purge_dups: purge_dups.xml comparison

comparison purge_dups.xml @ 4:a315c25dc813 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"

author	iuc
date	Tue, 12 Oct 2021 19:07:05 +0000
parents	76d4cbefff85
children

comparison

equal deleted inserted replaced

-:76d4cbefff85
+:a315c25dc813
 <tool id="purge_dups" name="Purge overlaps" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
 <description>and haplotigs in an assembly based on read depth (purge_dups)</description>
 <macros>
-<token name="@TOOL_VERSION@">1.2.5</token>
+<import>macros.xml</import>
-<token name="@VERSION_SUFFIX@">3</token>
-<xml name="trimmers">
-<section name="section_hist" title="Histogram plot options" >
-<!--<param name="cutoffs_his" type="data" optional="true" format="txt" label="Read depth cutoffs file" />-->
-<param argument="--ymin" type="integer" optional="true" min="0" label="Specify a minimum for the Y axis"/>
-<param argument="--ymax" type="integer" optional="true" label="Specify a maximum for the Y axis"/>
-<param argument="--xmin" type="integer" optional="true" min="0" label="Specify a minimum for the X axis"/>
-<param argument="--xmax" type="integer" optional="true" label="Specify a maximum for the X axis"/>
-<param argument="--title" type="text" value="Read depth histogram plot" label="Histogram title"/>
-</section>
-</xml>
-<token name="@HIST_PLOT@"><![CDATA[
-python '$__tool_directory__/hist_plot.py'
---cutoffs cutoffs.tsv
-#if $function_select.section_hist.ymin
---ymin $function_select.section_hist.ymin
-#end if
-#if $function_select.section_hist.ymax
---ymax $function_select.section_hist.ymax
-#end if
-#if $function_select.section_hist.xmin
---xmin $function_select.section_hist.xmin
-#end if
-#if $function_select.section_hist.xmax
---xmax $function_select.section_hist.xmax
-#end if
-#if $function_select.section_hist.title
---title '${function_select.section_hist.title}'
-#end if
-depth.stat hist.png
-]]></token>
-<token name="@CALCUTS@"><![CDATA[
-calcuts
-#if $function_select.section_calcuts.min_depth:
--f $function_select.section_calcuts.min_depth
-#end if
-#if $function_select.section_calcuts.low_depth:
--l $function_select.section_calcuts.low_depth
-#end if
-#if $function_select.section_calcuts.transition:
--m $function_select.section_calcuts.transition
-#end if
-#if $function_select.section_calcuts.upper_depth:
--u $function_select.section_calcuts.upper_depth
-#end if
-$function_select.section_calcuts.ploidy
-]]></token>
-<xml name="calcuts">
-<section name="section_calcuts" title="Calcuts options">
-<param name="min_depth" type="float" label="Minimum depth count fraction to maximum depth coun" min="0" max="1" argument="-f" optional="true" help="Default = 0.1"/>
-<param name="low_depth" label="Lower bound for read depth" type="integer" argument="-l" optional="true"/>
-<param name="transition" label="Transition between haploid and diploid" type="integer" argument="-m" optional="true"/>
-<param name="upper_depth" label="Upper bound for read depth" type="integer" argument="-u" optional="true"/>
-<param name="ploidy" argument="-d" type="select" label="Ploidy">
-<option value="-d 0" selected="true">Diploid [0]</option>
-<option value="-d 1">Haploid [1]</option>
-</param>
-</section>
-</xml>
 </macros>
-<requirements>
+<expand macro="xrefs"/>
-<requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement>
+<expand macro="requirements"/>
-<requirement type="package" version="3.4.2">matplotlib-base</requirement>
-</requirements>
 <command detect_errors="exit_code"><![CDATA[
 #if $function_select.functions == 'purge_dups':
 #for $i, $file in enumerate($function_select.input):
 #if $file.is_of_type("paf"):
 gzip -c '${file}' > '${i}.gz' &&
 -c '${function_select.coverage}'
 #end if
 #if $function_select.cutoffs:
 -T '${function_select.cutoffs}'
 #end if
-#if $function_select.min_bad:
+-f $function_select.min_bad
--f $function_select.min_bad
+-a $function_select.min_align
-#end if
+-b $function_select.min_match
-#if $function_select.min_align:
+-m $function_select.min_chain
--a $function_select.min_align
+-M $function_select.max_gap
-#end if
-#if $function_select.min_match:
--b $function_select.min_match
-#end if
-#if $function_select.min_chain:
--m $function_select.min_chain
-#end if
-#if $function_select.max_gap:
--M $function_select.max_gap
-#end if
 #if $function_select.double_chain.chaining_rounds == 'two':
 -2
-#if $function_select.double_chain.max_gap_2:
+-G $function_select.double_chain.max_gap_2
--G $function_select.double_chain.max_gap_2
-#end if
 #end if
-#if $function_select.min_chain_score:
+-l $function_select.min_chain_score
--l $function_select.min_chain_score
+-E $function_select.max_extend
-#end if
-#if $function_select.max_extend:
--E $function_select.max_extend
-#end if
 #for $i, $file in enumerate($function_select.input):
 '${i}.gz'
