# HG changeset patch
# User ebi-gxa
# Date 1580312425 18000
# Node ID a34f243f55a4af23ba1cbdff5f72b9eab7a0b397
# Parent  75340a5e5fb04f2dc9c4fa73896fade41b2c5858
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 08ac0ad9182623944c4546f8ea8db6a1a537f7eb

diff -r 75340a5e5fb0 -r a34f243f55a4 monocle3-create.xml
--- a/monocle3-create.xml	Mon Sep 16 09:52:55 2019 -0400
+++ b/monocle3-create.xml	Wed Jan 29 10:40:25 2020 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="monocle3_create" name="Monocle3 create" version="@TOOL_VERSION@+galaxy0">
+<tool id="monocle3_create" name="Monocle3 create" version="@TOOL_VERSION@+galaxy1">
   <description>a Monocle3 object from input data</description>
   <macros>
     <import>monocle3-macros.xml</import>
@@ -26,19 +26,19 @@
 ]]></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" argument="--expression-matrix" type="data" format="tabular,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" argument="--cell-metadata" optional="true" type="data" format="tabular,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" argument="--gene-annotation" optional="true" type="data" format="tabular,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>
diff -r 75340a5e5fb0 -r a34f243f55a4 monocle3-macros.xml
--- a/monocle3-macros.xml	Mon Sep 16 09:52:55 2019 -0400
+++ b/monocle3-macros.xml	Wed Jan 29 10:40:25 2020 -0500
@@ -1,9 +1,11 @@
 <macros>
-  <token name="@TOOL_VERSION@">0.1.2</token>
+  <token name="@TOOL_VERSION@">0.1.3</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**
 
+0.1.3+galaxy0: Updated to monocle3-cli 0.0.5 to fix bug with tsv inputs.
+
 0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2
     ]]></token>
   <token name="@INPUT_OPTS@">
@@ -23,7 +25,7 @@
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.0.3">monocle3-cli</requirement>
+      <requirement type="package" version="0.0.5">monocle3-cli</requirement>
       <yield/>
     </requirements>
   </xml>
@@ -57,7 +59,7 @@
     </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>