Mercurial > repos > immuneml > immuneml_tools
diff immuneml_create_dataset.xml @ 0:629e7e403e19 draft
"planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
| author | immuneml |
|---|---|
| date | Thu, 01 Jul 2021 11:36:43 +0000 |
| parents | |
| children | ed3932e6d616 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/immuneml_create_dataset.xml Thu Jul 01 11:36:43 2021 +0000 @@ -0,0 +1,178 @@ +<tool id="immune_ml_dataset" name="Create dataset" version="@VERSION@.0"> + <description></description> + <macros> + <import>prod_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command><![CDATA[ + #set $input_orig_names = [] + #for $input in $interface_cond.data_input + #if $input + #set input_orig_names += ["./"+str($input.element_identifier)] + ([ -e ./"$input.element_identifier" ] && echo "File '$input.element_identifier' already exists in the input folder, skipping." || ln -s $input "$input.element_identifier") && + #end if + #end for + + #if $interface_cond.interface == "simple" + python3 '$__tool_directory__/build_dataset_yaml_wrapper.py' + --output_path . --file_name specs.yaml + #if $interface_cond.dataset_cond.dataset_type == "repertoire" + --is_repertoire True + --format "$interface_cond.dataset_cond.metadata_cond.data_format" + #if $interface_cond.dataset_cond.metadata_cond.data_format != "IReceptor" + --metadata_file "$interface_cond.dataset_cond.metadata_cond.metadata_input" && + cp $interface_cond.dataset_cond.metadata_cond.metadata_input "$interface_cond.dataset_cond.metadata_cond.metadata_input.element_identifier" + #end if + #else + --is_repertoire False + --format "$interface_cond.dataset_cond.data_format" + --metadata_columns "$interface_cond.dataset_cond.metadata_columns" + #if $interface_cond.dataset_cond.dataset_type == "sequence" + --paired False + #elif $interface_cond.dataset_cond.dataset_type == "receptor" + --paired True + --receptor_chains $interface_cond.dataset_cond.receptor_type + #end if + #end if + && mv ./specs.yaml create_dataset.yaml && + #else + cp $yaml_input create_dataset.yaml && + #end if + + immune-ml ./create_dataset.yaml ${html_outfile.files_path} --tool DatasetGenerationTool && + + mv ${html_outfile.files_path}/index.html ${html_outfile} && + mv ./create_dataset.yaml ${specs} + + ]]> + </command> + <inputs> + <conditional name="interface_cond"> + <param type="select" name="interface" label="Which interface would you like to use?" display="radio"> + <option value="simple">Simplified (limited options)</option> + <option value="advanced">Advanced (full control through YAML) </option> + </param> + <when value="simple"> + <conditional name="dataset_cond"> + <param type="select" name="dataset_type" label="Dataset type" display="radio" help="Repertoire datasets + should be used when making predictions per repertoire, such as predicting a disease state. Sequence or + receptor datasets should be used when predicting values for unpaired (single-chain) and paired immune + receptors respectively, like antigen specificity."> + <option value="repertoire">Repertoire dataset</option> + <option value="sequence">Sequence dataset (single chain)</option> + <option value="receptor">Receptor dataset (paired chains)</option> + </param> + <when value="repertoire"> + <conditional name="metadata_cond"> + <param type="select" name="data_format" label="Data format" display="radio"> + <option value="AIRR">AIRR</option> + <option value="IReceptor">iReceptor Gateway</option> + <option value="ImmunoSEQRearrangement">immunoSEQ: rearrangement-level files</option> + <option value="ImmunoSEQSample">immunoSEQ: sample-level files</option> + <option value="MiXCR">MiXCR</option> + <option value="VDJdb">VDJdb</option> + <option value="TenxGenomics">10x Genomics ‘Clonotype consensus annotations’ (CSV)</option> + </param> + <when value="AIRR"> + <param name="metadata_input" type="data" format="txt" label="Metadata file" multiple="false" help="The metadata file describes metadata information for all repertoires included in the dataset. Every repertoire ARR file described in the metadata file must be selected under 'Data files'."/> + </when> + <when value="ImmunoSEQRearrangement"> + <param name="metadata_input" type="data" format="txt" label="Metadata file" multiple="false" help="The metadata file describes metadata information for all repertoires included in the dataset. Every repertoire immunoSEQ rearrangement file described in the metadata file must be selected under 'Data files'."/> + </when> + <when value="ImmunoSEQSample"> + <param name="metadata_input" type="data" format="txt" label="Metadata file" multiple="false" help="The metadata file describes metadata information for all repertoires included in the dataset. Every repertoire immunoSEQ sample file described in the metadata file must be selected under 'Data files'."/> + </when> + <when value="MiXCR"> + <param name="metadata_input" type="data" format="txt" label="Metadata file" multiple="false" help="The metadata file describes metadata information for all repertoires included in the dataset. Every repertoire MiXCR file described in the metadata file must be selected under 'Data files'."/> + </when> + <when value="VDJdb"> + <param name="metadata_input" type="data" format="txt" label="Metadata file" multiple="false" help="The metadata file describes metadata information for all repertoires included in the dataset. Every repertoire VDJdb file described in the metadata file must be selected under 'Data files'."/> + </when> + <when value="TenxGenomics"> + <param name="metadata_input" type="data" format="txt" label="Metadata file" multiple="false" help="The metadata file describes metadata information for all repertoires included in the dataset. Every repertoire 10x Genomics file described in the metadata file must be selected under 'Data files'."