 #end for
 > dups.bed 2> purge_dups.log
 #else if $function_select.functions == 'split_fa':
 split_fa
-#if $function_select.split:
--n $function_select.split
-#end if
 '${function_select.input}' > split.fasta
 #else if $function_select.functions == 'pbcstat':
 #for $i, $file in enumerate($function_select.input):
 #if $file.is_of_type('paf'):
 gzip -c '${file}' > '${i}.gz' &&
 #else
 ln -s '${file}' '${i}.gz' &&
 #end if
 #end for
 pbcstat
-#if $function_select.max_cov:
+-M $function_select.pbcstat_options.max_cov
--M $function_select.max_cov
+-f $function_select.pbcstat_options.min_map_ratio
+#if $function_select.pbcstat_options.min_map_qual:
+-q $function_select.pbcstat_options.min_map_qual
 #end if
-#if $function_select.min_map_ratio:
+-l $function_select.pbcstat_options.flank
--f $function_select.min_map_ratio
+$function_select.pbcstat_options.primary_alignments
-#end if
-#if $function_select.min_map_qual:
--q $function_select.min_map_qual
-#end if
-#if $function_select.flank:
--l $function_select.flank
-#end if
-$function_select.primary_alignments
 #for $i, $file in enumerate($function_select.input):
 '${i}.gz'
 #end for
 && mv PB.stat depth.stat
 && @CALCUTS@ depth.stat > cutoffs.tsv 2>calcuts.log
 && @HIST_PLOT@
 #else if $function_select.functions == 'ngscstat':
 ngscstat
-#if $function_select.min_align_qual:
+-q $function_select.ngscstat_options.min_align_qual
--q $function_select.min_align_qual
-#end if
 ##        #if $function_select.max_depth:
 ##            -M $function_select.max_depth
 ##        #end if
-#if $function_select.max_insert:
+-L $function_select.ngscstat_options.max_insert
--L $function_select.max_insert
-#end if
 '${function_select.input}'
 && mv TX.stat depth.stat
 && @CALCUTS@ depth.stat > cutoffs.tsv 2>calcuts.log
 && @HIST_PLOT@
 #else if $function_select.functions == 'calcuts':
 @CALCUTS@ '${function_select.input}' > cutoffs.tsv 2>calcuts.log
 #else if $function_select.functions == 'get_seqs':
 get_seqs
-$function_select.coverage
+$function_select.advanced_options.coverage
-$function_select.haplotigs
+$function_select.advanced_options.haplotigs
-$function_select.end_trim
+$function_select.advanced_options.end_trim
-$function_select.split
+$function_select.advanced_options.split
-#if $function_select.length:
+-l $function_select.advanced_options.length
--l $function_select.length
+-m $function_select.advanced_options.min_ratio
-#end if
+-g $function_select.advanced_options.min_gap
-#if $function_select.min_ratio:
--m $function_select.min_ratio
-#end if
-#if $function_select.min_gap:
--g $function_select.min_gap
-#end if
 '${function_select.bed_input}' '${function_select.fasta_input}'
 #end if
 ]]></command>
 <inputs>
 <conditional name="function_select">
-<param type="select" name="functions" label="Select the purge_dups function">
+<param type="select" name="functions" label="Function mode">
+<option value="pbcstat">Calculate coverage cutoff, base-level read depth and create read depth histogram for PacBio data (calcuts+pbcstat)</option>
+<option value="ngscstat">Calculate coverage cutoff, base-level read depth and create read depth histogram for Illumina data (calcuts+ngscstat)</option>
+<option value="calcuts">Calculate coverage cutoffs (calcuts)</option>
+<option value="split_fa">Split assembly FASTA files by 'N's (split_fa)</option>
 <option value="purge_dups">Purge haplotigs and overlaps for an assembly (purge_dups)</option>
-<option value="split_fa">Split FASTA file by 'N's (split_fa)</option>
+<option value="get_seqs">Obtain sequences after purging (get_seqs)</option>
-<option value="pbcstat">Calculate coverage cutoff and create read depth histogram and base-levelread depth for PacBio data (calcuts+pbcstats)</option>
-<option value="ngscstat">Calculate coverage cutoff and create read depth histogram and base-level read detph for Illumina data (calcuts+ngscstat)</option>
-<option value="calcuts">calculate coverage cutoffs (calcuts)</option>
-<option value="get_seqs">Obtain seqeuences after purging (get_seqs)</option>
 </param>
 <when value="purge_dups">
 <param name="input" type="data" format="paf,paf.gz" multiple="true" label="PAF input file"/>
-<param name="coverage" type="data" format="tabular" optional="true" argument="-c" label="Base-level coverage file" />
+<param argument="-c" name="coverage" type="data"
-<param name="cutoffs" type="data" format="tabular" label ="Cutoffs file" optional="true" argument="-T"/>
+format="tabular" optional="true" label="Base-level coverage file"
-<param name="min_bad" type="float" min="0" max="1" argument="-f" optional="true" label="Minimum fraction of haploid/diploid/bad/repetitive bases in a sequence" help="Default = 0.8"/>
+help="This file is generated with purge_dups by using the 'Calculate coverage cutoff, base-level
