Mercurial > repos > iuc > stacks2_gstacks
diff stacks_gstacks.xml @ 0:d35cb34f2b85 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
| author | iuc |
|---|---|
| date | Mon, 01 Jul 2019 10:59:14 -0400 |
| parents | |
| children | 27359c6bf3e3 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stacks_gstacks.xml Mon Jul 01 10:59:14 2019 -0400 @@ -0,0 +1,382 @@ +<tool id="stacks2_gstacks" name="Stacks2: gstacks" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> + <description>Call variants, genotypes and haplotype</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="1.9">samtools</requirement> + </expand> + <expand macro="version_cmd"/> + <command detect_errors="aggressive"><![CDATA[ +@FASTQ_INPUT_FUNCTIONS@ + +mkdir bam_inputs stacks_outputs && +#if $mode_cond.mode_select == "denovo" and not $popmap: + ## since collections have no len .. yet + #try: + #set count = len($input_bam) + #except: + #set count = len($input_bam.keys()) + #end try + #if count == 1: + #for $bam in $input_bam: + ln -s '$bam' bam_inputs/catalog.bam && + #end for + #else + >&2 echo "exactly one (merged) bam file is needed in denovo mode if no population map is given" && + exit 1 && + #end if +#else + @BAM_INPUT@ +#end if + +gstacks + +#if $mode_cond.mode_select == "denovo": + -P bam_inputs + $mode_cond.ignore_pe_reads + #if $mode_cond.advanced_cond.advanced_select == "yes": + --kmer-length $mode_cond.advanced_cond.kmer_length + --max-debruijn-reads $mode_cond.advanced_cond.max_debruijn_reads + --min-kmer-cov $mode_cond.advanced_cond.min_kmer_cov + $mode_cond.advanced_cond.write_alignments + #end if +#else: + #if $popmap + -I bam_inputs + #else + $bamlist + #end if + #if $mode_cond.paired_cond.paired_select == '' + $mode_cond.paired_cond.rm_unpaired_reads + $mode_cond.paired_cond.rm_pcr_duplicates + #else: + $mode_cond.paired_cond.paired_select + #end if + #if $mode_cond.advanced_cond.advanced_select == "yes": + --min-mapq $mode_cond.advanced_cond.min_mapq + --max-clipped $mode_cond.advanced_cond.max_clipped + --max-insert-len $mode_cond.advanced_cond.max_insert_len + $mode_cond.advanced_cond.details + --phasing-cooccurrences-thr-range $mode_cond.advanced_cond.phasing_cooccurrences_thr_min,$mode_cond.advanced_cond.phasing_cooccurrences_thr_max + $mode_cond.advanced_cond.phasing_dont_prune_hets + #end if +#end if +#if $popmap + -M '$popmap' +#end if +-O stacks_outputs +-t \${GALAXY_SLOTS:-1} + +##Model options: +--model $model_cond.model +--var-alpha $model_cond.var_alpha +--gt-alpha $model_cond.gt_alpha + + +## the bam files generated by gstacks (--write-alignments) are seemingly buggy +## (https://groups.google.com/d/msg/stacks-users/CazwJY1DPGA/7vuahiB2GgAJ) +## so we fix them temporarily by piping them through samtools view (disabling all +## exit codes and stderr output) this adds the samtools requirement +## for later versions where this is fixed the output bam files could just be moved +## to stacks_outputs if this is still necessary +#if $mode_cond.mode_select == "denovo" and $mode_cond.advanced_cond.advanced_select == "yes" and $mode_cond.advanced_cond.write_alignments != "" + #if $popmap: + && for b in bam_inputs/*alns.bam; do (samtools view -b "\$b" || true) 2> /dev/null > stacks_outputs/\$(basename "\$b"); done + #else + && (samtools view -b bam_inputs/alignments.bam || true) 2> /dev/null > stacks_outputs/alignments.bam + #end if +#end if + + +## annoyingly gstacks creates stacks_output/gstacks.log +## instead of just writing to stderr as the other tools +## hence we do not use the tokens and return populations.log as log file and take the stderr +#if $output_log + && mv stacks_outputs/gstacks.log $output_log +#end if + +@EXTRACT_VCF@ + +## TODO extract individual distributions from stacks_outputs/gstacks.log.distribs +## alternative extra tool +## for i in \$(stacks-dist-extract stacks_outputs/gstacks.log.distribs) +## do +## stacks-dist-extract stacks_outputs/gstacks.log.distribs $i > stacks_outputs/gstacks.log.