diff blobtoolkit.xml @ 0:7d9ee8cd14b8 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9
author bgruening
date Mon, 30 Jan 2023 12:39:40 +0000
parents
children 840822c1e84a
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blobtoolkit.xml	Mon Jan 30 12:39:40 2023 +0000
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+<tool id="blobtoolkit" name="BlobToolKit" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>genome assembly QC</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro='requirements' />
+    <command detect_errors="exit_code"><![CDATA[
+        #if $mode_conditional.selector == 'create'
+            mkdir -p './Blobdir' &&
+            mkdir -p './taxdump' &&
+            ln -s '${mode_conditional.taxdump}' 'taxdump.tar' &&
+            tar -xf 'taxdump.tar' -C './taxdump' &&
+            ln -s '${mode_conditional.fasta}' 'assembly.fasta' &&
+            #if $mode_conditional.meta
+                ln -s '${mode_conditional.meta}' 'assembly.yaml' &&
+            #end if
+            blobtools create
+            --fasta 'assembly.fasta'
+            #if $mode_conditional.meta
+                --meta 'assembly.yaml'
+            #end if
+            --taxid $mode_conditional.taxid
+            --taxdump './taxdump'
+            './Blobdir'
+            && cp -r './taxdump' './Blobdir/'
+            && tar -zcf './Blobdir.tgz' './Blobdir'
+
+        #else if $mode_conditional.selector == 'add'
+            #if $mode_conditional.blobdir.is_of_type("tgz")
+                tar -zxf '${mode_conditional.blobdir}' -C './' &&
+            #else
+                tar -xf '${mode_conditional.blobdir}' -C './' &&
+            #end if
+            #if $mode_conditional.busco
+                ln -s '${mode_conditional.busco}' './busco_results.tab' && 
+            #end if
+            #if $mode_conditional.blast_input.selector == 'enabled'
+                ln -s '$mode_conditional.blast_input.hits' './blast_results.tab' &&
+            #end if
+            #if $mode_conditional.cov
+                ln -s '$mode_conditional.cov' './input.bam' &&
+                ln -s '$mode_conditional.cov.metadata.bam_index' './input.bam.bai' &&
+            #end if
+            #if $mode_conditional.bed
+                    mkdir -p './bed_files' &&
+                    #import re
+                    #for $i, $input in enumerate($mode_conditional.bed):
+                        #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier) + "." + str($i)
+                        ln -sf '${input}' './bed_files/${safename}.bed' &&
+                    #end for
+            #end if
+            blobtools add
+                --threads \${GALAXY_SLOTS:-8}
+                --taxdump './Blobdir/taxdump'
+                #if $mode_conditional.busco
+                    --busco './busco_results.tab'
+                #end if
+                #if $mode_conditional.blast_input.selector == 'enabled'
+                    --hits './blast_results.tab'
+                    #if $mode_conditional.blast_input.hits_cols
+                        --hits-cols '${$mode_conditional.blast_input.hits_cols}'
+                    #end if
+                    --taxrule $mode_conditional.blast_input.taxrule
+                    --evalue $mode_conditional.blast_input.evalue
+                    --hit-count $mode_conditional.blast_input.hit_count
+                    --bitscore $mode_conditional.blast_input.bitscore
+                #end if
+                #if $mode_conditional.bed
+                    --beddir './bed_files'
+                #end if
+                #if $mode_conditional.cov
+                    --cov './input.bam'
+                #end if
+                #if $mode_conditional.fasta
+                    --fasta '${mode_conditional.fasta}'
+                #end if
+                #if $mode_conditional.trnascan
+                    --trnascan '${mode_conditional.trnascan}'
+                #end if
+                #if $mode_conditional.text_input.selector == 'enabled'
+                    --text '${mode_conditional.text_input.text}'
+                    --text-cols '${mode_conditional.text_input.text_cols}'
+                    $mode_conditional.text_input.text_header
+                    $mode_conditional.text_input.text_no_array
+                    --text-delimiter $mode_conditional.text_input.text_delimiter
+                #end if
+                #if $mode_conditional.advanced_options.blobdb
+                    --blobdb '${mode_conditional.advanced_options.blobdb}'
+                #end if
+                #if $mode_conditional.advanced_options.synonyms
+                    --synonyms '${mode_conditional.advanced_options.synonyms}'
+                #end if
+                $mode_conditional.advanced_options.update_plot
+                #if $mode_conditional.advanced_options.pileup_args
+                    --pileup-args '${mode_conditional.advanced_options.pileup_args}'
+                #end if
+                $mode_conditional.advanced_options.replace
