name="input_type" value="single_end"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	249 <param name="read1" ftype="fastqsanger" value="bbnorm/input_R1.fastq"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	250 <param name="target" value="4"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	251 <section name="norm_params">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	252 <param name="deterministic" value="true"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	253 <param name="mindepth" value="0"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	254 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	255 <output name="output_normalised_R1" ftype="fastqsanger" value="bbnorm/normalised_R1.fastq"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	256 </test>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	257 <!-- Single end sequencing, compressed -->
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	258 <test expect_num_outputs="1">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	259 <param name="input_type" value="single_end"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	260 <param name="read1" ftype="fastqsanger.gz" value="bbnorm/input_R1.fastq.gz"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	261 <param name="target" value="4"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	262 <section name="norm_params">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	263 <param name="deterministic" value="true"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	264 <param name="mindepth" value="0"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	265 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	266 <output name="output_normalised_R1" ftype="fastqsanger.gz" value="bbnorm/normalised_R1.fastq"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	267 </test>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	268 <!-- PE as an interleaved file -->
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	269 <test expect_num_outputs="4">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	270 <param name="input_type" value="PE_1file"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	271 <param name="read1" ftype="fastqsanger" value="bbnorm/input_interleaved.fastq"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	272 <param name="target" value="4"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	273 <section name="norm_params">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	274 <param name="deterministic" value="true"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	275 <param name="mindepth" value="0"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	276 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	277 <section name="output_options">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	278 <param name="save_discarded_reads" value="true"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	279 <param name="save_kmer_hists" value="true"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	280 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	281 <output name="output_normalised_R1" ftype="fastqsanger" value="bbnorm/normalised_interleaved.fastq"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	282 <output name="output_discarded" ftype="fastqsanger" value="bbnorm/discarded.fastq"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	283 <output name="kmer_hist_input" ftype="tabular" file="bbnorm/kmer_hist_input.tabular"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	284 <output name="kmer_hist_output" ftype="tabular" file="bbnorm/kmer_hist_output.tabular"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	285 </test>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	286 <!-- PE as 2 files -->
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	287 <test expect_num_outputs="2">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	288 <param name="input_type" value="PE_2files"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	289 <param name="read1" ftype="fastqsanger" value="bbnorm/input_R1.fastq"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	290 <param name="read2" ftype="fastqsanger" value="bbnorm/input_R2.fastq"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	291 <param name="target" value="4"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	292 <section name="norm_params">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	293 <param name="deterministic" value="true"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	294 <param name="mindepth" value="0"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	295 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	296 <output name="output_normalised_R1" ftype="fastqsanger" value="bbnorm/normalised_R1.fastq"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	297 <output name="output_normalised_R2" ftype="fastqsanger" value="bbnorm/normalised_R2.fastq"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	298 </test>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	299 <!-- Paired end collection -->
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	300 <test expect_num_outputs="3">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	301 <param name="input_type" value="paired"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	302 <param name="reads_collection">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	303 <collection type="paired">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	304 <element name="forward" ftype="fastqsanger" value="bbnorm/input_R1.fastq"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	305 <element name="reverse" ftype="fastqsanger" value="bbnorm/input_R2.fastq"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	306 </collection>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	307 </param>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	308 <param name="target" value="4"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	309 <section name="norm_params">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	310 <param name="deterministic" value="true"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	311 <param name="mindepth" value="0"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	312 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	313 <output_collection name="output_pair" type="paired" count="2">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	314 <element name="forward" ftype="fastqsanger" value="bbnorm/normalised_R1.fastq"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	315 <element name="reverse" ftype="fastqsanger" value="bbnorm/normalised_R2.fastq"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	316 </output_collection>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	317 </test>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	318 </tests>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	319 <help>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	320 What it does
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	321
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	322 BBNorm downsamples a provided sequencing output, while paying attention to potential heteregeneities in sequencing depth obtained from the wet-lab workflow. The reads corresponding to regions with low coverage will be kept as is, whereas some of the reads contributing to an above-threshold coverage depth will be subsampled. The resulting data set is expected to be smaller in size, whereas the genome regions with low coverage levels will still be represented in the subsampled dataset. This provides a more uniform coverage depth against all genomic coordinates while the computational resources needed for subsequent steps such as assembly can be substantially reduced without losing coverage anywhere.
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	323
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	324 -----
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	325
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	326 If the target sequencing depth is 2X, a Martian genome sequencing result is expected to be down-sampled as follows:
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	327
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	328 input.fastq::
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	329
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	330 @read_header_1
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	331 AAAAATTTTTCCCCCGGGGGAAATTT
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ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	333 FFFFFFFFFFFFFFFEFFFFFF,FFE
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	334 @read_header_2
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	335 TTTTTCCCCCGGGGGAAATTTCCCGGG
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ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	337 FFFFFFFFFFFFFFFEFFFFFFEFFDD
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	338 @read_header_3
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	339 TTTTTCCCCCGGGGGAAATTTCCCGGG
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	340 +
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	341 FFFFFFFFFFFCEFFEFFFFFFEFFEE
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	342 @read_header_4
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	343 TTTTTCCCCCGGGGGAAATTTCCCGGG
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	344 +
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	345 FFFFFDDFFFFFFFFEFFFFFFEFFEF
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	346 @read_header_5
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	347 TTTTTCCCCCGGGGGAAATTTCCCGGG
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	348 +
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	349 FFFFFEFFFFEEFFFEFFFFFFDFFFF
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	350 @read_header_6
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	351 AAAAATTTTTCCCCCGGGGGAAATTT
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	352 +
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	353 FFFFFFFFFFFFFFFEFFFFFFEFFD
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	354
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	355
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	356 output.fastq::
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	357
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	358 @read_header_1
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	359 AAAAATTTTTCCCCCGGGGGAAATTT
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ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	361 FFFFFFFFFFFFFFFEFFFFFF,FFE
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	362 @read_header_2
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	363 TTTTTCCCCCGGGGGAAATTTCCCGGG
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ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	366 @read_header_3
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	367 TTTTTCCCCCGGGGGAAATTTCCCGGG
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ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	369 FFFFFFFFFFFCEFFEFFFFFFEFFEE
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	370 @read_header_6
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	371 AAAAATTTTTCCCCCGGGGGAAATTT
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ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	373 FFFFFFFFFFFFFFFEFFFFFFEFFD
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	374
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	375
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	376 Indications
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	377
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	378 BBNorm is mainly intended for use in assembly pipelines out of short reads. It might be useful when there is too much data that increases computation time or a highly skewed coverage distribution by subsampling from the existing data. As opposed to keeping a randomly selected subset of reads, such as retaining the first n-many elements, this is a weighted resampling that tries to reduce coverage around coordinates of very high sequencing depth.
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	379
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	380
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	381 Contraindications
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	382
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	383 * The data already has a roughly uniform coverage that does not need to be normalised further.
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	384 * You do not have any excess data to discard: BBnorm does not increase data quantity by imputation or by repeatedly sampling with replacement.
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	385 * Your pipeline reports results that rely on quantification of abundance (ex: differential expression profiling or ChIP-Seq)
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	386 * You want to do variant discovery. Reduction of sequencing depth might bias significance levels, or even obscure the existence of rare variants altogether.
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	387 * The sequencing platform has a very high error rate (ex: ONT) that might mislead this algorithm.
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	388
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	389 </help>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	390 <expand macro="citations"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	391 </tool>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	392

Mercurial > repos > iuc > bbtools_bbnorm

annotate bbnorm.xml @ 0:ac326f8788a2 draft