\$i.tsv +## done +## TODO make optional output collection + ]]></command> + + <inputs> + <expand macro="bam_input_macro"/> + <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" /> + + <conditional name="mode_cond"> + <param name="mode_select" type="select" label="Mode"> + <option value="denovo" selected="true">De novo mode</option> + <option value="refbased">Reference-based</option> + </param> + <when value="denovo"> + <param argument="--ignore-pe-reads" name="ignore_pe_reads" type="boolean" checked="false" truevalue="--ignore-pe-reads" falsevalue="" label="Ignore paired-end reads" help="ignore paired-end reads even if present in the input" /> + <conditional name="advanced_cond"> + <param name="advanced_select" type="select" label="Advanced options"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param argument="--kmer-length" name="kmer_length" type="integer" value="31" min="2" max="31" label="K-mer length for the de Bruijn graph" /> + <param argument="--max-debruijn-reads" name="max_debruijn_reads" type="integer" value="1000" min="1" label="Maximum number of reads to use in the de Bruijn graph" /> + <param argument="--min-kmer-cov" name="min_kmer_cov" type="integer" value="2" label="Minimum coverage to consider a kmer" /> + <param argument="--write-alignments" name="write_alignments" type="boolean" checked="false" truevalue="--write-alignments" falsevalue="" label="save read alignments" help="heavy BAM files"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="refbased"> + <conditional name="paired_cond"> + <param name="paired_select" type="select" label="Paired end options" help="select single/paired for single end data or to select advanced paired end options, --unpaired: treat reverse reads as if they were forward reads; --ignore-pe-reads: ignore paired-end reads even if present in the input"> + <option value="" selected="true">single/paired</option> + <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option> + <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option> + </param> + <when value=""> + <param argument="--rm-unpaired-reads" name="rm_unpaired_reads" type="boolean" checked="false" truevalue="--rm-unpaired-reads" falsevalue="" label="Discard unpaired reads" /> + <param argument="--rm-pcr-duplicates" name="rm_pcr_duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="Remove read pairs of the same sample that have the same insert length" help="implies --rm-unpaired-reads" /> + </when> + <when value="--unpaired"/> + <when value="--ignore-pe-reads"/> + </conditional> + <conditional name="advanced_cond"> + <param name="advanced_select" type="select" label="Advanced options"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param argument="--min-mapq" name="min_mapq" type="integer" value="10" min="0" max="255" label="Minimum PHRED-scaled mapping quality to consider a read" /> + <param argument="--max-clipped" name="max_clipped" type="float" value="0.2" min="0.0" max="1.1" label="Maximum soft-clipping level" help="in fraction of read length" /> + <param argument="--max-insert-len" name="max_insert_len" type="integer" value="1000" min="0" label="Maximum allowed sequencing insert length" /> + <param argument="--details" type="boolean" checked="false" truevalue="--details" falsevalue="" label="Write a heaview output" /> + <param name="phasing_cooccurrences_thr_min" type="integer" value="1" min="0" label="Edge coverage min" help="(--phasing-cooccurrences-thr-range)" /> + <param name="phasing_cooccurrences_thr_max" type="integer" value="2" min="0" label="Edge coverage max" help="range of edge coverage thresholds to iterate over when building the graph of allele cooccurrences for SNP phasing (--phasing-cooccurrences-thr-range)"/> + <param argument="--phasing-dont-prune-hets" name="phasing_dont_prune_hets" type="boolean" checked="false" truevalue="--phasing-dont-prune-hets" falsevalue="" label="Don't try to ignore dubious heterozygote genotypes during phasing" /> + </when> + <when value="no"/> + </conditional> + </when> + </conditional> + + <conditional name="model_cond"> + <param argument="--model" type="select" label="Model to use to call