+                './Blobdir'
+            && tar -zcf './Blobdir.tgz' './Blobdir'
+
+        #else if $mode_conditional.selector == 'filter'
+            #if $mode_conditional.blobdir.is_of_type("tgz")
+                tar -zxf '${mode_conditional.blobdir}' -C './' &&
+            #else
+                tar -xf '${mode_conditional.blobdir}' -C './' &&
+            #end if            
+            #if $mode_conditional.filter_options.fasta
+                ln -s '${mode_conditional.filter_options.fasta}' './input.fasta' &&
+            #end if
+            #if $mode_conditional.filter_options.fastq_filter.selector == 'enabled'
+                ln -s '${mode_conditional.filter_options.fastq}' './input.fastq' &&
+                ln -s '$mode_conditional.filter_options.cov' './input.bam' &&
+                ln -s '$mode_conditional.filter_options.cov.metadata.bam_index' './input.bam.csi' &&
+            #end if
+            blobtools filter
+            #if $mode_conditional.filter_options.param
+                --param $mode_conditional.filter_options.param
+            #end if
+            #if $mode_conditional.filter_options.json
+                --json $mode_conditional.filter_options.json
+            #end if
+            #if $mode_conditional.filter_options.list
+                --list $mode_conditional.filter_options.list
+            #end if
+            $mode_conditional.filter_options.invert
+            #if $mode_conditional.filter_options.fasta
+                --fasta './input.fasta'
+            #end if
+            #if $mode_conditional.filter_options.fastq_filter.selector == 'enabled'
+                --fastq './input.fastq'
+                --cov './input.bam'
+            #end if
+            #if $mode_conditional.filter_options.text_input.selector == 'enabled'
+                --text '${mode_conditional.filter_options.text_input.text}'
+                --text-cols '${mode_conditional.filter_options.text_input.text_cols}'
+                $mode_conditional.filter_options.text_input.text_header
+                --text-delimiter $mode_conditional.filter_options.text_input.text_delimiter
+            #end if
+            ./Blobdir
+            #if $mode_conditional.remove_options.remove_selector or $mode_conditional.remove_options.field
+                && blobtools remove
+                #for $param in $mode_conditional.remove_options.remove_selector
+                    $param
+                #end for 
+                #if $mode_conditional.remove_options.field
+                    --field $mode_conditional.remove_options.field
+                #end if
+                ./Blobdir
+            #end if
+            && tar -zcf './Blobdir.tgz' './Blobdir'
+
+        #else if $mode_conditional.selector == 'plots'
+            #if $mode_conditional.blobdir.is_of_type("tgz")
+                tar -zxf '${mode_conditional.blobdir}' -C './' &&
+            #else
+                tar -xf '${mode_conditional.blobdir}' -C './' &&
+            #end if            
+            blobtools view
+            --format $mode_conditional.format
+            --view 'blob'
+            ./Blobdir
+            && mv ./Blobdir.blob.circle* ./Blobdir.blob.circle
+            && blobtools view
+            --format $mode_conditional.format
+            --view 'cumulative'
+            ./Blobdir
+            && mv ./Blobdir.cumulative* Blobdir.cumulative
+            && blobtools view
+            --format $mode_conditional.format
+            --view 'snail'
+            ./Blobdir
+            && mv ./Blobdir.snail* Blobdir.snail
+        #end if
+    ]]></command>
+    <inputs>
+        <conditional name="mode_conditional">
+            <param name="selector" type="select" label="Select mode" help="Select a BlobToolKit module">
+                <option value="create">Create a BlobToolKit dataset</option>
+                <option value="add">Add data to a BlobToolKit dataset</option>
+                <option value="filter">Edit a BlobToolKit dataset</option>
+                <option value="plots">Generate plots</option>
+            </param>
+            <when value="create">
+                <param argument="--fasta" type="data" format="fasta" label="Genome assembly file" help="FASTA sequence file" />
+                <param argument="--meta" type="data" format="yaml" label="Metadata file" optional="true" help="Optional metadata dataset"/>
+                <param argument="--taxid" type="integer" value="" label="NCBI taxonomy ID" help="Add ranks to metadata for a taxid"/>
+                <param argument="--taxdump" type="data" format="tar,tgz,gz" label="NCBI taxdump directory" help="It should be compressed in tar.gz format"/>
+            </when>
+            <when value="add">
+                <param name="blobdir" type="data" format="tgz" label="Blobdir.tgz file" help="This file should be generated by Blobtool create" />
+                <param argument="--busco" type="data" format="tsv,tabular,txt" optional="true" label="BUSCO full table file"/>
