--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/monocle3-create.xml	Mon Sep 16 09:52:55 2019 -0400
@@ -0,0 +1,82 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="monocle3_create" name="Monocle3 create" version="@TOOL_VERSION@+galaxy0">
+  <description>a Monocle3 object from input data</description>
+  <macros>
+    <import>monocle3-macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+ln -s '${expression_matrix}' expression_matrix.'${expression_matrix_format}' &&
+#if $cell_metadata
+ln -s '${cell_metadata}' cell_metadata.'${cell_metadata_format}' &&
+#end if
+#if $gene_annotation
+ln -s '${gene_annotation}' gene_annotation.'${gene_annotation_format}' &&
+#end if
+LANG=en_US.UTF-8 monocle3 create
+    --expression-matrix expression_matrix.'${expression_matrix_format}'
+#if $cell_metadata
+    --cell-metadata cell_metadata.'${cell_metadata_format}'
+#end if
+#if $gene_annotation
+    --gene-annotation gene_annotation.'${gene_annotation_format}'
+#end if
+    @OUTPUT_OPTS@
+    @VERBOSE@
+]]></command>
+
+  <inputs>
+    <param name="expression_matrix" argument="--expression-matrix" type="data" format="tsv,csv,rdata" label="Expression matrix, genes as rows, cells as columns. Required input. Provide as TSV, CSV or RDS."/>
+    <param name="expression_matrix_format" type="select" label="Format of expression matrix">
+      <option value="rds" selected="true">RDS</option>
+      <option value="tsv">TSV</option>
+      <option value="csv">CSV</option>
+    </param>
+    <param name="cell_metadata" argument="--cell-metadata" optional="true" type="data" format="tsv,csv,rdata" label="Per-cell annotation, optional. Row names must match the column names of the expression matrix. Provide as TSV, CSV or RDS."/>
+    <param name="cell_metadata_format" type="select" label="Format of cell metadata">
+      <option value="rds" selected="true">RDS</option>
+      <option value="tsv">TSV</option>
+      <option value="csv">CSV</option>
+    </param>
+    <param name="gene_annotation" argument="--gene-annotation" optional="true" type="data" format="tsv,csv,rdata" label="Per-gene annotation, optional. Row names must match the row names of the expression matrix. Provide as TSV, CSV or RDS."/>
+    <param name="gene_annotation_format" type="select" label="Format of gene annotation">
+      <option value="rds" selected="true">RDS</option>
+      <option value="tsv">TSV</option>
+      <option value="csv">CSV</option>
+    </param>
+    <expand macro="output_object_params"/>
+    <expand macro="verbose_flag"/>
+  </inputs>
+
+  <outputs>
+    <data name="output_rds" format="rdata" from_work_dir="output.RDS" label="${tool.name} on ${on_string}: ${output_object_format}"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="expression_matrix" value="expression.RDS"/>
+      <param name="cell_metadata" value="cells.RDS"/>
+      <param name="gene_annotation" value="genes.RDS"/>
+      <param name="output_object_format" value="cds3"/>
+      <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+===========================================================================
+Create Monocle3 object from input expression/metadata (`new_cell_data_set`)
+===========================================================================
+
+Create a Monocle3 cds3 object from input expression data and optional metadata.
+The expression matrix, with genes as rows and cells as columns, is the only mandatory
+input. The cell metadata (with row names matching the column names of the expression
+matrix) and gene annotation (with row names matching the row names of the expression
+matrix) are optional. These files can be provided as RDS objects, or CSV/TSV. Select the
+format of your input files in the corresponding drop-downs.
+
+@HELP@
+
+@VERSION_HISTORY@
+]]></help>
+  <expand macro="citations"/>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/monocle3-macros.xml	Mon Sep 16 09:52:55 2019 -0400
@@ -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>