changeset 0:c0441ea8f37a draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"

--- /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>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/monocle3-macros.xml	Mon Sep 16 09:50:52 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>