+                <conditional name="blast_input">
+                    <param name="selector" type="select" label="BLAST/Diamond hits">
+                        <option value="enabled">Enabled</option>
+                        <option value="disabled" selected="true">Disabled</option>
+                    </param>
+                    <when value="enabled">
+                        <param argument="--hits" type="data" format="tsv,tabular" optional="true" label="BLAST/Diamond hits dataset" help="Tabular BLAST/Diamond output file"/>
+                        <param argument="--taxrule" type="select" label="BLAST hits to taxa rule" help="Rule to use when assigning BLAST hits to taxa">
+                            <option value="bestsum">Bestsum</option>
+                            <option value="bestsumorder">Bestsumorder</option>
+                            <option value="bestdistsum">Bestdistsum</option>
+                            <option value="bestdistsumorder">Bestdistsumorder</option>
+                            <option value="blastp">Blastp</option>
+                        </param>              
+                        <param argument="--evalue" type="float" min="0" value="1" label="E-value cutoff"
+                            help="The smaller the E-value, the better the match. Any hits with an evalue weaker than the value specified will be excluded"/>
+                        <param argument="--bitscore" type="float" min="0" value="1" label="Bitscore cutoff" 
+                            help="The higher the bit-score, the better the sequence similarity. Any hits with an bitscore lower the value specified will be excluded"/>
+                        <param argument="--hit-count" type="integer" min="1" value="10" label="Hits to a given taxon" optional="true" 
+                            help="By default the 10 highest scoring hits to a given taxon will be used when applying the --taxrule"/>
+                        <param argument="--hits-cols" type="text" value="1=qseqid,2=staxids,3=bitscore,5=sseqid,10=qstart,11=qend,14=evalue" optional="true" 
+                            label="BLAST/Diamond file column order" help="More information in the help section">
+                            <sanitizer invalid_char="">
+                                <valid initial="string.letters,string.digits">
+                                    <add value="=" />
+                                    <add value="," />
+                                </valid>
+                            </sanitizer>
+                            <validator type="regex">[0-9a-z=,]+</validator>
+                        </param>
+                    </when>
+                    <when value="disabled"/>
+                </conditional>
+                <param argument="--bed" type="data" format="bed" multiple="true" optional="true" label="BED file of coverages per scaffold"/>
+                <param argument="--cov" type="data" format="bam,sam,cram" optional="true" label="BAM/SAM/CRAM read alignment file"/>
+                <param argument="--fasta" type="data" format="fasta" optional="true" label="FASTA sequence" help="FASTA sequence file" />
+                <param argument="--trnascan" type="data" format="tsv,tabular" optional="true" label="tRNAscan2-SE" help="tRNAscan-SE is employed for identifying and annotating tRNA genes in genomes"/>
+                <expand macro="macro_text_input">
+                    <param argument="--text-no-array" type="boolean" truevalue="--text-no-array" falsevalue="" checked="false" label="Prevent duplicated identifiers" 
+                        help="Prevent fields in files with duplicate identifiers being loaded as array fields" />
+                </expand>
+                <section name="advanced_options" title="Advanced options">
+                    <param argument="--blobdb" type="data" format="json" optional="true" label="Blobtools v1 database" help="This file should have been generated with the previous Blobtools tool version"/>
+                    <param argument="--synonyms" type="data" format="tsv" optional="true" label="Identifier and sinonyms" help="TSV file containing current identifiers and synonyms"/>
+                    <param argument="--update-plot" type="boolean" truevalue="--update-plot" falsevalue="" checked="false" label="Update plot" help="Flag to use new taxrule as default category" />
+                    <param argument="--pileup-args" type="text" value="" optional="true" label="Samtools Pileup" help="Key/value pairs to pass to samtools pileup">
+                        <sanitizer invalid_char="">
+                            <valid initial="string.letters,string.digits">
+                                <add value="=" />
+                                <add value="," />
+                                <add value="-" />
+                            </valid>
+                        </sanitizer>
+                        <validator type="regex">[0-9a-zA-Z=,-]+</validator>
+                    </param>