-<param name="min_align" type="integer" label="Minimum alignment score" argument="-a" optional="true"/>
+read depth and create read depth histogram' option"/>
-<param name="min_match" type="integer" label="Minimum max match score" argument="-b" optional="true"/>
+<param argument="-T" name="cutoffs" type="data"
-<param name="min_chain" label="Minimum matching bases for chaining" type="integer" argument="-m" optional="true"/>
+format="tabular" optional="true" label ="Cutoffs file"
-<param name="max_gap" label="Maximum gap size for chaining" type="integer" argument="-M" optional="true"/>
+help="This file is generated with purge_dups by using the 'Calculate coverage cutoff, base-level
+read depth and create read depth histogram' option"/>
+<param argument="-f" name="min_bad" type="float"
+min="0" max="1" value="0.8" label="Minimum fraction of haploid/diploid/bad/repetitive bases in a sequence"
+help="This parameter is set for a suspect haplotigs. If 80% (default value) of a scaffold is high coverage
+(defined by the sixth column of the cutoff file), it's a repetitive contig. If 80% is low coverage (defined
+in the first column of the cutoff file), it's a junk contig. If 80%  is above diploid coverage(defined in
+the fourth column of the cutoff file), it's a diploid, otherwise it's a suspect haplotig"/>
+<param argument="-a" name="min_align" type="integer"
+min="0" value="70" label="Minimum alignment score"
+help="If its alignment score is larger than this parameter and max match score larger than
+the 'mininum max match score' (-b), it is marked as a repeat; if the alignment score is larger than this parameter
+and max match score no larger than the 'mininum max match score', it is marked as a haplotig.
+Otherwise it is left as a candidate primary contig. If after purging, the complete genes reported by BUSCO are
+too low, you can try to increase this parameter"/>
+<param argument="-b" name="min_match" type="integer"
+min="0" value="200" label="Minimum max match score"
+help="If its alignment score is larger than the 'minimum align score' (-a) and max match score larger than
+this parameter, it is marked as a repeat; if the alignment score is larger than the 'minimum
+align'  and max match score no larger than this parameter, it is marked as a haplotig.
+Otherwise it is left as a candidate primary contig."/>
+<param argument="-m" name="min_chain" type="integer"
+min="0" value="500" label="Minimum matching bases for chaining"
+help="In the first round, it will asset chains consistent alignments within this parameter value"/>
+<param argument="-M" name="max_gap" type="integer"
+min="0" value="20000" label="Maximum gap size for chaining"
+help="In the first round, it will asset chains consistent alignments within this parameter value"/>
 <conditional name="double_chain">
 <param type="select" name="chaining_rounds" label="Rounds of chaining">
 <option value="one">1 round</option>
 <option value="two">2 rounds</option>
 </param>
 <when value="two">
-<param name="max_gap_2" argument="-G" optional="true" label="Maximum gap size for second round of chaining" type="integer"/>
+<param argument="-G" name="max_gap_2" type="integer"
+min="0" value="50000" label="Maximum gap size for second round of chaining"
+help="In the second round, it will asset chains consistent alignments within this parameter value"/>
 </when>
 <when value="one"/>
 </conditional>
-<param name="min_chain_score" argument="-l" optional="true" label="Minimum chaining score for a match" type="integer" />
+<param argument="-l" name="min_chain_score" type="integer"
-<param name="max_extend" argument="-E" optional="true" label="Maximum extension for contig ends" type="integer" />
+min="0" value="10000" label="Minimum chaining score for a match"
+help="This parameter control the overlap size. You should decrease its value to allow more overlaps"/>
+<param argument="-E" name="max_extend" type="integer"
+min="0" value="15000" label="Maximum extension for contig ends"
+help="If the chained alignment is within this value to the contig ends, it will extended to the ends"/>
+<param name="log_file" type="boolean" truevalue="true" falsevalue="false" label="Generate log file"/>
 </when>
 <when value="split_fa">
-<param name="input" type="data" format="fasta" label="Base-level coverage file"/>
+<param name="input" type="data" format="fasta,fasta.gz" label="Assembly FASTA file" help="The sequence will be cleaved in those position in which the nucleotides is an 'N' or an 'n'."/>
-<param name="split" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Base-level coverage file" />
+<!-- This option disables the cleaving process, and yield the original sequence
+<param argument="-n" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Block split by N" help="Enable this option if you do not want break your scaffols into contigs."/>
+-->
 </when>
