Mercurial > repos > iuc > mirnature
diff mirnature.xml @ 0:dd2f87ccbd2c draft default tip
planemo upload for repository https://github.com/Bierinformatik/miRNAture commit 9e4e624a3a486cbd805bc3beb00e9903f315efe0
| author | iuc |
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| date | Sun, 11 Dec 2022 22:28:10 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mirnature.xml Sun Dec 11 22:28:10 2022 +0000 @@ -0,0 +1,246 @@ +<tool id="mirnature" name="miRNAture" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> + <description>Computational detection of canonical microRNAs</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="aggressive"><![CDATA[ + #import re + mkdir -p uncompress && + mkdir -p queries_to_test && + mkdir -p temporal && + mkdir -p output && + + cp '$speG' temporal/genome.fasta && + #if $blast_strategy: + cp '$queries_to_blast' queries_to_test/Unknown_species.fa && + echo "Unknown_species.fa miRNA Unknown species" > queries_to_test/queries_description.txt && + #end if + + #if str('$database_source.database_source_selector') == "cached": + ln -s '$dataset.fields.path' uncompress/data.gz && + #else: + ln -s '$dataset' uncompress/data.gz && + #end if + tar -xf uncompress/data.gz --directory uncompress/ && + rm uncompress/data.gz && + ## Change name of user folder to Dataset + mv uncompress/* uncompress/Dataset && + + miRNAture + -stage '$stage' + #if $subset_models + -sublist '$subset_models' + #end if + -nbitscore_cut '$nbitscore' + -dataF 'uncompress/Dataset/' + -speG 'temporal/genome.fasta' + -speN '$speN' + -speT '$speT' + -pe '1' + -workdir 'output/' + -m "${",".join(map(str, $homology_mode)) + ",final"}" + #if $blast_strategy: + -strategy "${",".join(map(str, $blast_strategy)) + ",ALL"}" + -blstq 'queries_to_test/' + #end if + -rep '$repeat_filter' > '$std_output' + ]]></command> + + <inputs> + <!--File--> + <param argument="-speG" format="fasta" multiple="true" type="data" + label="Input genome or sequence" + help="Input sequence to be processed by miRNAture" /> + + <!--TEXT--> + <param argument="-speN" type="text" label="Scientific species name written separated by '_', such as: Homo_sapiens" > + <validator type="regex" message="Only letters and underscores are allowed">^[\(\w\)]+$</validator> + </param> + <param argument="-speT" type="text" label="Species tag to identify through experiment (i.e short 4 letters tag)" > + <validator type="regex" message="Please write only letters">^[a-zA-Z]+$</validator> + </param> + + <!--NUM--> + <param argument="-nbitscore_cut" name="nbitscore" type="float" label="nBitscore" + value="1" min="0" max="1" help="Control of normalized bitscore (nbitscore) threshold to filter Rfam candidates" /> + + <param argument="-rep" name="repeat_filter" type="select" label="Repeats filter" help="Repetition cutoff" > + <option value="relax,150,100">relax</option> + <option value="default,200,100">default</option> + </param> + + <param format="txt" multiple="true" name="subset_models" type="data" + label="List of miRNA models to be searched" + help="Input sequence to be processed by miRNAture" optional="true"/> + + <conditional name="database_source"> + <param argument="-dataF" name="database_source_selector" type="select" label="Choose the source for the database"> + <option value="cached">Pre-defined datasets</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="dataset" type="select" help="Select a pre-calculated dataset to run miRNAture (i.e. https://doi.org/10.5281/zenodo.7180160)" label="Pre-calculated datasets" > + <options from_data_table="mirnature_selection" /> + <validator message="No reference dataset is available for miRNAture" type="no_options" /> + </param> + </when> + <when value="history"> + <param name="dataset" format="gz" type="data" label="Input user Pre-calculated dataset" help="Please submit the pre-calculated data to run miRNAture (i.e https://doi.org/10.5281/zenodo.7180160)" /> + </when> + </conditional> + +<!