/> + </when> + </conditional> + </when> + <when value="sequence"> + <param type="select" name="data_format" label="Data format" display="radio"> + <option value="AIRR">AIRR</option> + <option value="IReceptor">iReceptor Gateway</option> + <option value="ImmunoSEQRearrangement">ImmunoSEQ: rearrangement-level files</option> + <option value="ImmunoSEQSample">ImmunoSEQ: sample-level files</option> + <option value="MiXCR">MiXCR</option> + <option value="VDJdb">VDJdb</option> + <option value="TenxGenomics">10xGenomics ‘Clonotype consensus annotations’ (CSV)</option> + </param> + <param type="text" name="metadata_columns" optional="false" label="Metadata columns" help="Please + specify the names of the columns that contain metadata. The metadata columns specified here can be + used as labels for prediction. Multiple metadata columns may be specified and separated by comma, + for example: Epitope,Epitope gene,Epitope species"/> + </when> + <when value="receptor"> + <param type="select" name="data_format" label="Data format" display="radio"> + <option value="AIRR">AIRR</option> + <option value="IReceptor">iReceptor Gateway</option> + <option value="VDJdb">VDJdb</option> + <option value="TenxGenomics">10xGenomics ‘Clonotype consensus annotations’ (CSV)</option> + </param> + <param type="select" name="receptor_type" label="Receptor type" display="radio"> + <option value="TRA_TRB">T cell alpha/beta</option> + <option value="TRG_TRD">T cell gamma/delta</option> + <option value="IGH_IGL">B cell heavy/light</option> + <option value="IGH_IGK">B cell heavy/kappa</option> + </param> + <param type="text" name="metadata_columns" optional="false" label="Metadata columns" help="Please + specify the names of the columns that contain metadata. The metadata columns specified here can be + used as labels for prediction. Multiple metadata columns may be specified and separated by comma, + for example: Epitope,Epitope gene,Epitope species"/> + </when> + </conditional> + <param name="data_input" type="data" multiple="true" label="Data files" min="1" max="2000" help="This field should include individual repertoire or receptor files, or iReceptor zip files. Multiple files can be selected by holding down the control/command or shift key, or by clicking 'browse datasets' (folder button on the right). Important: make sure all the files you want to include in the dataset are highlighted in blue or gray."/> + </when> + <when value="advanced"> + <param name="yaml_input" type="data" format="txt" label="YAML specification" multiple="false"/> + <param name="data_input" type="data" multiple="true" label="Data and metadata files" optional="true" help="This field should include individual repertoire or receptor files, or iReceptor zip files, and optionally a metadata file. Multiple files can be selected by holding down the control/command or shift key, or by clicking 'browse datasets' (folder button on the right). Important: make sure all the files you want to include in the dataset are highlighted."/> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="specs" label="create_dataset.yaml"/> + <data format="iml_dataset" name="html_outfile" label="ImmuneML dataset"/> + </outputs> + + + <help><![CDATA[ + + In Galaxy, an immuneML dataset is simply a Galaxy collection containing all relevant files (including an optional metadata file). + The Create dataset Galaxy tool allows users to import data from various formats and create immuneML datasets in Galaxy. + These datasets are in an optimized binary (Pickle) format, which ensures that you can quickly import the dataset into + Galaxy tools without having to repeatedly specify the import parameters. + + Before creating a dataset, the relevant data files must first be uploaded to the Galaxy interface. This can be done either + by uploading files from your local computer (use the 'Upload file' tool under the 'Get local data' menu), or by fetching + remote data from the iReceptor Plus Gateway or VDJdb (see `How to import remote AIRR datasets in Galaxy <https://docs.immuneml.uio.no/galaxy/galaxy_import_remote_data.html>`_). + + The imported immuneML dataset is stored in a Galaxy collection, which will appear as a history item on the right side of the screen, + and can later be selected as input to other tools. + + The tool has a simplified and an advanced interface. The simplified interface is fully button-based, and relies + on default settings for importing datasets. The advanced interface gives full control over import settings through a YAML + specification. In most cases, the simplified interface will suffice. + + For the exhaustive documentation of this tool and more information about immuneML datasets, see the tutorial `How to make an immuneML dataset in Galaxy <https://docs.immuneml.uio.no/galaxy/galaxy_dataset.html>`_. + + **Tool output** + + This Galaxy tool will produce the following history elements: + + - ImmuneML dataset: a sequence, receptor or repertoire dataset which can be used as an input to other immuneML tools. The history element contains a summary HTML page describing general characteristics of the dataset, including the name of the dataset + (which is used in the dataset definition of a yaml specification), the dataset type and size, available labels, and a link to download the raw data files. + + - create_dataset.yaml: the YAML specification file that was used by immuneML to create the dataset. + This file can be downloaded and altered (for example to export files in AIRR format, or use non-standard import parameters), + and run again using the 'Advanced' interface. + + ]]> + </help> + +</tool>