 <when value="pbcstat">
 <param name="input" type="data" format="paf,paf.gz" multiple="true" label="PAF input file"/>
-<param name="max_cov" type="integer" label="Maximum coverage" argument="-M" optional="true"/>
+<section name="pbcstat_options" title="PBCSTAT options" expanded="true">
-<param name="min_map_ratio" argument="-f" type="float" min="0" max="1" value="0" label="Minimum mapping length ratio"/>
+<param argument="-M" name="max_cov" type="integer" min="0" value="500" label="Maximum coverage"/>
-<param name="min_map_qual" type="integer"  argument="-q" optional="true" label="Minimum mapping quality"/>
+<param argument="-f" name="min_map_ratio"  type="float" min="0" max="1" value="0" label="Minimum mapping length ratio"/>
-<param name="flank" type="integer" argument="-l" optional="true" label="Flanking space" />
+<param argument="-q" name="min_map_qual" type="integer"  optional="true" label="Minimum mapping quality"/>
-<param name="primary_alignments" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Use only primary alignments" />
+<param argument="-l" name="flank"  type="integer" min="0" value="0" label="Flanking space" />
+<param argument="-p" name="primary_alignments" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Use only primary alignments" />
+</section>
 <expand macro="calcuts" />
 <expand macro="trimmers"/>
+<expand macro="output_macro">
+<option value="pbcstat_coverage" selected="true">PBCSTAT base coverage</option>
+<option value="pbcstat_wig">PBCSTAT base coverage (WIG)</option>
+<option value="depth_stats">PBCSTAT depths</option>
+</expand>
 </when>
 <when value="ngscstat">
 <param name="input" type="data" format="bam" label="BAM input file"/>
-<param name="min_align_qual" type="integer"  argument="-q" optional="true" label="Minimum alignment quality" />
+<section name="ngscstat_options" title="NGSCSTAT options" expanded="true">
-<!-- Param exists in help text, but isn't actually part of the code. Maybe in the next release? -->
+<param argument="-q" name="min_align_qual" type="integer" min="0" value="30" label="Minimum alignment quality" />
-<!-- <param name="max_depth" type="integer" label="Maximum read depth" argument="-M" optional="true"/> -->
+<!-- Param exists in help text, but isn't actually part of the code. Maybe in the next release? -->
-<param name="max_insert" type="integer"  argument="-L" optional="true" label="Maximum insert size"/>
+<!-- <param name="max_depth" type="integer" label="Maximum read depth" argument="-M" optional="true"/> -->
+<param argument="-L" name="max_insert" type="integer" min="0" value="1000" label="Maximum insert size"/>
+</section>
 <expand macro="calcuts" />
 <expand macro="trimmers"/>
+<expand macro="output_macro">
+<option value="ngscstat_coverage" selected="true">NGSCSTAT base coverage</option>
+</expand>
 </when>
 <when value="calcuts">
-<param name="input" type="data" format="tabular" label="STAT input file"/>
+<param name="input" type="data" format="tabular" label="Depths input file"/>
 <expand macro="calcuts" />
 </when>
 <when value="get_seqs">
-<param name="fasta_input" type="data" format="fasta" label="Fasta input file"/>
+<param name="fasta_input" type="data" format="fasta" label="Assembly FASTA file"/>
-<param name="bed_input" type="data" format="bed" label="Bed input file"/>
+<param name="bed_input" type="data" format="bed" label="BED input file" help="Generated by the 'purge_dups' function mode."/>
-<param name="coverage" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Keep high coverage contigs in the primary contig set"/>
+<section name="advanced_options" title="Advanced options">
-<param name="haplotigs" type="boolean" argument="-a" truevalue="-a" falsevalue="" checked="false" label="Do not add prefix to haplotigs"/>
+<param argument="-c" name="coverage" type="boolean"
-<param name="length" type="integer" argument="-l" optional="true" label="Minimum primary contig length" help="Default: 1000"/>
+truevalue="-c" falsevalue="" checked="false" label="Keep high coverage contigs in the primary contig set"/>
-<param name="min_ratio" type="float" min="0" max="1" argument="-m" optional="true" label="Minimum ratio of remaining primary contig length to the original contig length"/>
+<param argument="-a" name="haplotigs" type="boolean"  truevalue="-a" falsevalue="" checked="false" label="Do not add prefix to haplotigs"/>
-<param name="end_trim" type="boolean" argument="-e" truevalue="-e" falsevalue="" checked="true" label="Trim end sequences" help="Only remove sequences at end of halplotigs If you also want to remove the duplications in the middle, set to false, however that may delete false positive duplications."/>
+<param argument="-l" name="length" type="integer" min="0" value="10000" label="Minimum primary contig length" />