--Static list--> + <param argument="-stage" type="select" label="Select one miRNAture stage"> + <option value="complete">complete</option> + <option value="homology">homology</option> + </param> + <!--Check Boxes--> + <param argument="-mode" name="homology_mode" type="select" multiple="true" label="Homology mode"> + <option value="blast">blast</option> + <option value="rfam">rfam</option> + <option value="mirbase">mirbase</option> + <option value="hmm">hmm</option> + </param> + <param argument="-strategy" name="blast_strategy" optional="true" type="select" multiple="true" + label="Select one or more pre-calculated set of blastn parameters, accordingly to the miRNAture publication."> + <option value="1">1</option> + <option value="2">2</option> + <option value="3">3</option> + <option value="4">4</option> + <option value="5">5</option> + <option value="6">6</option> + <option value="7">7</option> + <option value="8">8</option> + <option value="9">9</option> + </param> + <param argument="-blstq" format="fasta" multiple="true" name="queries_to_blast" type="data" label="Query sequences" + help="Query sequences to search in target genome" optional="true" /> +</inputs> + +<outputs> + <data name="std_output" format="txt" label="Standard output miRNAture" /> + <collection name="gff3_files_h" type="list" label="${tool.name} on ${on_string}: GFF3 file"> + <discover_datasets pattern="(?P<designation>.+)\.gff3" directory="output/miRNA_prediction/Final_Candidates/" format="gff3" visible="true" /> + <filter> stage == "homology" </filter> + </collection> + <collection name="tab_files_h" type="list" label="${tool.name} on ${on_string}: Additional Files"> + <discover_datasets pattern="(?P<designation>.+)\-potential\.txt" directory="output/miRNA_prediction/Final_Candidates/" format="txt" visible="true" /> + <filter> stage == "homology" </filter> + </collection> + <collection name="yaml_files_h" type="list" label="${tool.name} on ${on_string}: YAML file"> + <discover_datasets pattern="(?P<designation>.+)\.yaml" directory="output" format="yaml" visible="true"/> + <filter> stage == "homology" </filter> + </collection> + <collection name="gff3_files_c" type="list" label="${tool.name} on ${on_string}: GFF3 file"> + <discover_datasets pattern="(?P<designation>.+)\.gff3" directory="output/miRNA_prediction/Final_Candidates/" format="gff3" visible="true" /> + <discover_datasets pattern="(?P<designation>.+)\.gff3" directory="output/Final_miRNA_evaluation/" ext="gff3" format="gff3" visible="true" /> + <filter> stage == "complete" </filter> + </collection> + <collection name="bed_files_c" type="list" label="${tool.name} on ${on_string}: BED file"> + <discover_datasets pattern="(?P<designation>.+)\.bed" directory="output/Final_miRNA_evaluation/" ext="bed" format="bed" visible="true" /> + <filter> stage == "complete" </filter> + </collection> + <collection name="fasta_files_c" type="list" label="${tool.name} on ${on_string}: Fasta files"> + <discover_datasets pattern="(?P<designation>.+)\.fasta" directory="output/Final_miRNA_evaluation/Fasta" ext="fasta" format="fasta" visible="true" /> + <filter> stage == "complete" </filter> + </collection> + <collection name="statistics_files_c" type="list" label="${tool.name} on ${on_string}: Summary file"> + <discover_datasets pattern="(?P<designation>.+)\.txt" directory="output/Final_miRNA_evaluation/" ext="txt" format="txt" visible="true" /> + <filter> stage == "complete" </filter> + </collection> + <collection name="yaml_files_c" type="list" label="${tool.name} on ${on_string}: YAML file"> + <discover_datasets pattern="(?P<designation>.+)\.yaml" directory="output" ext="yaml" format="yaml" visible="true"/> + <filter> stage == "complete" </filter> + </collection> +</outputs> + +<tests> + <!