comparison blobtoolkit.xml @ 3:f6cc3378ec15 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit d4e8bcb01de330e345970d3df6b75392c7fe2275

2:a4e7a0877d0c

<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[

                --meta 'assembly.yaml'
            #end if
            --taxid $mode_conditional.taxid
            --taxdump './taxdump'
            './Blobdir'
            && tar -C ./Blobdir -zcvf Blobdir.tgz .
        #else if $mode_conditional.selector == 'add'
            mkdir -p './Blobdir' &&
            mkdir -p './taxdump' &&
            ln -s '${mode_conditional.taxdump}' 'taxdump.tar' &&
            tar -xf 'taxdump.tar' -C './taxdump' &&

                #if $mode_conditional.advanced_options.pileup_args
                    --pileup-args '${mode_conditional.advanced_options.pileup_args}'
                #end if
                $mode_conditional.advanced_options.replace
                './Blobdir'
            && tar -C ./Blobdir -zcvf Blobdir.tgz .

        #else if $mode_conditional.selector == 'filter'
            mkdir -p './Blobdir' &&
            #if $mode_conditional.blobdir.is_of_type("tgz")

                #if $mode_conditional.remove_options.field
                    --field $mode_conditional.remove_options.field
                #end if
                ./Blobdir
            #end if
            && tar -C ./Blobdir -zcvf Blobdir.tgz .
        #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>
            </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="--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">

                            <valid initial="string.letters,string.digits"/>
                        </sanitizer>
                        <validator type="regex">[0-9a-zA-Z]+</validator>
                    </param>
                </section>
            </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>
    </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="100"/>
        </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="taxdump" value="small_taxdump.tar.gz"/>
                <param name="busco" value="busco_full_table.tabular"/>

                    <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="100"/>
        </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">

                </section>
                <section name="remove_options">
                    <param name="remove_selector" value="--all"/>
                </section>
            </conditional>
            <output name="blobdir">
                <assert_contents>
                    <has_size value="620" delta="50"/>
                </assert_contents>
            </output>
        </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">

                </section>
                <section name="remove_options">
                    <param name="remove_selector" value="--all"/>
                </section>
            </conditional>
            <output name="blobdir">
                <assert_contents>
                    <has_size value="620" delta="50"/>
                </assert_contents>
            </output>
        </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.

3:f6cc3378ec15

<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[

                --meta 'assembly.yaml'
            #end if
            --taxid $mode_conditional.taxid
            --taxdump './taxdump'
            './Blobdir'
            
            && tar -C ./Blobdir -zcvf Blobdir.tgz .

        #else if $mode_conditional.selector == 'plot'
            mkdir -p blobtk_files && 
            tar -xvf '$blobdir_input' -C blobtk_files &&
            blobtk plot --blobdir blobtk_files  --view '$plot_view'
            
        #else if $mode_conditional.selector == 'add'
            mkdir -p './Blobdir' &&
            mkdir -p './taxdump' &&
            ln -s '${mode_conditional.taxdump}' 'taxdump.tar' &&
            tar -xf 'taxdump.tar' -C './taxdump' &&

                #if $mode_conditional.advanced_options.pileup_args
                    --pileup-args '${mode_conditional.advanced_options.pileup_args}'
                #end if
                $mode_conditional.advanced_options.replace
                './Blobdir'

            #if $mode_conditional.blobtk_plot_options.blobtk_plot == 'yes'
                && blobtk plot --blobdir './Blobdir' --view $blobtk_plot_options.plot_view
            #end if
            
            && tar -C ./Blobdir -zcvf Blobdir.tgz .

        #else if $mode_conditional.selector == 'filter'
            mkdir -p './Blobdir' &&
            #if $mode_conditional.blobdir.is_of_type("tgz")

                #if $mode_conditional.remove_options.field
                    --field $mode_conditional.remove_options.field
                #end if
                ./Blobdir
            #end if

            #if $mode_conditional.blobtk_plot_options.blobtk_plot == 'yes'
                && blobtk plot --blobdir ./Blobdir --view $blobtk_plot_options.plot_view
            #end if

            && tar -C ./Blobdir -zcvf Blobdir.tgz .
        #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="plot">Plot a BlobToolKit dataset</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="--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>
                <expand macro="blobtk_plotting"></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">