+                    <param argument="--replace" type="boolean" truevalue="--replace" falsevalue="" checked="false" label="Replace fields" help="Allow existing fields to be overwritten" />
+                </section>
+            </when>
+            <when value="filter">
+                <param name="blobdir" type="data" format="tgz" label="Blobdir file" help="This file should be generated by the moudule create" />
+                <section name="filter_options" title="Filter mode options" expanded="true">
+                    <param argument="--param" type="text" value="" optional="true" label="Parameter value" help="String of type param=value. Individual param=value pairs can be specified to 
+                        filter based on Variable or Category fields">
+                        <sanitizer invalid_char="">
+                            <valid initial="string.letters,string.digits">
+                                <add value="=" />
+                                <add value="," />
+                                <add value="-" />
+                            </valid>
+                        </sanitizer>
+                        <validator type="regex">[0-9a-zA-Z=,-]+</validator>
+                    </param>
+                    <param argument="--list" type="text" value="" optional="true" label="List of identifiers" help="Space separated list of identifiers">
+                        <sanitizer invalid_char="">
+                            <valid initial="string.letters,string.digits">
+                                <add value=" " />
+                                <add value="-" />
+                                <add value="_" />
+                            </valid>
+                        </sanitizer>
+                        <validator type="regex">[0-9a-zA-Z _-]+</validator>
+                    </param>
+                    <param argument="--json" type="data" format="json" optional="true" label="JSON format list file" help="JSON format list file as generated by BlobtoolKit Viewer"/>
+                    <param argument="--fasta" type="data" format="fasta" multiple="true" optional="true" label="Assembly to be filtered" help="FASTA format assembly file to be filtered"/>
+                    <conditional name="fastq_filter">
+                        <param name="selector" type="select" label="Filter FASTQ reads">
+                            <option value="disabled">Disabled</option>
+                            <option value="enabled">Enabled</option>
+                        </param>
+                        <when value="disabled"/>
+                        <when value="enabled">
+                            <param argument="--fastq" type="data" format="fastq" optional="true" label="Reads to be filtered" help="FASTQ format read file to be filtered"/>
+                            <param argument="--cov" type="data" format="bam,sam,cram" optional="true" label="BAM/SAM/CRAM read alignment file" />
+                        </when>
+                    </conditional>
+                    <expand macro="macro_text_input"/>
+                    <param argument="--summary-rank" type="text" value="phylum" label="Sumamry rank" help="Taxonomic level for summary">
+                        <sanitizer invalid_char="">
+                            <valid initial="string.letters"/>
+                        </sanitizer>
+                        <validator type="regex">[a-zA-Z]+</validator>
+                    </param>
+                    <param argument="--invert" type="boolean" truevalue="--invert" falsevalue="" checked="false" label="Invert filter" help="Invert the filter (exclude matching records)"/>
+                </section>
+                <section name="remove_options" title="Remove mode options" expanded="true">
+                    <param name="remove_selector" type="select" multiple="true" display="checkboxes" label="Fields to remove">
+                        <option value="--all">Remove all fields except identifiers (--all)</option>
+                        <option value="--busco">Remove all BUSCO fields (--busco)</option>
+                        <option value="--cov">Remove all cov and read_cov fields (--cov)</option>
+                        <option value="--fasta">Remove gc, length and ncount fields (--fasta)</option>
+                        <option value="--hits">Remove all taxonomy fields (--hits)</option>
+                    </param>
+                    <param argument="--field" type="text" value="" optional="true" label="Remove fields by ID">
+                        <sanitizer invalid_char="">
+                            <valid initial="string.letters,string.digits"/>
+                        </sanitizer>
+                        <validator type="regex">[0-9a-zA-Z]+</validator>
+                    </param>
+                </section>
+            </when>
+            <when value="plots">
+                <param name="blobdir" type="data" format="tgz" label="Blobdir file" help="This file should be generated by the moudule create" />
