comparison lotus2.xml @ 15:6e9fd3e0dcbb draft

"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"

14:30340f534fbe

<tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.01">
    <description>fast OTU processing pipeline</description>
    <macros>
        <token name="@VERSION@">2.09.2</token>
        <xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz">
            <conditional name="refDB_cond">
                <param argument="-refDB" type="select" label="Taxonomy reference database">
                    <option value="cached">Use a built-in taxonomy database</option>
                    <option value="history">Use a taxonomy from history</option>

    -reversePrimer '$reversePrimer'
#end if
#if $offtarget_cond.offtargetDB != 'no':
    -offtargetDB '$offtarget_cond.ref_file'
#end if

-clustering $clu_args.clu_cond.clustering
#if $clu_args.clu_cond.clustering in ('1', '3'):
    #if str($clu_args.clu_cond.id):
        -id $clu_args.clu_cond.id

#if str($tax_args.LCA_frac):
    -LCA_frac $tax_args.LCA_frac
#end if
-lulu $tax_args.lulu
-buildPhylo $tax_args.buildPhylo

; EXIT_VALUE=\$? ;

zip -8 -r -v output.zip output/
&&
exit \$EXIT_VALUE

            </when>
            <when value="history">
                <param name="ref_file" type="data" format="fasta,fasta.gz" label="FASTA reference genome" />
            </when>
        </conditional>
        <section name="clu_args" title="Clustering Options">
            <conditional name="clu_cond">
                <param argument="-clustering" type="select" label="Clustering algorithm">
                    <option value="1">UPARSE</option>
                    <option value="2">swarm</option>
                    <option value="3">cd-hit</option>
                    <option value="6">unoise3</option>
                    <option value="7" selected="true">dada2</option>
                </param>
                <when value="1">
                    <expand macro="id_macro" />
                </when>
                <when value="2">
                    <param argument="-swarm_distance" type="integer" min="1" value="1" optional="true" label="Clustering threshold for OTUs when using swarm clustering (optional)" />
                </when>
                <when value="3">
                    <expand macro="id_macro" />
                </when>
                <when value="6">
                </when>
                <when value="7">
                </when>
            </conditional>
            <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads (optional)" help="E.g. 4:1,4:2,3:3 . See http://lotus2.earlham.ac.uk/images/Derep_options.pdf for how to specify this parameter. If not specified, LotuS2 will select an appropriate default for the chosen clustering algorithm." />
            <param argument="-deactivateChimeraCheck" type="select" label="Chimera check">
                <option value="" selected="true">(Default)</option>

                    <!-- <option value="4">VSEARCH LCA against custom reference database</option> -->
                </param>
                <when value="0">
                    <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for RDP (optional)"/>
                </when>
                <when value="1">
                    <expand macro="refDB_macro" ref_fasta_formats="fasta" />
                </when>
                <when value="2">
                    <expand macro="refDB_macro" />
                </when>
                <when value="3">
                    <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for UTAX (optional)"/>
                </when>
                <when value="4">
                    <expand macro="refDB_macro" />
                </when>
            </conditional>
            <conditional name="amplicon_cond">
                <param argument="-amplicon_type" type="select" label="Amplicon type">
                    <option value="" selected="true">(Default)</option>
                    <option value="LSU">LSU Large subunit (23S/28S)</option>

            <param argument="-buildPhylo" type="select" label="Build OTU phylogeny">
                <option value="0">Disable</option>
                <option value="1" selected="true">Use fasttree2</option>
                <option value="2">Use iqtree2</option>
            </param>
        </section>
    </inputs>

    <outputs>
        <data name="outputs" format="zip" label="${tool.name} on ${on_string}: Complete LotuS2 output" from_work_dir="output.zip" />

        <data name="runlog" format="txt" label="${tool.name} on ${on_string}: main log file" from_work_dir="output/LotuSLogS/LotuS_run.log" />
    </outputs>

    <tests>
        <test>
            <param name="paired_or_single" value="single"/>
            <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/>
            <param name="platform" value="454" />
            <param name="clustering" value="3" />
            <output name="otu" file="OTU.txt" compare="sim_size" />
            <output name="otu_fna" file="OTU.fna" compare="sim_size" />
            <output name="mapping" file="mapping.txt" />
        </test>
        <test>
            <param name="paired_or_single" value="paired_collection"/>
            <param name="pair_input">
                <collection type="list:paired">
                    <element name="Anh_sample">
                        <collection type="paired">
                            <element name="forward" value="Anh_sample1.fastq.gz" ftype="fastqsanger.gz" />
                            <element name="reverse" value="Anh_sample2.fastq.gz" ftype="fastqsanger.gz" />
                        </collection>
                    </element>
                </collection>
            </param>
            <param name="mapping" value="mapping_paired.txt" />
            <param name="platform" value="454" />
            <param name="clustering" value="3" />
            <output name="otu" file="OTU_paired.txt" compare="sim_size" />
            <output name="otu_fna" file="OTU_paired.fna" compare="sim_size" />
        </test>
    </tests>

15:6e9fd3e0dcbb

<tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.09">
    <description>fast OTU processing pipeline</description>
    <macros>
        <token name="@VERSION@">2.19</token>
        <xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz">
            <conditional name="refDB_cond">
                <param argument="-refDB" type="select" label="Taxonomy reference database">
                    <option value="cached">Use a built-in taxonomy database</option>
                    <option value="history">Use a taxonomy from history</option>