-<param name="split" type="boolean" argument="-s" truevalue="-s" falsevalue="" checked="false" label="Split contigs"/>
+<param argument="-m" name="min_ratio" type="float"
-<param name="min_gap" type="integer" argument="-g" optional="true" help="default=10k" label="Minimum gap size between duplications" />
+min="0" max="1" value="0.05" label="Minimum ratio of remaining primary contig length to the original contig length"/>
+<param argument="-e" name="end_trim" type="boolean"
+truevalue="-e" falsevalue="" checked="true" label="Trim end sequences"
+help="Only remove sequences at end of halplotigs. If you also want to remove the duplications in the middle,
+set to false, however that may delete false positive duplications."/>
+<param argument="-s" name="split" type="boolean"  truevalue="-s" falsevalue="" checked="false" label="Split contigs"/>
+<param argument="-g" name="min_gap" type="integer" min="0" value="10000" label="Minimum gap size between duplications" />
+</section>
 </when>
 </conditional>
 </inputs>
 <outputs>
 <!-- Get Seqs -->
-<data name="get_seqs_hap" format="fasta" from_work_dir="hap.fa" label="${tool.name} on ${on_string}: get seqs haplotype fasta" >
+<data name="get_seqs_hap" format="fasta" from_work_dir="hap.fa" label="${tool.name} on ${on_string}: get_seqs haplotype" >
 <filter>function_select['functions'] == 'get_seqs'</filter>
 </data>
-<data name="get_seqs_purged" format="fasta" from_work_dir="purged.fa" label="${tool.name} on ${on_string}: get seqs purged fasta">
+<data name="get_seqs_purged" format="fasta" from_work_dir="purged.fa" label="${tool.name} on ${on_string}: get_seqs purged sequences">
 <filter>function_select['functions'] == 'get_seqs'</filter>
 </data>
 <!-- Split FA -->
-<data name="split_fasta" format="fasta" from_work_dir="split.fasta" label="${tool.name} on ${on_string}: split fasta">
+<data name="split_fasta" format="fasta" from_work_dir="split.fasta" label="${tool.name} on ${on_string}: split FASTA">
 <filter>function_select['functions'] == 'split_fa'</filter>
 </data>
 <!-- Ngscstat -->
-<data name="ngscstat_cov" format="tabular" from_work_dir="TX.base.cov" label="${tool.name} on ${on_string}: ngscstat base coverage file">
+<data name="ngscstat_cov" format="tabular" from_work_dir="TX.base.cov" label="${tool.name} on ${on_string}: NGSCSTAT base coverage">
 <filter>function_select['functions'] == 'ngscstat'</filter>
-</data>
+<filter>'ngscstat_coverage' in function_select['output_options']</filter>
-<data name="stat_file" format="tabular" from_work_dir="depth.stat"  label="${tool.name} on ${on_string}: stat file">
+</data>
+<data name="stat_file" format="tabular" from_work_dir="depth.stat"  label="${tool.name} on ${on_string}: depths">
 <filter>function_select['functions'] == 'ngscstat' or function_select['functions'] == 'pbcstat'</filter>
+<filter>'depth_stats' in function_select['output_options']</filter>
 </data>
 <!-- Pbcstat -->
-<data name="pbcstat_cov" format="tabular" from_work_dir="PB.base.cov"  label="${tool.name} on ${on_string}: pbcstat base coverage file">
+<data name="pbcstat_cov" format="tabular" from_work_dir="PB.base.cov"  label="${tool.name} on ${on_string}: PBCSTAT base coverage">
 <filter>function_select['functions'] == 'pbcstat'</filter>
-</data>
+<filter>'pbcstat_coverage' in function_select['output_options']</filter>
-<data name="pbcstat_wig" format="wig" from_work_dir="PB.cov.wig" label="${tool.name} on ${on_string}: pbcstat base wig file">
+</data>
+<data name="pbcstat_wig" format="wig" from_work_dir="PB.cov.wig" label="${tool.name} on ${on_string}: PBCSTAT base coverage (WIG)">
 <filter>function_select['functions'] == 'pbcstat'</filter>
+<filter>'pbcstat_wig' in function_select['output_options']</filter>
 </data>
 <data name="hist" format="png" from_work_dir="hist.png" label="${tool.name} on ${on_string}: histogram plot">
 <filter>function_select['functions'] == 'pbcstat' or function_select['functions'] == 'ngscstat'</filter>
+<filter>'histogram' in function_select['output_options']</filter>
 </data>
 <!-- Calcuts -->
-<data name="calcuts_log" format="txt" from_work_dir="calcuts.log" label="${tool.name} on ${on_string}: calcuts log file">
+<data name="calcuts_log" format="txt" from_work_dir="calcuts.log" label="${tool.name} on ${on_string}: calcuts log">
 <filter>function_select['functions'] in ('pbcstat', 'ngscstat', 'calcuts')</filter>
-</data>
+<filter>'calcuts_log' in function_select['output_options']</filter>
-<data name="calcuts_tab" format="tabular" from_work_dir="cutoffs.tsv" label="${tool.name} on ${on_string}: calcuts cutoff file">
+</data>
+<data name="calcuts_cutoff" format="tabular" from_work_dir="cutoffs.tsv" label="${tool.name} on ${on_string}: calcuts cutoff">
 <filter>function_select['functions'] in ('pbcstat', 'ngscstat', 'calcuts')</filter>
+<filter>'calcuts_cutoff' in function_select['output_options']</filter>
