diff seurat_run_pca.xml @ 1:c4607a42113e draft

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

--- a/seurat_run_pca.xml	Wed Apr 03 11:15:42 2019 -0400
+++ b/seurat_run_pca.xml	Mon Nov 25 06:08:09 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="seurat_run_pca" name="Seurat RunPCA" version="2.3.1+galaxy1">
+<tool id="seurat_run_pca" name="Seurat RunPCA" version="@SEURAT_VERSION@_@VERSION@+galaxy0">
     <description>run a PCA dimensionality reduction</description>
     <macros>
         <import>seurat_macros.xml</import>
@@ -8,32 +8,37 @@
     <command detect_errors="exit_code"><![CDATA[
 seurat-run-pca.R
 
---input-object-file '$input'
+@INPUT_OBJECT@
 #if $pc_genes:
-    --pc-genes '$pc-genes'
+    --pc-genes '$pc_genes'
 #end if
---output-object-file '$output'
+#if $pc_cells
+  --pc-cells '$pc_cells'
+#end if
+@OUTPUT_OBJECT@
 --output-embeddings-file output_embed
 --output-loadings-file output_load
 --output-stdev-file output_sdev
 #if $pcs_compute:
     --pcs-compute '$pcs_compute'
 #end if
-#if $use_imputed:
-'$use_imputed'
+#if $reverse_pca
+  '$reverse_pca'
 #end if
 
 ]]></command>
 
     <inputs>
-        <param name="input" type="data" format="rdata" label="RDS object" />
-        <param name="pc_genes" type="data" format="tabular, txt" optional="True" label="Genes to scale" help="File of gene names to scale/center. Default is all genes in object." />
+        <expand macro="input_object_params"/>
+        <expand macro="output_object_params"/>
+        <param name="pc_genes" type="data" format="tabular,txt" optional="True" label="Genes to scale" help="File with gene names to scale/center. Default is all genes in object@data." />
+        <param label="Cells to scale" optional="true" name="pc_cells" argument="--pc-cells" type="text" help="File with cell names to scale/center. Default is all cells in object@data."/>
         <param name="pcs_compute" type="integer" optional="True" label="Principal components" help="Total Number of PCs to compute and store (20 by default). Less PCs might be faster, but will explain less variance."/>
-        <param name="use_imputed" type="boolean" truevalue="--use-imputed TRUE" falsevalue="" checked="false" label="Use imputed" help="Run PCA on imputed values."/>
+        <param label="Reverse PCA" optional="true" name="reverse_pca" argument="--reverse-pca" type="boolean" truevalue="--reverse-pca" checked="false" help="Run PCA on reverse matrix (gene x cell; FALSE by default means cell x gene)."/>
     </inputs>
 
     <outputs>
-        <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
+        <expand macro="output_files"/>
         <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/>
         <data name="output_load" format="csv" from_work_dir="output_load" label="${tool.name} on ${on_string}: Seurat Loadings"/>
         <data name="output_sdev" format="csv" from_work_dir="output_sdev" label="${tool.name} on ${on_string}: Seurat Std dev"/>
@@ -42,7 +47,7 @@
     <tests>
         <test>
             <param name="input" ftype="rdata" value="out_scale.rds"/>
-            <output name="output" ftype="rdata" value="out_runpca.rds" compare="sim_size"/>
+            <output name="rds_seurat_file" ftype="rdata" value="out_runpca.rds" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -50,12 +55,9 @@
 
 **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 runs a PCA dimensionality reduction.
 
-This tool runs a PCA dimensionality reduction
+@SEURAT_INTRO@
 
 -----