    -reversePrimer '$reversePrimer'
#end if
#if $offtarget_cond.offtargetDB != 'no':
    -offtargetDB '$offtarget_cond.ref_file'
#end if
-useMini4map $useMini4map

-clustering $clu_args.clu_cond.clustering
#if $clu_args.clu_cond.clustering in ('1', '3'):
    #if str($clu_args.clu_cond.id):
        -id $clu_args.clu_cond.id

#if str($tax_args.LCA_frac):
    -LCA_frac $tax_args.LCA_frac
#end if
-lulu $tax_args.lulu
-buildPhylo $tax_args.buildPhylo
#if $tax_args.taxExcludeGrep:
    -taxExcludeGrep '$tax_args.taxExcludeGrep'
#end if
; EXIT_VALUE=\$? ;

zip -8 -r -v output.zip output/
&&
exit \$EXIT_VALUE

            </when>
            <when value="history">
                <param name="ref_file" type="data" format="fasta,fasta.gz" label="FASTA reference genome" />
            </when>
        </conditional>
        <param argument="-useMini4map" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use minimap2 instead of VSEARCH to map back reads to OTUs" />
        <section name="clu_args" title="Clustering Options">
            <conditional name="clu_cond">
                <param argument="-clustering" type="select" label="Clustering algorithm">
                    <option value="2">swarm</option>
                    <option value="3">cd-hit</option>
                    <option value="6">unoise3</option>
                    <option value="7" selected="true">dada2</option>
                    <option value="8">vsearch</option>
                </param>
                <when value="2">
                    <param argument="-swarm_distance" type="integer" min="1" value="1" optional="true" label="Clustering threshold for OTUs when using swarm clustering (optional)" />
                </when>
                <when value="3">
                    <expand macro="id_macro" />
                </when>
                <when value="6">
                </when>
                <when value="7">
                </when>
                <when value="8">
                </when>
            </conditional>
            <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads (optional)" help="E.g. 4:1,4:2,3:3 . See http://lotus2.earlham.ac.uk/images/Derep_options.pdf for how to specify this parameter. If not specified, LotuS2 will select an appropriate default for the chosen clustering algorithm." />
            <param argument="-deactivateChimeraCheck" type="select" label="Chimera check">
                <option value="" selected="true">(Default)</option>

                    <!-- <option value="4">VSEARCH LCA against custom reference database</option> -->
                </param>
                <when value="0">
                    <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for RDP (optional)"/>
                </when>
                <!-- <when value="1">
                    <expand macro="refDB_macro" ref_fasta_formats="fasta" />
                </when> -->
                <when value="2">
                    <expand macro="refDB_macro" />
                </when>
                <!-- <when value="3">
                    <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for UTAX (optional)"/>
                </when>
                <when value="4">
                    <expand macro="refDB_macro" />
                </when> -->
            </conditional>
            <conditional name="amplicon_cond">
                <param argument="-amplicon_type" type="select" label="Amplicon type">
                    <option value="" selected="true">(Default)</option>
                    <option value="LSU">LSU Large subunit (23S/28S)</option>

            <param argument="-buildPhylo" type="select" label="Build OTU phylogeny">
                <option value="0">Disable</option>
                <option value="1" selected="true">Use fasttree2</option>
                <option value="2">Use iqtree2</option>
            </param>
            <param argument="-taxExcludeGrep" type="text" value="" label="Taxonomic groups to exclude, as a regular expression" help="OTUs matching this regular expression will be assigned as unknown, and by default removed">
                <sanitizer>
                    <valid initial="default">
                        <add value="|" />
                        <add value="$" />
                    </valid>
                </sanitizer>
            </param>
        </section>
    </inputs>

    <outputs>
        <data name="outputs" format="zip" label="${tool.name} on ${on_string}: Complete LotuS2 output" from_work_dir="output.zip" />

        <data name="runlog" format="txt" label="${tool.name} on ${on_string}: main log file" from_work_dir="output/LotuSLogS/LotuS_run.log" />
    </outputs>

    <tests>
        <test>
            <conditional name="inputs">
                <param name="paired_or_single" value="single"/>
                <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/>
            </conditional>
            <param name="platform" value="454" />
            <section name="clu_args">
                <conditional name="clu_cond">
                    <param name="clustering" value="3" />
                </conditional>
                <param name="derepMin" value="1" />
            </section>
            <output name="otu" file="OTU.txt" compare="sim_size" />
            <output name="otu_fna" file="OTU.fna" compare="sim_size" />
            <output name="mapping" file="mapping.txt" />
        </test>
        <test>
            <conditional name="inputs">
                <param name="paired_or_single" value="paired_collection"/>
                <param name="pair_input">
                    <collection type="list:paired">
                        <element name="Anh_sample">
                            <collection type="paired">
                                <element name="forward" value="Anh_sample1.fastq.gz" ftype="fastqsanger.gz" />
                                <element name="reverse" value="Anh_sample2.fastq.gz" ftype="fastqsanger.gz" />
                            </collection>
                        </element>
                    </collection>
                </param>
            </conditional>
            <param name="map" value="mapping_paired.txt" />
            <param name="platform" value="454" />
            <section name="clu_args">
                <conditional name="clu_cond">
                    <param name="clustering" value="3" />
                </conditional>
                <param name="derepMin" value="1" />
            </section>
            <output name="otu" file="OTU_paired.txt" compare="sim_size" />
            <output name="otu_fna" file="OTU_paired.fna" compare="sim_size" />
        </test>
    </tests>