 </data>
 <!-- Purge dups -->
-<data name="purge_dups_log" format="txt" from_work_dir="purge_dups.log" label="${tool.name} on ${on_string}: purge_dups log file">
+<data name="purge_dups_log" format="txt" from_work_dir="purge_dups.log" label="${tool.name} on ${on_string}: purge_dups log">
 <filter>function_select['functions'] == 'purge_dups'</filter>
-</data>
+<filter>function_select['log_file']</filter>
-<data name="purge_dups_bed" format="bed" from_work_dir="dups.bed" label="${tool.name} on ${on_string}: purge_dups bed file">
+</data>
+<data name="purge_dups_bed" format="bed" from_work_dir="dups.bed" label="${tool.name} on ${on_string}: purge_dups BED">
 <filter>function_select['functions'] == 'purge_dups'</filter>
 </data>
 </outputs>
 <tests>
-<!-- Purge dups -->
+<!-- Test 1 Purge dups -->
-<test expect_num_outputs="2">
+<test expect_num_outputs="1">
 <conditional name="function_select">
 <param name="functions" value="purge_dups"/>
-<param name="input" value="test.paf"/>
+<param name="input" value="assembly_test.paf"/>
 <param name="coverage" value="test.cov" ftype="tabular"/>
 <param name="cutoffs" value="cutoffs.tsv" ftype="tabular"/>
 <param name="min_bad" value="0.01"/>
 <param name="min_align" value="10"/>
 <param name="min_match" value="100"/>
 <param name="max_gap_2" value="1001"/>
 </conditional>
 <param name="min_chain_score" value="1"/>
 <param name="max_extend" value="100"/>
 </conditional>
-<output name="purge_dups_bed" value="purge_dups_out.bed"/>
+<output name="purge_dups_bed" value="purge_dups_01.bed" ftype="bed"/>
 </test>
-<!-- Purge dups gzip -->
+<!-- Test 2 Purge dups gzip -->
 <test expect_num_outputs="2">
 <conditional name="function_select">
 <param name="functions" value="purge_dups"/>
-<param name="input" value="test.paf.gz" ftype="paf.gz"/>
+<param name="input" value="assembly_test.paf.gz" ftype="paf.gz"/>
 <param name="coverage" value="test.cov" ftype="tabular"/>
 <param name="cutoffs" value="cutoffs.tsv" ftype="tabular"/>
 <param name="min_bad" value="0.01"/>
 <param name="min_align" value="10"/>
 <param name="min_match" value="100"/>
 <param name="chaining_rounds" value="two"/>
 <param name="max_gap_2" value="1001"/>
 </conditional>
 <param name="min_chain_score" value="1"/>
 <param name="max_extend" value="100"/>
-</conditional>
+<param name="log_file" value="true"/>
-<output name="purge_dups_bed" value="purge_dups_out.bed"/>
+</conditional>
-</test>
+<output name="purge_dups_bed" value="purge_dups_02.bed" ftype="bed"/>
-<!-- Purge dups multiple input -->
+<output name="purge_dups_log" value="purge_dups_log_02.txt" ftype="txt"/>
-<test expect_num_outputs="2">
+</test>
+<!-- Test 3 Purge dups multiple input -->
+<test expect_num_outputs="1">
 <conditional name="function_select">
 <param name="functions" value="purge_dups"/>
-<param name="input" value="test.paf,test2.paf.gz"/>
+<param name="input" value="assembly_test.paf,test2.paf.gz"/>
 </conditional>
-<output name="purge_dups_bed" value="purge_dups_out_2.bed"/>
+<output name="purge_dups_bed" value="purge_dups_03.bed" ftype="bed"/>
 </test>
-<!-- Split fa -->
+<!-- Test 4 Split fa -->
 <test expect_num_outputs="1">
 <conditional name="function_select">
 <param name="functions" value="split_fa"/>
-<param name="input" value="test.fasta"/>
+<param name="input" value="assembly_test.fasta"/>
-<param name="split" value="-n"/>
+</conditional>
-</conditional>
+<output name="split_fasta" value="split_04.fasta" ftype="fasta"/>
-<output name="split_fasta" value="split_out.fasta"/>
+</test>
-</test>
+<!-- Test 5 pbcstat -->
-<!-- pbcstat -->
 <test expect_num_outputs="6">
 <conditional name="function_select">
 <param name="functions" value="pbcstat"/>
-<param name="input" value="test.paf"/>
+<param name="input" value="assembly_test.paf"/>
-<param name="max_cov" value="1000"/>
+<section name="pbcstat_options">
-<param name="min_map_ratio" value="0.01"/>
+<param name="max_cov" value="1000"/>
-<param name="min_map_qual" value="1"/>
+<param name="min_map_ratio" value="0.01"/>
-<param name="flank" value="1"/>
+<param name="min_map_qual" value="1"/>
-<param name="primary_alignments" value="-p"/>
+<param name="flank" value="1"/>
+<param name="primary_alignments" value="-p"/>
+</section>
 <section name="section_calcuts">
 <param name="min_depth" value="0.01"/>
 <param name="low_depth" value="1"/>
 <param name="transition" value="1"/>
 <param name="upper_depth" value="100"/>
 <param name="ploidy" value="-d 0"/>
 </section>
-</conditional>
+<param name="output_options" value="pbcstat_coverage,pbcstat_wig,depth_stats,histogram,calcuts_cutoff,calcuts_log"/>
-<output name="calcuts_tab" value="calcuts_out.tsv"/>
+</conditional>
-<output name="pbcstat_cov" value="out.cov"/>
+<output name="calcuts_cutoff" value="calcuts_cutoff_05.tabular" ftype="tabular"/>
