Mercurial > repos > ebi-gxa > scanpy_run_diffmap
view scanpy-run-diffmap.xml @ 9:1709957891e5 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"
author | ebi-gxa |
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date | Thu, 12 Mar 2020 05:15:56 -0400 |
parents | c869331377bf |
children | 713e94af9d6c |
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<?xml version="1.0" encoding="utf-8"?> <tool id="scanpy_run_diffmap" name="Scanpy DiffusionMap" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@"> <description>calculate diffusion components</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 embed diffmap --n-comps ${n_comps} #if $use_graph --use-graph '${use_graph}' #end if #if $key_added --key-added '${key_added}' #end if $export_embed @INPUT_OPTS@ @OUTPUT_OPTS@ ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> <param name="n_comps" argument="--n-comps" type="integer" min="2" value="10" label="Number of diffusion components to calculate"/> <param name="export_embed" argument="--export-embedding" type="boolean" checked="false" truevalue="--export-embedding embed.tsv" falsevalue="" label="Export embeddings as a tab-separated text table"/> <param name="use_graph" argument="--use-graph" value="neighbors" type="text" label="Name of the slot that holds the KNN graph"/> <param name="key_added" argument="--key-added" type="text" optional="true" label="Additional suffix to the name of the slot to save the calculated trajectory"/> </inputs> <outputs> <expand macro="output_data_obj" description="Diffussion Map"/> <data name="output_embed" format="tsv" from_work_dir="embed.tsv" label="${tool.name} on ${on_string}: diffmap embedding"> <filter>export_embed</filter> </data> </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="leiden"/> <param name="root_value" value="1"/> <param name="use_graph" value="neighbors"/> <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/> </test> </tests> <help><![CDATA[ ==================================================== Calculate Diffusion Components (`scanpy.tl.diffmap`) ==================================================== Calculate diffusion components from single cell KNN graphs. This requires to run `Scanpy ComputeGraph`, first. It yields `X_diffmap`, the dimension-reduced representation in diffusion components space. @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations"> <citation type="doi">10.1186/s13059-019-1663-x</citation> </expand> </tool>