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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 08ac0ad9182623944c4546f8ea8db6a1a537f7eb
author | ebi-gxa |
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date | Wed, 29 Jan 2020 10:38:45 -0500 |
parents | c0441ea8f37a |
children | a7d4f80d1265 |
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<?xml version="1.0" encoding="utf-8"?> <tool id="monocle3_diffExp" name="Monocle3 diffExp" version="@TOOL_VERSION@+galaxy0"> <description> of genes along a trajectory</description> <macros> <import>monocle3-macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ LANG=en_US.UTF-8 monocle3 diffExp --neighbor-graph '$(neighbor_graph)' --reduction-method '$(reduction_method)' #if $knn --knn '$(knn)' #end if --method '$(method)' --alternative '$(alternative)' @INPUT_OPTS@ output.tsv @VERBOSE@ ]]></command> <inputs> <expand macro="input_object_params"/> <param name="neighbor_graph" argument="--neighbor-graph" type="select" label="What neighbor graph to use, principal graph recommended for trajectory analysis."> <option value="knn" selected="true">KNN</option> <option value="principal_graph">Principal graph</option> </param> <param name="reduction_method" argument="--reduction-method" type="select" label="The reduction method to base the analysis on."> <option value="UMAP" selected="true">UMAP</option> </param> <param name="knn" argument="--knn" optional="true" type="integer" value="20" label="Number of nearest neighbors used for building the kNN graph which is passed to knn2nb function during the Moran's I (Geary's C) test procedure."/> <param name="method" argument="--method" type="select" label="A character string specifying the method for detecting significant genes showing correlated expression along the principal graph embedded in the low dimensional space."> <option value="Moran_I" selected="true">Moran_I</option> </param> <param name="alternative" argument="--alternative" type="select" label="A character string specifying the alternative hypothesis."> <option value="greater" selected="true">greater</option> <option value="less">less</option> <option value="two.sided">two-sided</option> </param> <expand macro="verbose_flag"/> </inputs> <outputs> <data name="output_tsv" format="tsv" from_work_dir="output.tsv" label="${tool.name} on ${on_string}: tsv"/> </outputs> <tests> <test> <param name="input_object_file" value="input.RDS"/> <param name="input_object_format" value="cds3"/> <param name="neighbor_graph" value="knn"/> <param name="reduction_method" value="UMAP"/> <param name="knn" value="20"/> <param name="method" value="Moran_I"/> <param name="alternative" value="greater"/> <output name="output_tsv" file="output.tsv" ftype="tsv" compare="sim_size"/> </test> </tests> <help><![CDATA[ ======================================================================== Monocle3 differential expression testing along trajectory (`graph_test`) ======================================================================== Identify differentially expressed genes along the inferred trajectory. @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations"/> </tool>