-<output name="pbcstat_wig" value="out.wig"/>
+<output name="calcuts_log" value="calcuts_log_05.txt" ftype="txt"/>
-<output name="stat_file" value="pbcstats.tabular"/>
+<output name="pbcstat_cov" value="pbcstat_cov_05.tabular" ftype="tabular"/>
-<output name="hist" value="hist.png" ftype="png" compare="sim_size"/>
+<output name="pbcstat_wig" value="pbcstat_cov_05.wig" ftype="wig"/>
-</test>
+<output name="stat_file" value="pbcstats_05.tabular" ftype="tabular"/>
-<!-- pbcstat gzip -->
+<output name="hist" value="hist_05.png" ftype="png" compare="sim_size"/>
-<test expect_num_outputs="6">
+</test>
+<!-- Test 6 pbcstat gzip -->
+<test expect_num_outputs="2">
 <conditional name="function_select">
 <param name="functions" value="pbcstat"/>
-<param name="input" value="test.paf.gz" ftype="paf.gz"/>
+<param name="input" value="assembly_test.paf.gz" ftype="paf.gz"/>
-<param name="max_cov" value="1000"/>
+<section name="pbcstat_options">
-<param name="min_map_ratio" value="0.01"/>
+<param name="max_cov" value="1000"/>
-<param name="min_map_qual" value="1"/>
+<param name="min_map_ratio" value="0.01"/>
-<param name="flank" value="1"/>
+<param name="min_map_qual" value="1"/>
-<param name="primary_alignments" value="-p"/>
+<param name="flank" value="1"/>
+<param name="primary_alignments" value="-p"/>
+</section>
 <section name="section_calcuts">
 <param name="min_depth" value="0.01"/>
 <param name="low_depth" value="1"/>
 <param name="transition" value="1"/>
 <param name="upper_depth" value="100"/>
 <param name="ploidy" value="-d 0"/>
 </section>
 </conditional>
-<output name="calcuts_tab" value="calcuts_out.tsv"/>
+<param name="output_options" value="pbcstat_coverage,calcuts_cutoff"/>
-<output name="pbcstat_cov" value="out.cov"/>
+<output name="calcuts_cutoff" value="calcuts_cutoff_06.tabular" ftype="tabular"/>
-<output name="pbcstat_wig" value="out.wig"/>
+<output name="pbcstat_cov" value="pbcstat_cov_06.tabular" ftype="tabular"/>
 </test>
-<!-- Pbcstat multiple input -->
+<!-- Test 7 Pbcstat multiple input -->
-<test expect_num_outputs="6">
+<test expect_num_outputs="2">
 <conditional name="function_select">
 <param name="functions" value="pbcstat"/>
-<param name="input" value="test.paf,test2.paf.gz"/>
+<param name="input" value="assembly_test.paf,test2.paf.gz"/>
 <section name="section_calcuts">
 <param name="min_depth" value="0.01"/>
 <param name="low_depth" value="1"/>
 <param name="transition" value="1"/>
 <param name="upper_depth" value="100"/>
 <param name="ploidy" value="-d 0"/>
 </section>
 </conditional>
-<output name="calcuts_tab" value="calcuts_out.tsv"/>
+<param name="output_options" value="pbcstat_coverage,calcuts_cutoff"/>
-<output name="pbcstat_cov" value="out2.cov"/>
+<output name="calcuts_cutoff" value="calcuts_cutoff_07.tabular" ftype="tabular"/>
-<output name="stat_file" value="pbcstats2.tabular"/>
+<output name="pbcstat_cov" value="pbcstat_cov_07.tabular" ftype="tabular"/>
-<output name="pbcstat_wig" value="out2.wig"/>
+</test>
-</test>
+<!-- Test 8 ngscstat -->
-<!-- ngscstat -->
+<test expect_num_outputs="2">
-<test expect_num_outputs="5">
 <conditional name="function_select">
 <param name="functions" value="ngscstat"/>
 <param name="input" value="test.bam"/>
-<param name="min_align_qual" value="10"/>
+<section name="ngscstat_options">
-<param name="max_insert" value="100"/>
+<param name="min_align_qual" value="10"/>
+<param name="max_insert" value="100"/>
+</section>
 <section name="section_calcuts">
 <param name="min_depth" value="0.01"/>
 <param name="low_depth" value="1"/>
 <param name="transition" value="1"/>
 <param name="upper_depth" value="100"/>
 <param name="ploidy" value="-d 0"/>
 </section>
 </conditional>
-<output name="calcuts_tab" value="calcuts_out.tsv"/>
+<param name="output_options" value="ngscstat_coverage,calcuts_cutoff"/>
-<output name="ngscstat_cov" value="ngsc_out.cov"/>
+<output name="calcuts_cutoff" value="calcuts_cutoff_08.tabular" ftype="tabular"/>
-<output name="stat_file" value="tx_stats.tabular"/>
+<output name="ngscstat_cov" value="ngsc_cov_08.tabular" ftype="tabular"/>
-<output name="hist" value="hist.png" ftype="png" compare="sim_size"/>
+</test>
-</test>
+<!-- Test 9 Calcuts -->
-<!-- Calcuts -->
 <test expect_num_outputs="2">
 <conditional name="function_select">
 <param name="functions" value="calcuts"/>
 <param name="input" value="test.stat"/>
 <section name="section_calcuts">
 <param name="transition" value="1"/>
 <param name="upper_depth" value="100"/>
 <param name="ploidy" value="-d 0"/>
 </section>
 </conditional>
-<output name="calcuts_tab" value="calcuts_out.tsv"/>
+<output name="calcuts_cutoff" value="calcuts_cutoff_09.tabular" ftype="tabular"/>
-</test>
+<output name="calcuts_log" value="calcuts_log_09.txt" ftype="txt"/>
-<!-- Get seqs -->
+</test>
+<!-- Test 10 Get seqs -->
 <test expect_num_outputs="2">
