bbtools_bbnorm: bbnorm.xml annotate

annotate bbnorm.xml @ 5:71bd084b9eba draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 4aa44523d9df9bf1773ed724735120476d773a19

author	iuc
date	Thu, 06 Mar 2025 11:49:14 +0000
parents	78e3ecfdf6df
children

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"/>
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	7 <expand macro="bio.tools"/>
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	8 <expand macro="requirements"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	9 <stdio>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	10 <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	11 </stdio>
3 78e3ecfdf6df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 4c1b74f1d14c5cac8ed806de0bb207d00e7a0e51 iuc parents: 1 diff changeset	12 <command detect_errors="aggressive"><![CDATA[
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	13 ## 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	14 ## 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	15 #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	16 #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	17 #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	18 #else:
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	19 #set read1 = $input_type_cond.read1
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	20 #if str($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	21 #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	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 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	24
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	25 #if $read1.ext.endswith('.gz'):
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	26 #set read1_file = 'forward.fastq.gz'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	27 #else
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	28 #set read1_file = 'forward.fastq'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	29 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	30 ln -s '${read1}' '${read1_file}' &&
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	31
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	32 #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	33 #if $read2.ext.endswith('.gz'):
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	34 #set read2_file = 'reverse.fastq.gz'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	35 #else
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	36 #set read2_file = 'reverse.fastq'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	37 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	38 ln -s '${read2}' '${read2_file}' &&
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	39 #end if
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
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	42 ## 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	43 ## 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	44 ## 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	45 ## 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	46 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	47 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	48 fi &&
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	49
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	50 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	51
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	52 #### Input parameters
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	53 #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	54 in='${read1_file}'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	55 interleaved=f
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	56 #else:
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	57 #if str($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	58 in='${read1_file}'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	59 interleaved=t
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	60 #else:
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	61 in1='${read1_file}'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	62 in2='${read2_file}'
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	63 interleaved=f
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 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	66
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	67 #### Output options
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	68 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	69 #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	70 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	71 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	72 #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	73 outt=discarded.fastq
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	74 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	75 touppercase=t
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	76 #if $output_options.save_kmer_hists:
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	77 hist=kmer_hist_input.tabular
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	78 histout=kmer_hist_output.tabular
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	79 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	80
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	81 #### Hashing parameters
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	82 k=$hashing_params.k
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	83 bits=$hashing_params.bits
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	84 hashes=$hashing_params.hashes
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	85 #if str($hashing_params.prefilter) == "true":
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	86 prefilter=t
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	87 prehashes=$hashing_params.prehashes
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	88 prefilterbits=$hashing_params.prefilterbits
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	89 prefiltersize=$hashing_params.prefiltersize
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	90 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	91 buildpasses=$hashing_params.buildpasses
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	92 minq=$hashing_params.minq
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	93 minprob=$hashing_params.minprob
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	94 rdk=$hashing_params.rdk
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	95
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	96 ### Normalization parameters
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	97 fixspikes=$norm_params.fixspikes
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	98 target=$target
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	99 maxdepth=$norm_params.maxdepth
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	100 mindepth=$norm_params.mindepth
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	101 minkmers=$norm_params.minkmers
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	102 percentile=$norm_params.percentile
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	103 uselowerdepth=$norm_params.uselowerdepth
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	104 deterministic=$norm_params.deterministic
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	105 passes=$norm_params.passes
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	106
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	107 ### Error detection parameters
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	108 hdp=$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	109 ldp=$error_det_params.ldp
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	110 tossbadreads=$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	111 requirebothbad=$error_det_params.requirebothbad
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	112 errordetectratio=$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	113 highthresh=$error_det_params.highthresh
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	114 lowthresh=$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	115
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	116 ### Error correction parameters
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	117 #if str($error_corr_params.ecc.ecc) == "true":
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	118 ecc=t
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	119 ecclimit=$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	120 errorcorrectratio=$error_corr_params.errorcorrectratio
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	121 echighthresh=$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	122 eclowthresh=$error_corr_params.eclowthresh
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	123 eccmaxqual=$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	124 meo=$error_corr_params.meo
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	125 mue=$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	126 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	127 #end if