variants and genotypes"> + <option value="marukilow" selected="true">marukilow</option> + <option value="marukihigh">marukihigh</option> + <option value="snp">snp</option> + </param> + <when value="marukilow"> + <expand macro="variant_calling_options_vg" varalpha_default="0.01"/> + </when> + <when value="marukihigh"> + <expand macro="variant_calling_options_vg"/> + </when> + <when value="snp"> + <expand macro="variant_calling_options_vg"/> + </when> + </conditional> + <param name="add_log_distribs" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Add log distribs output as dataset" /> + <expand macro="in_log"/> + </inputs> + <outputs> + <expand macro="out_log"/> + <expand macro="gstacks_outputs_full_macro"/> + </outputs> + + <tests> + <!-- denovomode, w popmap --> + <test expect_num_outputs="3"> + <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> + <conditional name="mode_cond"> + <param name="mode_select" value="denovo"/> + </conditional> + <param name="add_log" value="yes" /> + <param name="add_log_distribs" value="yes" /> + <output name="output_log" ftype="txt" file="gstacks/gstacks.log" lines_diff="8"/> + <output name="distribs" ftype="txt" file="gstacks/gstacks.log.distribs" compare="sim_size"/> + <output_collection name="gstacks_out" type="list" count="2"> + <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="2"/> + <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz"/> + </output_collection> + </test> + <!-- denovomode, w popmap, write alignments --> + <test expect_num_outputs="3"> + <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> + <conditional name="mode_cond"> + <param name="mode_select" value="denovo"/> + <conditional name="advanced_cond"> + <param name="advanced_select" value="yes"/> + <param name="write_alignments" value="--write-alignments" /> + </conditional> + </conditional> + <param name="add_log" value="yes" /> + <assert_command> + <has_text text="--write-alignments" /> + </assert_command> + <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output> + <output_collection name="gstacks_out" type="list" count="2"/> + <output_collection name="gstacks_alns_out" type="list" count="2"> + <element name="PopA_01" file="gstacks/PopA_01.alns.bam" ftype="bam" /> + <element name="PopA_02" file="gstacks/PopA_02.alns.bam" ftype="bam" /> + </output_collection> + </test> + <!-- denovomode, wo popmap (allows for only one input), ignore PE, advanced, alt model --> + <test expect_num_outputs="3"> + <param name="input_bam" value="tsv2bam/PopA_01.matches.bam" ftype="bam"/> + <conditional name="mode_cond"> + <param name="mode_select" value="denovo" /> + <param name="ignore_pe_reads" value="--ignore-pe-reads" /> + <conditional name="advanced_cond"> + <param name="advanced_select" value="yes"/> + <param name="kmer_length" value="23" /> + <param name="max_debruijn_reads" value="666"/> + <param name="min_kmer_cov" value="3" /> + <param name="write_alignments" value="--write-alignments" /> + </conditional> + </conditional> + <conditional name="model_cond"> + <param name="model" value="marukihigh"/> + <param name="var_alpha" value="0.1" /> + <param name="gt_alpha" value="0.1" /> + </conditional> + <param name="add_log" value="yes" /> + <assert_command> + <has_text text="--ignore-pe-reads" /> + <has_text text="--rm-pcr-duplicates" /> + <has_text text="--kmer-length 23" /> + <has_text text="--max-debruijn-reads 666" /> + <has_text text="--min-kmer-cov 3" /> + <has_text text="--write-alignments" /> + <has_text text="--model marukihigh" /> + <has_text text="--var-alpha 0.1" /> + <has_text text="--gt-alpha 0.1" /> + </assert_command> + <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output> + <output_collection name="gstacks_out" type="list" count="2"/> + <output name="gstacks_aln_out" ftype="bam" file="gstacks/alignments.bam" /> + </test> + <!