Mercurial > repos > ebi-gxa > scanpy_integrate_harmony
diff scanpy-integrate-harmony.xml @ 0:8b3a52fbb482 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author | ebi-gxa |
---|---|
date | Mon, 07 Sep 2020 13:10:56 +0000 |
parents | |
children | f1298838e93b |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy-integrate-harmony.xml Mon Sep 07 13:10:56 2020 +0000 @@ -0,0 +1,134 @@ +<?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-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" file="harmony.h5" ftype="h5" compare="sim_size"/> + </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>