Mercurial > repos > iuc > purge_dups
diff purge_dups.xml @ 0:8ec117da1796 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
| author | iuc |
|---|---|
| date | Fri, 05 Feb 2021 17:52:51 +0000 |
| parents | |
| children | 29151e779524 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/purge_dups.xml Fri Feb 05 17:52:51 2021 +0000 @@ -0,0 +1,330 @@ +<tool id="purge_dups" name="Purge haplotigs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> + <description>and overlaps in an assembly based on read depth</description> + <macros> + <token name="@TOOL_VERSION@">1.2.5</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if $function_select.functions == "purge_dups": + purge_dups + #if $function_select.coverage: + -c '$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 + #end if + #if $function_select.min_align: + -a $function_select.min_align + #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 + #end if + #end if + #if $function_select.min_chain_score: + -l $function_select.min_chain_score + #end if + #if $function_select.max_extend: + -E $function_select.max_extend + #end if + '$function_select.input' > 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": + pbcstat + #if $function_select.max_cov: + -M $function_select.max_cov + #end if + #if $function_select.min_map_ratio: + -f $function_select.min_map_ratio + #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 + $function_select.primary_alignments + '$function_select.input' + #else if $function_select.functions == "ngscstat": + ngscstat + #if $function_select.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 $function_select.max_insert + #end if + '$function_select.input' + #else if $function_select.functions == "calcuts": + calcuts + #if $function_select.min_depth: + -f $function_select.min_depth + #end if + #if $function_select.low_depth: + -l $function_select.low_depth + #end if + #if $function_select.transition: + -m $function_select.transition + #end if + #if $function_select.upper_depth: + -u $function_select.upper_depth + #end if + $function_select.ploidy + '$function_select.input' > cutoffs.tsv 2>calcuts.log + #else if $function_select.functions == "get_seqs": + get_seqs + $function_select.coverage + $function_select.haplotigs + $function_select.end_trim + $function_select.split + #if $function_select.length: + -l $function_select.length + #end if + #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"> + <option value="purge_dups">purge haplotigs and overlaps for an assembly</option> + <option value="split_fa">split FASTA file by 'N's</option> + <option value="pbcstat">create read depth histogram and base-level read depth for pacbio data</option> + <option value="ngscstat">create read depth histogram and base-level read detph for illumina data</option> + <option value="calcuts">calculate coverage cutoffs</option> + <option value="get_seqs">obtain seqeuences after purging</option> + </param> + <when value="purge_dups"> + <param name="input" type="data" format="paf" label="PAF input file"/> + <param name="coverage" type="data" format="tabular" optional="true" argument="-c" label="Base-level coverage file" /> + <param name="cutoffs" type="data" format="tabular" label ="Cutoffs file" optional="true" argument="-T"/> + <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"/> + <param name="min_align" type="integer" label="Minimum alignment score" argument="-a" optional="true"/> + <param name="min_match" type="integer" label="Minimum max match score" argument="-b" optional="true"/> + <param name="min_chain" label="Minimum matching bases for chaining" type="integer" argument="-m" optional="true"/> + <param name="max_gap" label="Maximum gap size for chaining" type="integer" argument="-M" optional="true"/> + <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"/> + </when> + <when value="one"/> + </conditional> + <param name="min_chain_score" argument="-l" optional="true" label="Minimum chaining score for a match" type="integer" /> + <param name="max_extend" argument="-E" optional="true" label="Maximum extension for contig ends" type="integer" /> + </when> + <when value="split_fa"> + <param name="input" type="data" format="fasta" label="Base-level coverage file"/> + <param name="split" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Base-level coverage file" /> + </when> + <when value="pbcstat"> + <param name="input" type="data" format="paf" label="PAF input file"/> + <param name="max_cov" type="integer" label="Maximum coverage" argument="-M" optional="true"/> + <param name="min_map_ratio" argument="-f" type="float" min="0" max="1" value="0" label="Minimum mapping length ratio"/> + <param name="min_map_qual" type="integer" argument="-q" optional="true" label="Minimum mapping quality"/> + <param name="flank" type="integer" argument="-l" optional="true" label="Flanking space" /> + <param name="primary_alignments" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Use only primary alignments" /> + </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" /> + <!-- Param exists in help text, but isn't actually part of the code. Maybe in the next release? --> + <!