-- refbased wo popmap, paired options, removing all unpaired reads results in an error --> + <test expect_failure="true" expect_exit_code="1"> + <param name="input_bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/> + <conditional name="mode_cond"> + <param name="mode_select" value="refbased"/> + <conditional name="paired_cond"> + <param name="paired_select" value=""/> + <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes to much of the test data and gstacks fails--> + <param name="rm_pcr_duplicates" value="--rm-pcr-duplicates" /> + </conditional> + </conditional> + <param name="add_log" value="yes" /> + <assert_command> + <has_text text="-I bam_inputs" /> + <not_has_text text="-B " /> + <has_text text="--rm-unpaired-reads" /> + <has_text text="--rm-pcr-duplicates" /> + </assert_command> + </test> + <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model --> + <test expect_num_outputs="2"> + <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> + <conditional name="mode_cond"> + <param name="mode_select" value="refbased"/> + <conditional name="paired_cond"> + <param name="paired_select" value="--unpaired"/> + </conditional> + <conditional name="advanced_cond"> + <param name="advanced_select" value="yes" /> + <param name="min_mapq" value="23" /> + <param name="max_clipped" value="0.23" /> + <param name="max_insert_len" value="666" /> + <param name="details" value="--detailed"/> + <param name="phasing_cooccurrences_thr_min" value="2"/> + <param name="phasing_cooccurrences_thr_max" value="3"/> + <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets" /> + </conditional> + </conditional> + <param name="model_cond|model" value="snp"/> + <param name="model_cond|gt_alpha" value="0.1" /> + <param name="model_cond|var_alpha" value="0.1" /> + <param name="add_log" value="yes" /> + <assert_command> + <not_has_text text="-I bam_inputs" /> + <has_text text="-B " /> + <has_text text="--unpaired" /> + <has_text text="--min-mapq 23" /> + <has_text text="--max-clipped 0.23" /> + <has_text text="--max-insert-len 666" /> + <has_text text="--detailed" /> + <has_text text="--phasing-cooccurrences-thr-range 2,3" /> + <has_text text="--phasing-dont-prune-hets" /> + <has_text text="--model snp" /> + <has_text text="--gt-alpha 0.1" /> + </assert_command> + <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output> + <output_collection name="gstacks_out" type="list" count="2"/> + </test> + <!-- refbased wo popmap (here bam names don't matter), \-\-ignorepe --> + <test expect_num_outputs="2"> + <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/> + <conditional name="mode_cond"> + <param name="mode_select" value="refbased"/> + <conditional name="paired_cond"> + <param name="paired_select" value="--ignore-pe-reads"/> + </conditional> + </conditional> + <param name="add_log" value="yes" /> + <assert_command> + <has_text text="-I bam_inputs" /> + <not_has_text text="-B " /> + <has_text text="--ignore-pe-reads" /> + </assert_command> + <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output> + <output_collection name="gstacks_out" type="list" count="2"/> + </test> + </tests> + + <help> +<![CDATA[ +.. class:: infomark + +**What it does** + +For de novo analyses, this program will pull in paired-end reads, if available, +assemble the paired-end contig and merge it with the single-end locus, align +reads to the locus, and call SNPs. + +For reference-aligned analyses, this program will build loci from the single +and/or paired-end reads before calling SNPs. The single- and paired-end reads +must be aligned and stored together in the intput BAM or SAM files and the +reads must be sorted. The gstacks program will detect if single- or paired-end +reads are present. + +In either mode, gstacks is able to remove PCR duplicates if requested. + +-------- + +**Input files** + +If a population map is given BAM records must be assigned to samples using BAM "reads groups" +(gstacks uses the ID/identifier and SM/sample name fields). Read groups +must be consistent if repeated different files. +Otherwise read groups are unneeded and ignored. + +**Output files** + +- Assembled contigs and variant sites + +- Optional outputs: Read alignments and log.distribs + +@STACKS_INFOS@ +]]> + </help> + <expand macro="citation" /> +</tool>