| Next changeset 1:3e737c810a54 (2020-01-29) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114" |
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added:
monocle3-macros.xml monocle3-plotCells.xml |
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| diff -r 000000000000 -r 896359db6339 monocle3-macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monocle3-macros.xml Mon Sep 16 09:51:16 2019 -0400 |
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| @@ -0,0 +1,64 @@ +<macros> + <token name="@TOOL_VERSION@">0.1.2</token> + <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/monocle3/ and https://github.com/ebi-gene-expression-group/monocle-scripts</token> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** + +0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2 + ]]></token> + <token name="@INPUT_OPTS@"> + --input-object-format '${input_object_format}' '${input_object_file}' + </token> + <token name="@OUTPUT_OPTS@"> + --output-object-format '${output_object_format}' output.RDS +#if $introspective + --introspective +#end if + </token> + <token name="@VERBOSE@"> +#if $verbose + --verbose +#end if + </token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.0.3">monocle3-cli</requirement> + <yield/> + </requirements> + </xml> + + <xml name="citations"> + <citations> + <yield /> + <citation type="doi">10.1038/nmeth.4402</citation> + <citation type="bibtex"> + @misc{githubscanpy-scripts, + author = {Ni Huang, Krzysztof Polanski, EBI Gene Expression Team}, + year = {2019}, + title = {Monocle3-cli: command line interface for Monocle3}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/monocle-scripts}, + }</citation> + </citations> + </xml> + + <xml name="input_object_params"> + <param name="input_object_file" argument="input-object-file" type="data" format="rdata" label="Input object in RDS format"/> + <param name="input_object_format" argument="--input-object-format" type="select" label="Format of input object"> + <option value="cds3" selected="true">Monocle3 object in RDS</option> + </param> + </xml> + + <xml name="output_object_params"> + <param name="output_object_format" argument="--output-object-format" type="select" label="Format of output object"> + <option value="cds3" selected="true">Monocle3 object in RDS</option> + </param> + <param name="introspective" argument="--introspective" type="boolean" checked="true" label="Print introspective information of output object"/> + </xml> + + <xml name="verbose_flag"> + <param name="verbose" argument="--verbose" type="boolean" checked="false" label="Emit verbose output"/> + </xml> +</macros> |
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| diff -r 000000000000 -r 896359db6339 monocle3-plotCells.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monocle3-plotCells.xml Mon Sep 16 09:51:16 2019 -0400 |
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| @@ -0,0 +1,114 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="monocle3_plotCells" name="Monocle3 plotCells" version="@TOOL_VERSION@+galaxy0"> + <description> in the reduced dimensionality space</description> + <macros> + <import>monocle3-macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +LANG=en_US.UTF-8 monocle3 plotCells + --reduction-method '$(reduction_method)' + --norm-method '$(norm_method)' +#if $xdim + --xdim '$(xdim)' +#end if +#if $ydim + --ydim '$(ydim)' +#end if +#if $color_cells_by + --color-cells-by '$(color_cells_by)' +#end if +#if $genes + --genes '$(genes)' +#end if +#if $cell_size + --cell-size '$(cell_size)' +#end if +#if $alpha + --alpha '$(alpha)' +#end if +#if $label_cell_groups + --label-cell-groups +#end if +#if $no_trajectory_graph + --no-trajectory-graph +#end if +#if $label_groups_by_cluster + --label-groups-by-cluster +#end if +#if $label_leaves + --label-leaves +#end if +#if $label_roots + --label-roots +#end if +#if $label_branch_points + --label-branch-points +#end if + + @INPUT_OPTS@ + output.png + + @VERBOSE@ +]]></command> + + <inputs> + <expand macro="input_object_params"/> + <param name="xdim" argument="--xdim" optional="true" type="integer" value="1" label="The column of reducedDimS(cds) to plot on the horizontal axis."/> + <param name="ydim" argument="--ydim" optional="true" type="integer" value="2" label="The column of reducedDimS(cds) to plot on the vertical axis."/> + <param name="reduction_method" argument="--reduction-method" type="select" label="The dimensionality reduction for plotting."> + <option value="UMAP" selected="true">UMAP</option> + <option value="tSNE">tSNE</option> + <option value="PCA">PCA</option> + <option value="LSI">LSI</option> + </param> + <param name="color_cells_by" argument="--color-cells-by" optional="true" type="text" value="pseudotime" label="The cell attribute (e.g. the column of pData(cds)) to map to each cell's color, or one of {cluster, partition, pseudotime}."/> + <param name="genes" argument="--genes" optional="true" type="text" label="A list of gene IDs/short names to plot, one per panel."/> + <param name="norm_method" argument="--norm-method" type="select" label="Determines how to transform expression values for plotting."> + <option value="log" selected="true">Size factor correction and log transformation</option> + <option value="size_only">Size factor correction only</option> + </param> + <param name="cell_size" argument="--cell-size" optional="true" type="float" value="1.5" label="The size of the point for each cell."/> + <param name="alpha" argument="--alpha" optional="true" type="float" value="1" label="The alpha aesthetics for the original cell points, useful to highlight the learned principal graph."/> + <param name="label_cell_groups" argument="--label-cell-groups" type="boolean" checked="true" label="If set, display the cell group names directly on the plot. Otherwise include a color legend on the side of the plot."/> + <param name="no_trajectory_graph" argument="--no-trajectory-graph" type="boolean" checked="false" label="When this option is set, skip displaying the trajectory graph inferred by learn_graph()."/> + <param name="label_groups_by_cluster" argument="--label-groups-by-cluster" type="boolean" checked="false" label="If set, and setting --color-cells-by to something other than cluster, label the cells of each cluster independently. Can result in duplicate labels being present in the manifold."/> + <param name="label_leaves" argument="--label-leaves" type="boolean" checked="false" label="If set, label the leaves of the principal graph."/> + <param name="label_roots" argument="--label-roots" type="boolean" checked="false" label="If set, label the roots of the principal graph."/> + <param name="label_branch_points" argument="--label-branch-points" type="boolean" checked="false" label="If set, label the branch points of the principal graph."/> + <expand macro="verbose_flag"/> + </inputs> + + <outputs> + <data name="output_tsv" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: png"/> + </outputs> + + <tests> + <test> + <param name="input_object_file" value="input.RDS"/> + <param name="input_object_format" value="cds3"/> + <param name="reduction_method" value="UMAP"/> + <param name="xdim" value="1"/> + <param name="ydim" value="2"/> + <param name="color_cells_by" value="pseudotime"/> + <param name="norm_method" value="log"/> + <param name="cell_size" value="1.5"/> + <param name="alpha" value="1"/> + <output name="output_tsv" file="output.tsv" ftype="tsv" compare="sim_size"/> + </test> + </tests> + + <help><![CDATA[ +===================================== +Monocle3 cell plotting (`plot_cells`) +===================================== + +Display various information about cells (clustering, pseudotime, the inferred graph, +user-provided annotations, gene expression) in reduced dimensions. + +@HELP@ + +@VERSION_HISTORY@ +]]></help> + <expand macro="citations"/> +</tool> |