 <conditional name="function_select">
 <param name="functions" value="get_seqs"/>
 <param name="fasta_input" value="split_out.fasta"/>
 <param name="bed_input" value="dups.bed"/>
-<param name="coverage" value="-c"/>
+<section name="advanced_options">
-<param name="length" value="10"/>
+<param name="coverage" value="-c"/>
-<param name="haplotigs" value="-a"/>
+<param name="length" value="10"/>
-<param name="min_ratio" value=".01"/>
+<param name="haplotigs" value="-a"/>
-<param name="end_trim" value="-e"/>
+<param name="min_ratio" value=".01"/>
-<param name="split" value="-s"/>
+<param name="end_trim" value="-e"/>
-<param name="min_gap" value="100000"/>
+<param name="split" value="-s"/>
-</conditional>
+<param name="min_gap" value="100000"/>
-<output name="get_seqs_purged" value="purged_out.fa"/>
+</section>
-</test>
+</conditional>
-<!-- pbcstat histogram options-->
+<output name="get_seqs_purged" value="get_seqs_purged_10.fa" ftype="fasta"/>
-<test expect_num_outputs="6">
+<output name="get_seqs_hap" value="get_seqs_hap_10.fa" ftype="fasta"/>
+</test>
+<!-- Test 11 pbcstat histogram options-->
+<test expect_num_outputs="1">
 <conditional name="function_select">
 <param name="functions" value="pbcstat"/>
-<param name="input" value="test.paf"/>
+<param name="input" value="assembly_test.paf"/>
-<param name="max_cov" value="1000"/>
+<section name="pbcstat_options">
-<param name="min_map_ratio" value="0.01"/>
+<param name="max_cov" value="1000"/>
-<param name="min_map_qual" value="1"/>
+<param name="min_map_ratio" value="0.01"/>
-<param name="flank" value="1"/>
+<param name="min_map_qual" value="1"/>
-<param name="primary_alignments" value="-p"/>
+<param name="flank" value="1"/>
+<param name="primary_alignments" value="-p"/>
+</section>
 <section name="section_calcuts">
 <param name="min_depth" value="0.01"/>
 <param name="low_depth" value="1"/>
 <param name="transition" value="1"/>
 <param name="upper_depth" value="100"/>
 <param name="ymax" value="100"/>
 <param name="xmax" value="100"/>
 <param name="cutoffs_his" value="calcuts_out.tsv"/>
 </section>
 </conditional>
-<output name="calcuts_tab" value="calcuts_out.tsv"/>
+<param name="output_options" value="histogram"/>
-<output name="pbcstat_cov" value="out_hist_options.cov"/>
+<output name="hist" value="hist_11.png" ftype="png" compare="sim_size"/>
-<output name="pbcstat_wig" value="out_hist_options.wig"/>
-<output name="stat_file" value="pbcstats_hist_options.tabular"/>
-<output name="hist" value="hist_options.png" ftype="png" compare="sim_size"/>
 </test>
 </tests>
 <help><![CDATA[
 .. class:: infomark
-**What it does**
+**Purpose**
 The purge_dups tools are designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.
+purge_dups can significantly improve genome assemblies by removing overlaps and haplotigs caused by sequence divergence
+in heterozygous regions. This both removes false duplications in primary draft assemblies while retaining completeness and sequence
+integrity, and can improve scaffolding.
+----
+.. class:: infomark
+**Pipeline Guide**
+Given a primary assembly, and an alternative assembly (optional, if you have one), follow the steps shown below to build your
+own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 5 is optional,
+we highly recommend our users to do so, because assemblers may produce overrepresented sequences. In such a case, the final
+step 5 can be applied to remove those seqeuences.
+- Step 1: Calculate the coverage cutoffs and base coverages.
+- Step 2: Split an assembly with the **split_fasfa** function and do a self-self alignment by using minimap2.
+- Step 3: Purge haplotigs and overlaps with the **purge_dups** function.
+- Step 4: Get purged primary and haplotig sequences from the draft assembly with the **get_seqs** function.
+- Step 5: Merge hap.fa file, generated in the previous step, and the alternate assembly, and redo the above steps to get a decent haplotig set.
+----
+.. class:: infomark
+**Limitations**
+- Read depth cutoffs calculation: the coverage cutoffs can be larger for a low heterozygosity species, which causes the purged assembly size smaller than expected. In such a case, please use script/hist_plot.py to make the histogram plot and set coverage cutoffs manually.
+- Repeats: purge_dups has a limited ability to process repeats.
+----
+.. class:: infomark
+**Purged assembly validation**
+There are many ways to validate the purged assembly. One way is to make a coverage plot for it, the 2nd way is to run `BUSCO <https://busco.ezlab.org/>`_. A thid option is to use `Merqury <https://github.com/marbl/merqury>`_
 ]]></help>
-<citations>
+<expand macro="citations"/>
-<citation type="doi">10.1093/bioinformatics/btaa025</citation>
-</citations>
 </tool>

Mercurial > repos > iuc > purge_dups

comparison purge_dups.xml @ 4:a315c25dc813 draft