diff seurat_normalise_data.xml @ 1:48174ec556de draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f

--- a/seurat_normalise_data.xml	Wed Apr 03 11:20:42 2019 -0400
+++ b/seurat_normalise_data.xml	Mon Nov 25 06:13:04 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="seurat_normalise_data" name="Seurat NormaliseData" version="2.3.1+galaxy1">
+<tool id="seurat_normalise_data" name="Seurat NormaliseData" version="@SEURAT_VERSION@_@VERSION@+galaxy0">
     <description>normalise data</description>
     <macros>
         <import>seurat_macros.xml</import>
@@ -8,7 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
 seurat-normalise-data.R
 
---input-object-file '$input'
+@INPUT_OBJECT@
 #if $norm:
     --normalization-method $norm
 #end if
@@ -18,12 +18,17 @@
 #if $scale:
     --scale-factor $scale
 #end if
---output-object-file '$output'
+@OUTPUT_OBJECT@
 ]]></command>
 
     <inputs>
-        <param name="input" argument="--input-object-file" type="data" format="rdata" label="Seurat RDS object" help="Possibly the output of Seurat filter cells or Seurat create object." />
-        <param name="norm" argument="--normalization-method" type="text" optional="True" label="Normalisation method" help = "Method for normalization. Default is log-normalization (LogNormalize)."/>
+        <expand macro="input_object_params"/>
+        <expand macro="output_object_params"/>
+        <param name="norm" argument="--normalization-method" type="select" optional="True" label="Normalisation method" help = "Method for normalization. Default is log-normalization (LogNormalize). Can be 'CLR' or 'RC' additionally.">
+          <option value="LogNormalize" selected="true">Log Normalise</option>
+          <option value="CLR">CLR</option>
+          <option value="RC">RC</option>
+        </param>
         <param name="assay" argument="--assay-type" type="text" optional="True" label="Assay type" help = "Type of assay to normalize for (default is RNA), but can be changed for multimodal analyses.">
             <validator type="regex" message="Please only use letters">^[\(\w\)]+$</validator>
         </param>
@@ -31,13 +36,13 @@
     </inputs>
 
     <outputs>
-        <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: RDS file"/>
+        <expand macro="output_files"/>
     </outputs>
 
     <tests>
         <test>
             <param name="input" ftype="rdata" value="seurat.rds"/>
-            <output name="output" ftype="rdata" value="out_norm.rds" compare="sim_size"/>
+            <output name="rds_seurat_file" ftype="rdata" value="out_norm.rds" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -45,12 +50,9 @@
 
 **What it does**
 
-Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
-It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
-interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
-types of single cell data.
+This tool normalises a Seurat RDS object.
 
-This tool normalises a Seurat RDS object.
+@SEURAT_INTRO@
 
 -----