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	128 ]]></command>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	129 <inputs>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	130 <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	131 <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	132 <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	133 <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	134 <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	135 <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	136 </param>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	137 <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	138 <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	139 </when>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	140 <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	141 <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	142 </when>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	143 <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	144 <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	145 <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	146 </when>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	147 <when value="paired">
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	148 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Collection of forward and reverse reads" collection_type="paired"/>
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	149 </when>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	150 </conditional>
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	151 <param argument="target" type="integer" min="1" value="100" 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))"/>
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	152 <section name="norm_params" title="Normalization parameters">
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	153 <param argument="maxdepth" type="integer" min="-1" value="-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))"/>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	154 <param argument="mindepth" type="integer" min="0" value="5" 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))"/>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	155 <param argument="minkmers" type="integer" min="0" value="15" label="Reads must have at least this many kmers over min depth to be retained."/>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	156 <param argument="percentile" type="integer" min="1" max="100" value="54" 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."/>
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	157 <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	158 <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	159 <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	160 <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	161 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	162 <section name="hashing_params" title="Hashing parameters">
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	163 <param argument="k" type="integer" min="1" value="31" label="kmer length" help="Values under 32 are most efficient, but arbitrarily high values are supported."/>
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	164 <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	165 <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	166 <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	167 <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	168 <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	169 <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	170 </param>
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	171 <param argument="hashes" type="integer" min="1" value="3" 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."/>
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	172 <conditional name="prefilter">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	173 <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	174 <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	175 <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	176 </param>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	177 <when value="false"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	178 <when value="true">
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	179 <param argument="prehashes" type="integer" min="1" value="2" label="Number of hashes for the prefilter"/>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	180 <param argument="prefilterbits" type="integer" min="1" value="2" label="Bits per cell in prefilter"/>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	181 <param argument="prefiltersize" type="float" min="0" max="1" value="0.35" label="Fraction of memory to allocate for the prefilter."/>
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	182 </when>
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	183 </conditional>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	184 <param argument="buildpasses" type="integer" min="1" value="1" label="Number of passes" help="More passes can sometimes increase accuracy by iteratively removing low-depth kmers"/>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	185 <param argument="minq" type="integer" min="0" value="6" label="Ignore kmers containing bases with quality below this threshold"/>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	186 <param argument="minprob" type="float" min="0" max="1" value="0.5" label="Ignore kmers with overall probability of correctness below this threshold"/>
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	187 <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	188 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	189 <section name="error_det_params" title="Error detection parameters">
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	190 <param argument="hdp" type="integer" min="0" max="100" value="90" label="highdepthpercentile" help="Position in sorted kmer depth array used as proxy of a read's high kmer depth."/>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	191 <param argument="ldp" type="integer" min="0" max="100" value="25" label="lowdepthpercentile" help="Position in sorted kmer depth array used as proxy of a read's low kmer depth."/>
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	192 <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	193 <param argument="requirebothbad" type="boolean" checked="false" label="Only toss bad pairs if both reads are bad."/>
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	194 <param argument="errordetectratio" type="integer" min="0" value="125" 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."/>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	195 <param argument="highthresh" type="integer" min="0" value="12" label="Threshold for high kmer" help="A high kmer at this or above are considered non-error."/>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	196 <param argument="lowthresh" type="integer" min="0" value="3" label="Threshold for low kmer" help="Kmers at this and below are always considered errors."/>
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	197 </section>
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.">
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	201 <option value="true">Correct errors when possible</option>
0 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">
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	206 <param argument="ecclimit" type="integer" min="1" value="3" label="Correct up to this many errors per read." help="If more are detected, the read will remain unchanged."/>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	207 <param argument="errorcorrectratio" type="integer" min="0" value="140" label="Depth ratio" help="Adjacent kmers with a depth ratio of at least this much between will be classified as an error."/>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	208 <param argument="echighthresh" type="integer" min="0" value="22" label="Threshold for high kmer" help="A kmer at this or above may be considered non-error."/>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	209 <param argument="eclowthresh" type="integer" min="0" value="2" label="Threshold for low kmer." help="kmers at this depth or below will be considered as errors."/>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	210 <param argument="eccmaxqual" type="integer" min="0" value="127" label="Do not correct bases with quality above this value."/>
0 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 <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	218 <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	219 <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	220 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	221 </inputs>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	222 <outputs>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	223 <data name="output_normalised_R1" format_source="read1" from_work_dir="normalised_R1.fastq" label="${tool.name} on ${on_string} (normalised R1 reads)">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	224 <filter>input_type_cond['input_type'] != 'paired'</filter>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	225 </data>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	226 <data name="output_normalised_R2" format_source="read2" from_work_dir="normalised_R2.fastq" label="${tool.name} on ${on_string} (normalised R2 reads)">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	227 <filter>input_type_cond['input_type'] == 'PE_2files'</filter>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	228 </data>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	229 <collection name="output_pair" type="paired" format_source="reads_collection" label="${tool.name} on ${on_string} (normalised reads)">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	230 <filter>input_type_cond['input_type'] == 'paired'</filter>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	231 <data name="forward" from_work_dir="normalised_R1.fastq" label="${tool.name} on ${on_string} (normalised R1 reads)"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	232 <data name="reverse" from_work_dir="normalised_R2.fastq" label="${tool.name} on ${on_string} (normalised R2 reads)"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	233 </collection>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	234 <data name="output_discarded" format="fastqsanger" from_work_dir="discarded.fastq" label="${tool.name} on ${on_string} (discarded reads)">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	235 <filter>output_options['save_discarded_reads'] is True</filter>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	236 </data>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	237 <data name="kmer_hist_input" format="tabular" from_work_dir="kmer_hist_input.tabular" label="${tool.name} on ${on_string} (kmer histogram input)">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	238 <filter>output_options['save_kmer_hists'] is True</filter>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	239 </data>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	240 <data name="kmer_hist_output" format="tabular" from_work_dir="kmer_hist_output.tabular" label="${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	241 <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	242 </data>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	243 </outputs>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	244 <tests>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	245 <!