+                <param argument="--format" type="select" label="Image format">
+                    <option value="png">PNG</option>
+                    <option value="svg">SVG</option>
+                </param>
+                <param argument="--param" type="text" optional="true" label="Query parameter" help="Query string parameter."/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="blobdir" format="tgz" from_work_dir="./Blobdir.tgz" label="${tool.name} on ${on_string}: Blobdir.tgz">
+            <filter>mode_conditional['selector'] == 'create' or mode_conditional['selector'] == 'add' or mode_conditional['selector'] == 'filter'</filter>
+        </data>
+        <data name="plot_circle" format="png" from_work_dir="./Blobdir.blob.circle" label="${tool.name} on ${on_string}: blob plot">
+            <filter>mode_conditional['selector'] == 'plots'</filter>
+            <change_format>
+                <when input="$mode_conditional.format" value="svg" format="svg"/>
+            </change_format>
+        </data>
+        <data name="plot_cumulative" format="png" from_work_dir="./Blobdir.cumulative" label="${tool.name} on ${on_string}: cumulative plot">
+            <filter>mode_conditional['selector'] == 'plots'</filter>
+            <change_format>
+                <when input="$mode_conditional.format" value="svg" format="svg"/>
+            </change_format>
+        </data>
+        <data name="plot_snail" format="png" from_work_dir="./Blobdir.snail" label="${tool.name} on ${on_string}: snail plot">
+            <filter>mode_conditional['selector'] == 'plots'</filter>
+            <change_format>
+                <when input="$mode_conditional.format" value="svg" format="svg"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="mode_conditional">
+                <param name="selector" value="create"/>
+                <param name="fasta" value="assembly.fasta.gz"/>
+                <param name="meta" value="assembly.yaml"/>
+                <param name="taxid" value="801"/>
+                <param name="taxdump" value="small_taxdump.tar.gz"/>
+            </conditional>
+            <output name="blobdir" file="test01_blobdir.tar.gz" compare="sim_size" delta="1000"/>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="mode_conditional">
+                <param name="selector" value="add"/>
+                <param name="blobdir" value="test01_blobdir.tar.gz"/>
+                <param name="busco" value="busco_full_table.tabular"/>
+                <param name="cov" value="bam_file.bam"/>
+                <param name="fasta" value="contig.fasta"/>
+                <section name="advanced_options">
+                    <param name="update_plot" value="false"/>
+                </section>
+                <conditional name="blast_input">
+                    <param name="selector" value="enabled"/>
+                    <param name="hits" value="blast_results.tabular"/>
+                    <param name="taxrule" value="bestsum"/>
+                    <param name="evalue" value="1"/>
+                    <param name="bitscore" value="1"/>
+                    <param name="hit_count" value="10"/>
+                    <param name="hits_cols" value="1=qseqid,2=staxids,3=bitscore,5=sseqid,10=qstart,11=qend,14=evalue"/>
+                </conditional>
+            </conditional>
+            <output name="blobdir" file="test02_blobdir.tar.gz"  compare="sim_size" delta="1000"/>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="mode_conditional">
+                <param name="selector" value="filter"/>
+                <param name="blobdir" value="test02_blobdir.tar.gz"/>
+                <section name="filter_options">
+                    <param name="fasta" value="contig.fasta"/>
+                    <param name="summary_rank" value="phylum"/>
+                    <param name="invert" value="false"/>
+                </section>
+                <section name="remove_options">
+                    <param name="remove_selector" value="--all"/>
+                </section>
+            </conditional>
+            <output name="blobdir">
+                <assert_contents>
+                    <has_size value="672428" delta="1000"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="3">
+            <conditional name="mode_conditional">
+                <param name="selector" value="plots"/>
+                <param name="blobdir" value="test02_blobdir.tar.gz"/>
+                <param name="format" value="png"/>
+            </conditional>
+            <output name="plot_circle" file="test04_circle.png" ftype="png"/>
+            <output name="plot_cumulative" file="test04_cumulative.png" ftype="png"/>
+            <output name="plot_snail" file="test04_snail.png" ftype="png"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    BlobToolKit is a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. It can be used to process assembly, 
+    read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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