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comparison seurat_run_pca.xml @ 1:c4607a42113e draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
author ebi-gxa
date Mon, 25 Nov 2019 06:08:09 -0500
parents df80f3d2f9d4
children e534a73143b1
comparison
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0:df80f3d2f9d4 1:c4607a42113e
1 <tool id="seurat_run_pca" name="Seurat RunPCA" version="2.3.1+galaxy1"> 1 <tool id="seurat_run_pca" name="Seurat RunPCA" version="@SEURAT_VERSION@_@VERSION@+galaxy0">
2 <description>run a PCA dimensionality reduction</description> 2 <description>run a PCA dimensionality reduction</description>
3 <macros> 3 <macros>
4 <import>seurat_macros.xml</import> 4 <import>seurat_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="version" /> 7 <expand macro="version" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 seurat-run-pca.R 9 seurat-run-pca.R
10 10
11 --input-object-file '$input' 11 @INPUT_OBJECT@
12 #if $pc_genes: 12 #if $pc_genes:
13 --pc-genes '$pc-genes' 13 --pc-genes '$pc_genes'
14 #end if 14 #end if
15 --output-object-file '$output' 15 #if $pc_cells
16 --pc-cells '$pc_cells'
17 #end if
18 @OUTPUT_OBJECT@
16 --output-embeddings-file output_embed 19 --output-embeddings-file output_embed
17 --output-loadings-file output_load 20 --output-loadings-file output_load
18 --output-stdev-file output_sdev 21 --output-stdev-file output_sdev
19 #if $pcs_compute: 22 #if $pcs_compute:
20 --pcs-compute '$pcs_compute' 23 --pcs-compute '$pcs_compute'
21 #end if 24 #end if
22 #if $use_imputed: 25 #if $reverse_pca
23 '$use_imputed' 26 '$reverse_pca'
24 #end if 27 #end if
25 28
26 ]]></command> 29 ]]></command>
27 30
28 <inputs> 31 <inputs>
29 <param name="input" type="data" format="rdata" label="RDS object" /> 32 <expand macro="input_object_params"/>
30 <param name="pc_genes" type="data" format="tabular, txt" optional="True" label="Genes to scale" help="File of gene names to scale/center. Default is all genes in object." /> 33 <expand macro="output_object_params"/>
34 <param name="pc_genes" type="data" format="tabular,txt" optional="True" label="Genes to scale" help="File with gene names to scale/center. Default is all genes in object@data." />
35 <param label="Cells to scale" optional="true" name="pc_cells" argument="--pc-cells" type="text" help="File with cell names to scale/center. Default is all cells in object@data."/>
31 <param name="pcs_compute" type="integer" optional="True" label="Principal components" help="Total Number of PCs to compute and store (20 by default). Less PCs might be faster, but will explain less variance."/> 36 <param name="pcs_compute" type="integer" optional="True" label="Principal components" help="Total Number of PCs to compute and store (20 by default). Less PCs might be faster, but will explain less variance."/>
32 <param name="use_imputed" type="boolean" truevalue="--use-imputed TRUE" falsevalue="" checked="false" label="Use imputed" help="Run PCA on imputed values."/> 37 <param label="Reverse PCA" optional="true" name="reverse_pca" argument="--reverse-pca" type="boolean" truevalue="--reverse-pca" checked="false" help="Run PCA on reverse matrix (gene x cell; FALSE by default means cell x gene)."/>
33 </inputs> 38 </inputs>
34 39
35 <outputs> 40 <outputs>
36 <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/> 41 <expand macro="output_files"/>
37 <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/> 42 <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/>
38 <data name="output_load" format="csv" from_work_dir="output_load" label="${tool.name} on ${on_string}: Seurat Loadings"/> 43 <data name="output_load" format="csv" from_work_dir="output_load" label="${tool.name} on ${on_string}: Seurat Loadings"/>
39 <data name="output_sdev" format="csv" from_work_dir="output_sdev" label="${tool.name} on ${on_string}: Seurat Std dev"/> 44 <data name="output_sdev" format="csv" from_work_dir="output_sdev" label="${tool.name} on ${on_string}: Seurat Std dev"/>
40 </outputs> 45 </outputs>
41 46
42 <tests> 47 <tests>
43 <test> 48 <test>
44 <param name="input" ftype="rdata" value="out_scale.rds"/> 49 <param name="input" ftype="rdata" value="out_scale.rds"/>
45 <output name="output" ftype="rdata" value="out_runpca.rds" compare="sim_size"/> 50 <output name="rds_seurat_file" ftype="rdata" value="out_runpca.rds" compare="sim_size"/>
46 </test> 51 </test>
47 </tests> 52 </tests>
48 <help><![CDATA[ 53 <help><![CDATA[
49 .. class:: infomark 54 .. class:: infomark
50 55
51 **What it does** 56 **What it does**
52 57
53 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 58 This tool runs a PCA dimensionality reduction.
54 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
55 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
56 types of single cell data.
57 59
58 This tool runs a PCA dimensionality reduction 60 @SEURAT_INTRO@
59 61
60 ----- 62 -----
61 63
62 **Inputs** 64 **Inputs**
63 65