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author | ebi-gxa |
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date | Tue, 27 Feb 2024 16:43:15 +0000 |
parents | 18e01a7c55c6 |
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<?xml version="1.0" encoding="utf-8"?> <tool id="scanpy_integrate_harmony" name="Scanpy Harmony" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>adjust principal components for variables that might introduce batch effect</description> <macros> <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ #if $batch_key ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-cli integrate harmony --batch-key '${batch_key}' #if $basis --basis '${basis}' #end if --adjusted-basis '${adjusted_basis}' #if not $settings.default #if $settings.theta --theta '${settings.theta}' #end if #if $settings.lambda --lambda '${settings.lambda}' #end if #if $settings.sigma --sigma '${settings.sigma}' #end if #if $settings.nclust --nclust '${settings.nclust}' #end if #if $settings.tau --tau '${settings.tau}' #end if #if $settings.block_size --block-size '${settings.block_size}' #end if #if $settings.max_iter_cluster --max-iter-cluster '${settings.max_iter_cluster}' #end if #if $settings.max_iter_harmony --max-iter-harmony '${settings.max_iter_harmony}' #end if #if $settings.epsilon_cluster --epsilon-cluster '${settings.epsilon_cluster}' #end if #if $settings.epsilon_harmony --epsilon-harmony '${settings.epsilon_harmony}' #end if #if $settings.random_state --random-state '${settings.random_state}' #end if #end if @INPUT_OPTS@ @OUTPUT_OPTS@ #else echo "No batch variables passed, simply passing original input as output unchanged." && cp '${input_obj_file}' output.h5 #end if ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> <param name="batch_key" type="text" argument="--batch-key" label="The name of the column in adata.obs that differentiates among experiments/batches."> <sanitizer> <valid initial="string.printable"/> </sanitizer> </param> <param name="basis" argument="--basis" type="text" value='X_pca' label="The name of the field in adata.obsm where the PCA table is stored. Defaults to 'X_pca', which is the default for sc.tl.pca()."> <sanitizer> <valid initial="string.printable"/> </sanitizer> </param> <param name="adjusted_basis" argument="--adjusted-basis" type="text" value='X_pca_harmony' label="he name of the field in adata.obsm where the adjusted PCA table will be stored after running this function."> <sanitizer> <valid initial="string.printable"/> </sanitizer> </param> <conditional name="settings"> <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/> <when value="false"> <param name="theta" argument="--theta" type="float" value="2.0" label="Diversity clustering penalty parameter" help="theta=0 does not encourage any diversity. Larger values of theta result in more diverse clusters." /> <param name="lambda" argument="--lambda" type="float" min="0" value="1.0" label="Ridge regression penalty parameter" help="Lambda must be strictly positive. Smaller values result in more aggressive correction." /> <param name="sigma" argument="--sigma" type="float" value="0.1" label="Ridge regression penalty parameter" help="Width of soft kmeans clusters. Sigma scales the distance from a cell to cluster centroids. Larger values of sigma result in cells assigned to more clusters. Smaller values of sigma make soft kmeans cluster approach hard clustering." /> <param name="nclust" argument="--nclust" type="integer" value="" optional="true" label="Number of clusters in model." help="nclust=1 equivalent to simple linear regression." /> <param name="tau" argument="--tau" type="integer" value="0" label="Protection against overclustering small datasets with large ones." help="'tau is the expected number of cells per cluster." /> <param name="block_size" argument="--block-size" type="float" value="0.05" label="What proportion of cells to update during clustering" min="0" max="1" help="Between 0 to 1, default 0.05. Larger values may be faster but less accurate." /> <param name="max_iter_cluster" argument="--max-iter-cluster" type="integer" value="20" label="Maximum number of rounds to run clustering at each round of Harmony" /> <param name="max_iter_harmony" argument="--max-iter-harmony" type="integer" value="10" label="Maximum number of rounds to run Harmony. One round of Harmony involves one clustering and one correction step." /> <param name="epsilon_cluster" argument="--epsilon-cluster" type="float" value="0.00001" label="Convergence tolerance for clustering round of Harmony" help="Set to -Inf to never stop early." /> <param name="epsilon_harmony" argument="--epsilon-harmony" type="float" value="0.00001" label="Convergence tolerance for Harmony." help="Set to -Inf to never stop early." /> <param name="random_state" argument="--random-state" type="integer" value="0" label="Seed for random number generator." /> </when> </conditional> </inputs> <outputs> <expand macro="output_data_obj" description="Batch-corrected for ${batch_key}"/> </outputs> <tests> <test> <param name="input_obj_file" value="find_cluster.h5"/> <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> <param name="batch_key" value="louvain"/> <output name="output_h5" ftype="h5"> <assert_contents> <has_h5_keys keys="obsm/X_pca_harmony"/> </assert_contents> </output> </test> <test> <param name="input_obj_file" value="find_cluster.h5"/> <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> <output name="output_h5" file="harmony_copy.h5" ftype="h5" compare="sim_size" delta_frac="0.1"/> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** Uses harmonypy [Korunsky19] to integrate different experiments at the principal components level. @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations"/> </tool>