Mercurial > repos > ebi-gxa > scanpy_run_dpt
view scanpy-run-dpt.xml @ 14:730d098a9f23 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 2db9e8cecb8d373874318e53ec2d4d7a64dd1b24-dirty"
author | ebi-gxa |
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date | Fri, 11 Sep 2020 11:04:10 +0000 |
parents | 820493156c4a |
children | 2e06dabb3f2f |
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<?xml version="1.0" encoding="utf-8"?> <tool id="scanpy_run_dpt" name="Scanpy DPT" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>diffusion pseudotime inference</description> <macros> <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-cli dpt --n-dcs $n_dcs --root '${root_attr}' '${root_value}' #if $n_branchings > 0 --n-branchings ${n_branchings} --min-group-size ${min_group_size} #end if #if $use_graph --neighbors-key '${use_graph}' #end if #if $key_added --key-added '${key_added}' #end if #if not $allow_kendall_tau_shift --disallow-kendall-tau-shift #end if @INPUT_OPTS@ @OUTPUT_OPTS@ ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> <param name="n_dcs" argument="--n-dcs" type="integer" min="2" value="10" label="Number of diffusion components to use"/> <param name="n_branchings" argument="--n-branchings" min="0" type="integer" value="0" label="Number of branchings to detect"/> <param name="min_group_size" argument="--min-group-size" type="float" min="0" max="1" value="0" label="The fraction of total cells under which further splitting is skipped during recursive splitting of branches" help="Ignored when `Number of branchings to detect` is 0"/> <param name="root_attr" argument="--root {attr} value" type="text" label="Name of attribute that defines clustering"/> <param name="root_value" argument="--root attr {value}" type="text" label="Name of the clustering that defines the root cell type"/> <param name="use_graph" argument="--neighbors-key" value="neighbors" type="text" label="Name of the slot that holds the KNN graph"/> <param name="key_added" argument="--key-added" type="text" optional="true" label="Additional suffix to the name of the slot to save the calculated pseudo-time"/> <param name="allow_kendall_tau_shift" type="boolean" checked="true" label="Allow Kendall Tau shift" help="If a very small branch is detected upon splitting, shift away from maximum correlation in Kendall tau criterion of [Haghverdi16] to stabilize the splitting" /> </inputs> <outputs> <expand macro="output_data_obj" description="Diffussion pseudotime inference"/> </outputs> <tests> <test> <param name="input_obj_file" value="diffmap.h5"/> <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> <param name="n_dcs" value="10"/> <param name="root_attr" value="louvain"/> <param name="root_value" value="1"/> <param name="use_graph" value="neighbors"/> <output name="output_h5" file="dpt.h5" ftype="h5" compare="sim_size"/> </test> </tests> <help><![CDATA[ ================================================ Calculate Diffusion Pseudotime (`scanpy.tl.dpt`) ================================================ Calculate diffusion pseudotime from single cell KNN graphs. This requires to run `Scanpy DiffusionMap` and `Scanpy FindCluster`, first. It yields `dpt_pseudotime`, diffusion pseudotime as an attribute for each cell. @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations"> <citation type="doi">10.1186/s13059-019-1663-x</citation> </expand> </tool>