Mercurial > repos > ebi-gxa > monocle3_diffexp
diff monocle3-diffExp.xml @ 0:c0441ea8f37a draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
author | ebi-gxa |
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date | Mon, 16 Sep 2019 09:50:52 -0400 |
parents | |
children | a7d4f80d1265 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monocle3-diffExp.xml Mon Sep 16 09:50:52 2019 -0400 @@ -0,0 +1,74 @@ +<?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>