-- <param name="max_depth" type="integer" label="Maximum read depth" argument="-M" optional="true"/> --> + <param name="max_insert" type="integer" argument="-L" optional="true" label="Maximum insert size"/> + </when> + <when value="calcuts"> + <param name="input" type="data" format="tabular" label="STAT input file"/> + <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> + </when> + <when value="get_seqs"> + <param name="fasta_input" type="data" format="fasta" label="Fasta input file"/> + <param name="bed_input" type="data" format="bed" label="Bed input file"/> + <param name="coverage" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Keep high coverage contigs in the primary contig set"/> + <param name="haplotigs" type="boolean" argument="-a" truevalue="-a" falsevalue="" checked="false" label="Do not add prefix to haplotigs"/> + <param name="length" type="integer" argument="-l" optional="true" label="Minimum primary contig length" help="Default: 1000"/> + <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 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 name="split" type="boolean" argument="-s" truevalue="-s" falsevalue="" checked="false" label="Split contigs"/> + <param name="min_gap" type="integer" argument="-g" optional="true" help="default=10k" label="Minimum gap size between duplications" /> + </when> + </conditional> + </inputs> + <outputs> + <!-- Get Seqs --> + <data name="get_seqs_hap" format="fasta" from_work_dir="hap.fa" label="${tool.name} on ${on_string}: get seqs haplotype fasta" > + <filter>function_select['functions'] == 'get_seqs'</filter> + </data> + <data name="get_seqs_purged" format="fasta" from_work_dir="purged.fa" label="${tool.name} on ${on_string}: get seqs purged fasta"> + <filter>function_select['functions'] == 'get_seqs'</filter> + </data> + <!-- Split FA --> + <data name="split_fasta" format="fasta" from_work_dir="split.fasta" label="${tool.name} on ${on_string}: split fasta"> + <filter>function_select['functions'] == 'split_fa'</filter> + </data> + <!-- Ngscstat --> + <data name="ngscstat_cov" format="tabular" from_work_dir="TX.base.cov" label="${tool.name} on ${on_string}: ngscstat base coverage file"> + <filter>function_select['functions'] == 'ngscstat'</filter> + </data> + <data name="ngscstat_stat" format="tabular" from_work_dir="TX.stat" label="${tool.name} on ${on_string}: ngscstat stat file"> + <filter>function_select['functions'] == 'ngscstat'</filter> + </data> + <!-- Pbcstat --> + <data name="pbcstat_cov" format="tabular" from_work_dir="PB.base.cov" label="${tool.name} on ${on_string}: pbcstat base coverage file"> + <filter>function_select['functions'] == 'pbcstat'</filter> + </data> + <data name="pbcstat_wig" format="wig" from_work_dir="PB.cov.wig" label="${tool.name} on ${on_string}: pbcstat base wig file"> + <filter>function_select['functions'] == 'pbcstat'</filter> + </data> + <data name="pbcstat_stat" format="tabular" from_work_dir="PB.stat" label="${tool.name} on ${on_string}: stat file"> + <filter>function_select['functions'] == 'pbcstat'</filter> + </data> + <!-- Calcuts --> + <data name="calcuts_log" format="txt" from_work_dir="calcuts.log" label="${tool.name} on ${on_string}: calcuts log file"> + <filter>function_select['functions'] == 'calcuts'</filter> + </data> + <data name="calcuts_tab" format="tabular" from_work_dir="cutoffs.tsv" label="${tool.name} on ${on_string}: calcuts cutoff file"> + <filter>function_select['functions'] == 'calcuts'</filter> + </data> + <!-- Purge dups --> + <data name="purge_dups_log" format="txt" from_work_dir="purge_dups.log" label="${tool.name} on ${on_string}: purge_dups log file"> + <filter>function_select['functions'] == 'purge_dups'</filter> + </data> + <data name="purge_dups_bed" format="bed" from_work_dir="dups.bed" label="${tool.name} on ${on_string}: purge_dups bed file"> + <filter>function_select['functions'] == 'purge_dups'</filter> + </data> + </outputs> + <tests> + <!-- Purge dups --> + <test expect_num_outputs="2"> + <conditional name="function_select"> + <param name="functions" value="purge_dups"/> + <param name="input" value="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="min_chain" value="1"/> + <param name="max_gap" value="1000"/> + <conditional name="double_chain"> + <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> + <output name="purge_dups_bed" value="purge_dups_out.bed"/> + </test> + <!-- 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="split" value="-n"/> + </conditional> + <output name="split_fasta" value="split_out.fasta"/> + </test> + <!-- pbcstat --> + <test expect_num_outputs="3"> + <conditional name="function_select"> + <param name="functions" value="pbcstat"/> + <param name="input" value="test.paf"/> + <param name="max_cov" value="1000"/> + <param name="min_map_ratio" value="0.01"/> + <param name="min_map_qual" value="1"/> + <param name="flank" value="1"/> + <param name="primary_alignments" value="-p"/> + </conditional> + <output name="pbcstat_cov" value="out.cov"/> + <output name="pbcstat_wig" value="out.wig"/> + </test> + <!-- ngscstat --> + <test expect_num_outputs="2"> + <conditional name="function_select"> + <param name="functions" value="ngscstat"/> + <param name="input" value="test.bam"/> + <param name="min_align_qual" value="10"/> + <param name="max_insert" value="100"/> + </conditional> + <output name="ngscstat_cov" value="ngsc_out.cov"/> + </test> + <!-- Calcuts --> + <test expect_num_outputs="2"> + <conditional name="function_select"> + <param name="functions" value="calcuts"/> + <param name="input" value="test.stat"/> + <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"/> + </conditional> + <output name="calcuts_tab" value="calcuts_out.tsv"/> + </test> + <!-- 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"/> + <param name="length" value="10"/> + <param name="haplotigs" value="-a"/> + <param name="min_ratio" value=".01"/> + <param name="end_trim" value="-e"/> + <param name="split" value="-s"/> + <param name="min_gap" value="100000"/> + </conditional> + <output name="get_seqs_purged" value="purged_out.fa"/> + </test> + </tests> + <help><![CDATA[ + .. class:: infomark + + **What it does** + + The purge_dups tools are designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth. + + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btaa025</citation> + </citations> +</tool>