-- HMM Rfam search --> + <test expect_exit_code="0"> + <param name="stage" value="homology"/> + <param name="subset_models" value="fam.txt"/> + <param name="nbitscore" value="1.0"/> + <param name="database_source_selector" value="history" /> + <param name="dataset" value="Dataset_mirnature_tutorial.tar.gz"/> + <param name="speG" value="genome.fasta"/> + <param name="speN" value="Unknown_species"/> + <param name="speT" value="Unsg"/> + <param name="homology_mode" value="hmm"/> + <param name="repeat_filter" value="relax"/> + <output name="std_output" file="test_hmm.txt" ftype="txt"/> + <output_collection name="gff3_files_h" count="1"/> + <output_collection name="yaml_files_h" count="1"/> + <output_collection name="tab_files_h" count="1"/> + </test> + <!-- Infernal Rfam search --> + <test expect_exit_code="0"> + <param name="stage" value="homology"/> + <param name="subset_models" value="fam.txt"/> + <param name="nbitscore" value="1.0"/> + <param name="database_source_selector" value="history" /> + <param name="dataset" value="Dataset_mirnature_tutorial.tar.gz"/> + <param name="speG" value="genome.fasta"/> + <param name="speN" value="Unknown_species"/> + <param name="speT" value="Unsp"/> + <param name="homology_mode" value="rfam"/> + <param name="repeat_filter" value="relax"/> + <output name="std_output" file="test_rfam.txt" ftype="txt"/> + <output_collection name="gff3_files_h" count="1"/> + <output_collection name="yaml_files_h" count="1"/> + <output_collection name="tab_files_h" count="1"/> + </test> + <!-- Infernal miRBase search --> + <test expect_exit_code="0"> + <param name="stage" value="homology"/> + <param name="subset_models" value="fam.txt"/> + <param name="nbitscore" value="1.0"/> + <param name="database_source_selector" value="history" /> + <param name="dataset" value="Dataset_mirnature_tutorial.tar.gz"/> + <param name="speG" value="genome.fasta"/> + <param name="speN" value="Unknown_species"/> + <param name="speT" value="Unsd"/> + <param name="homology_mode" value="mirbase"/> + <param name="repeat_filter" value="relax"/> + <output name="std_output" file="test_mirbase.txt" ftype="txt"/> + <output_collection name="gff3_files_h" count="1"/> + <output_collection name="yaml_files_h" count="1"/> + <output_collection name="tab_files_h" count="1"/> + </test> + <!-- Combined all homology search --> + <test expect_exit_code="0"> + <param name="stage" value="homology"/> + <param name="subset_models" value="fam.txt"/> + <param name="nbitscore" value="1.0"/> + <param name="database_source_selector" value="history" /> + <param name="dataset" value="Dataset_mirnature_tutorial.tar.gz"/> + <param name="speG" value="genome.fasta"/> + <param name="speN" value="Unknown_species"/> + <param name="speT" value="Unsp"/> + <param name="homology_mode" value="blast,hmm,rfam,mirbase"/> + <param name="blast_strategy" value="8,9"/> + <param name="queries_to_blast" value="test.fasta"/> + <param name="repeat_filter" value="relax"/> + <output name="std_output" file="test_all_homology.txt" ftype="txt"/> + <output_collection name="gff3_files_h" count="1"/> + <output_collection name="yaml_files_h" count="1"/> + <output_collection name="tab_files_h" count="1"/> + </test> +</tests> + +<help><![CDATA[ + +**miRNAture** detects *bona fide* miRNA candidates through sequence homology searches and validation steps using structural alignments +with pre-defined or/and modified miRNA-specific covariance models. The miRNAture pipeline is composed of three modules: + + #. Homology search operating on miRNA precursors + #. Prediction of the positioning of mature miRNAs within the precursor mature annotation + #. Evaluation scheme designed to identify false positive miRNA annotations. + +This multi-stage approach generates annotation files in BED/GFF3 from precursors and detected mature regions and corresponding FASTA files. +At the same time, a summary file with the MFE, precursor length and number of loci of each annotated miRNA family. + + ]]></help> + <expand macro="creators" /> + <expand macro="citations" /> +</tool>