-- Single end sequencing -->
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	246 <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	247 <param name="input_type" value="single_end"/>
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	248 <param name="read1" value="bbnorm/input_R1.fastq" ftype="fastqsanger"/>
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	249 <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	250 <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	251 <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	252 <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	253 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	254 <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	255 </test>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	256 <!-- 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	257 <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	258 <param name="input_type" value="single_end"/>
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	259 <param name="read1" value="bbnorm/input_R1.fastq.gz" ftype="fastqsanger.gz"/>
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	260 <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	261 <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	262 <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	263 <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	264 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	265 <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	266 </test>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	267 <!-- 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	268 <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	269 <param name="input_type" value="PE_1file"/>
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	270 <param name="read1" value="bbnorm/input_interleaved.fastq" ftype="fastqsanger"/>
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	271 <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	272 <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	273 <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	274 <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	275 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	276 <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	277 <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	278 <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	279 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	280 <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	281 <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	282 <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	283 <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	284 </test>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	285 <!-- 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	286 <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	287 <param name="input_type" value="PE_2files"/>
1 aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	288 <param name="read1" value="bbnorm/input_R1.fastq" ftype="fastqsanger"/>
aa7b97bc2f3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb iuc parents: 0 diff changeset	289 <param name="read2" value="bbnorm/input_R2.fastq" ftype="fastqsanger"/>
0 ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	290 <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	291 <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	292 <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	293 <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	294 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	295 <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	296 <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	297 </test>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	298 <!-- Paired end collection -->
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	299 <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	300 <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	301 <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	302 <collection type="paired">
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	303 <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	304 <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	305 </collection>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	306 </param>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	307 <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	308 <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	309 <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	310 <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	311 </section>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	312 <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	313 <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	314 <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	315 </output_collection>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	316 </test>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	317 </tests>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	318 <help>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	319 What it does
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	320
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	321 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	322
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 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	326
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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	336 FFFFFFFFFFFFFFFEFFFFFFEFFDD
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	337 @read_header_3
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	338 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	340 FFFFFFFFFFFCEFFEFFFFFFEFFEE
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	341 @read_header_4
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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	344 FFFFFDDFFFFFFFFEFFFFFFEFFEF
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	345 @read_header_5
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	346 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	348 FFFFFEFFFFEEFFFEFFFFFFDFFFF
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	349 @read_header_6
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	350 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	352 FFFFFFFFFFFFFFFEFFFFFFEFFD
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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	355 output.fastq::
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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	360 FFFFFFFFFFFFFFFEFFFFFF,FFE
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	361 @read_header_2
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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 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	368 FFFFFFFFFFFCEFFEFFFFFFEFFEE
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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	372 FFFFFFFFFFFFFFFEFFFFFFEFFD
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	373
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 Indications
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	376
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	377 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	378
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 Contraindications
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	381
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	382 * 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	383 * 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	384 * 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	385 * 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	386 * 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	387
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	388 </help>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	389 <expand macro="citations"/>
ac326f8788a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce iuc parents: diff changeset	390 </tool>

Mercurial > repos > iuc > bbtools_bbnorm

annotate bbnorm.xml @ 5:71bd084b9eba draft default tip