                            <valid initial="string.letters,string.digits"/>
                        </sanitizer>
                        <validator type="regex">[0-9a-zA-Z]+</validator>
                    </param>
                </section>
                <expand macro="blobtk_plotting"></expand>
            </when>
            <when value="plot">
                <param name="blobdir_input" type="data" format="tgz" label="Select the blobdir tar.gz file generated from blobtools"/>
                <param name="plot_view" type="select" label="Select the view type for the plot">
                    <option value="blob" selected="true">Blob view</option>
                    <option value="cumulative">Cumulative view</option>
                    <option value="legend">Legend view</option>
                    <option value="snail">Snail view</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="blobdir" format="tgz" from_work_dir="./Blobdir.tgz" label="${tool.name} on ${on_string}: Blobdir.tgz">
            <filter>mode_conditional['selector'] == 'create' or mode_conditional['selector'] == 'add' or mode_conditional['selector'] == 'filter'</filter>
        </data>
        <data name="output_svg" format="svg" from_work_dir="output.svg" label="${tool.name} on ${on_string}: Output Plot">
            <filter>
                ((
                (mode_conditional['selector'] == 'add' and mode_conditional['blobtk_plot_options']['blobtk_plot'] == 'yes') or 
                (mode_conditional['selector'] == 'filter' and mode_conditional['blobtk_plot_options']['blobtk_plot'] == 'yes') or
                (mode_conditional['selector'] == 'plot')
                ))
            </filter>
        </data>
    </outputs>
    <tests>
        <!-- Test 01: Testing blobtoolkit with create with no plotting enabled -->
        <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="100"/>
        </test>
        <!-- Test 02: Testing blobtoolkit with add with plotting enabled -->
        <test expect_num_outputs="2">
            <conditional name="mode_conditional">
                <param name="selector" value="add"/>
                <param name="blobdir" value="test01_blobdir.tar.gz"/>
                <param name="taxdump" value="small_taxdump.tar.gz"/>
                <param name="busco" value="busco_full_table.tabular"/>

                    <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 name="blobtk_plot_options">
                    <param name="blobtk_plot" value="yes"/>
                    <param name="plot_view" value="blob"/>
                </conditional>
            </conditional>
            <output name="blobdir" file="test02_blobdir.tar.gz"  compare="sim_size" delta="100"/>
            <output name="output_svg" file="test02_blob.svg"  compare="sim_size" delta="100"/>
        </test>
        <!-- Test 03: Testing blobtoolkit with filtering and plotting disabled -->
        <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">

                </section>
                <section name="remove_options">
                    <param name="remove_selector" value="--all"/>
                </section>
            </conditional>
            <conditional name="blobtk_plot_options">
                <param name="blobtk_plot" value="no"/>
            </conditional>
            <output name="blobdir">
                <assert_contents>
                    <has_size value="620" delta="50"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test 04: Testing blobtoolkit with filter with list and fasta filtering -->
        <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">

                </section>
                <section name="remove_options">
                    <param name="remove_selector" value="--all"/>
                </section>
            </conditional>
            <conditional name="blobtk_plot_options">
                <param name="blobtk_plot" value="no"/>
            </conditional>
            <output name="blobdir">
                <assert_contents>
                    <has_size value="620" delta="50"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test 05: Testing blobtoolkit blob plot -->
        <test expect_num_outputs="1">
            <conditional name="mode_conditional">
                <param name="selector" value="plot"/>
                <param name="blobdir_input" value="blobdir.tgz"/>
                <param name="plot_view" value="blob"/>
            </conditional>
            <output name="output_svg" ftype="svg" file="output.svg" compare="sim_size"/>
        </test>
        <!-- Test 06 :Testing blobtoolkit Snail plot -->
        <test expect_num_outputs="1">
            <conditional name="mode_conditional">
                <param name="selector" value="plot"/>
                <param name="blobdir_input" value="blobdir.tgz"/>
                <param name="plot_view" value="snail"/>
            </conditional>
                <output name="output_svg" ftype="svg">
                 <assert_contents>
                    <has_text text="Log10 scaffold count (total 242)"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test 07: Testing blobtoolkit legend plot -->
        <test expect_num_outputs="1">
            <conditional name="mode_conditional">
                <param name="selector" value="plot"/>
                <param name="blobdir_input" value="blobdir.tgz"/>
                <param name="plot_view" value="legend"/>
            </conditional>
            <output name="output_svg" ftype="svg" file="output_legend.svg" compare="sim_size"/>
        </test>
        <!-- Test 08: Testing blobtoolkit Cumulative plot -->
        <test expect_num_outputs="1">
            <conditional name="mode_conditional">
                <param name="selector" value="plot"/>
                <param name="blobdir_input" value="blobdir.tgz"/>
                <param name="plot_view" value="cumulative"/>
            </conditional>
            <output name="output_svg" ftype="svg" file="output_cumulative.svg" compare="sim_size"/>
        </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.