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view scanpy-run-fdg.xml @ 15:5d2c8acd2ae4 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit b03a24b2e459a00c79221b160d9187902a4098d0-dirty"
author | ebi-gxa |
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date | Wed, 25 Nov 2020 16:21:23 +0000 |
parents | dd27b39c5c12 |
children | a6190ae4fe16 |
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<?xml version="1.0" encoding="utf-8"?> <tool id="scanpy_run_fdg" name="Scanpy RunFDG" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>visualise cell clusters using force-directed graph</description> <macros> <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-cli embed fdg --key-added-ext '${key_added_ext}' #if $embeddings --export-embedding embeddings.tsv #end if #if $settings.default == "false" #if $settings.neighbors_key --neighbors-key '${settings.neighbors_key}' #end if #if $settings.obsp --obsp '${settings.obsp}' #end if --random-state ${settings.random_seed} --layout ${settings.layout} #if $settings.init_pos --init-pos '${settings.init_pos}' #end if #if $settings.root --root '${settings.root}' #end if #end if @INPUT_OPTS@ @OUTPUT_OPTS@ ]]></command> <inputs> <expand macro="input_object_params"/> <expand macro="output_object_params"/> <param name="embeddings" type="boolean" checked="true" label="Output embeddings in tsv format"/> <param name="key_added_ext" argument="--key-added-ext" type="text" optional="true" label="Additional suffix to the name of the slot to save the embedding"/> <conditional name="settings"> <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/> <when value="false"> <param name="neighbors_key" argument="--neighbors-key" value="neighbors" type="text" label="Name of the slot that holds the KNN graph"/> <param name="obsp" type="boolean" checked="false" label="Use .obsp[obsp] as adjacency" help="You can’t specify both obsp and neighbors-key at the same time."/> <param name="init_pos" argument="--init-pos" type="text" label="Method to initialise embedding, any key for adata.obsm or choose from the preset methods"> <option value="paga">paga</option> </param> <param name="layout" argument="--layout" type="select" label="Graph layout"> <option value="fa">fa</option> <option value="fr" selected="true">fr</option> <option value="grid_fr">grid fr</option> <option value="kk">kk</option> <option value="lgl">lgl</option> <option value="drl">drl</option> <option value="rt">rt</option> <option value="rt_circular">rt_circular</option> </param> <param name="root" argument="--root" type="integer" optional="true" label="Root for tree layouts"/> <param name="random_seed" argument="--random-state" type="integer" value="0" label="Seed for numpy random number generator"/> </when> </conditional> </inputs> <outputs> <expand macro="output_data_obj" description="FDG object"/> <data name="output_embed" format="tabular" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: FDG embeddings"> <filter>embeddings</filter> </data> </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="default" value="false"/> <param name="embeddings" value="true"/> <param name="random_seed" value="0"/> <output name="output_h5" file="run_fdg.h5" ftype="h5" compare="sim_size"/> <output name="output_embed" file="run_fdg.embeddings.tsv" ftype="tabular" compare="sim_size"> <assert_contents> <has_n_columns n="3"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ ================================================================================ Embed the neighborhood graph using Force-directed Graph (`scanpy.tl.draw_graph`) ================================================================================ For making FDG plots, please use `Scanpy PlotEmbed` with the output of this tool and enter "draw_graph_{layout}" as the name of the embedding to plot. It yields `X_draw_graph_{layout}`, FDG coordinates of data. @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations"/> </tool>