Mercurial > repos > ebi-gxa > seurat_run_tsne
comparison seurat_run_tsne.xml @ 1:13a27436f8ee draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
author | ebi-gxa |
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date | Mon, 25 Nov 2019 06:11:40 -0500 |
parents | 3aea769deab1 |
children | fd0fc93b3c87 |
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0:3aea769deab1 | 1:13a27436f8ee |
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1 <tool id="seurat_run_tsne" name="Seurat RunTSNE" version="2.3.1+galaxy1"> | 1 <tool id="seurat_run_tsne" name="Seurat RunTSNE" version="@SEURAT_VERSION@_@VERSION@+galaxy0"> |
2 <description>run t-SNE dimensionality reduction</description> | 2 <description>run t-SNE 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-tsne.R | 9 seurat-run-tsne.R |
10 | 10 |
11 --input-object-file '$input' | 11 @INPUT_OBJECT@ |
12 | |
13 #if $genes_use: | 12 #if $genes_use: |
14 --genes-use '$genes_use' | 13 --genes-use '$genes_use' |
15 #end if | 14 #end if |
16 | 15 |
17 #if str($adv.dims_use): | 16 #if str($adv.dims_use): |
21 #end if | 20 #end if |
22 | 21 |
23 #if not $adv.do_fast: | 22 #if not $adv.do_fast: |
24 --do-fast '$adv.do_fast' | 23 --do-fast '$adv.do_fast' |
25 #end if | 24 #end if |
25 #if $adv.tsne_method | |
26 --tsne-method '$adv.tsne_method' | |
27 #end if | |
28 #if $adv.dim_embed | |
29 --dim_embed '$adv.dim_embed' | |
30 #end if | |
31 #if $adv.random_seed | |
32 --random-seed '$adv.random_seed' | |
33 #end if | |
26 | 34 |
27 --output-object-file '$output' | 35 @OUTPUT_OBJECT@ |
28 --output-embeddings-file output_embed | 36 --output-embeddings-file output_embed |
29 ]]></command> | 37 ]]></command> |
30 | 38 |
31 <inputs> | 39 <inputs> |
32 <param name="input" argument="--input-obj-file" type="data" format="rdata" label="Seurat RDS object" help="The RDS/Rdata result of Seurat FindClusters."/> | 40 <expand macro="input_object_params"/> |
41 <expand macro="output_object_params"/> | |
33 <expand macro="genes-use-input"/> | 42 <expand macro="genes-use-input"/> |
34 <section name="adv" title="Advanced Options"> | 43 <section name="adv" title="Advanced Options"> |
35 <expand macro="dims-use-input"/> | 44 <expand macro="dims-use-input"/> |
36 <param name="do_fast" label="Faster execution" argument="--do-fast" checked="true" type="boolean" truevalue="" falsevalue="FALSE" help="If TRUE, uses the Barnes-hut implementation, which runs faster, but is less flexible. TRUE by default."/> | 45 <param name="do_fast" label="Faster execution" argument="--do-fast" checked="true" type="boolean" truevalue="" falsevalue="FALSE" help="If TRUE, uses the Barnes-hut implementation, which runs faster, but is less flexible. TRUE by default."/> |
46 <param label="tSNE method" optional="true" name="tsne_method" argument="--tsne-method" type="select" help="Select the method to use to compute the tSNE. Available methods are: Rtsne, Flt-SNE"> | |
47 <option value="Rtsne" selected="true">Rtsne</option> | |
48 <option value="Flt-SNE">Flt-SNE</option> | |
49 </param> | |
50 <param label="tSNE dimensions" optional="true" name="dim_embed" argument="--dim_embed" type="select" help="The dimensional space of the resulting tSNE embedding (default is 2). For example, set to 3 for a 3d tSNE"> | |
51 <option value="2" selected="true">2</option> | |
52 <option value="3">3</option> | |
53 </param> | |
54 <param label="Random seed" optional="true" name="random_seed" argument="--random-seed" type="integer" help="Seed of the random number generator"/> | |
37 </section> | 55 </section> |
38 </inputs> | 56 </inputs> |
39 | 57 |
40 <outputs> | 58 <outputs> |
41 <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/> | 59 <expand macro="output_files"/> |
42 <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/> | 60 <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/> |
43 </outputs> | 61 </outputs> |
44 | 62 |
45 <tests> | 63 <tests> |
46 <test> | 64 <test> |
47 <param name="input" ftype="rdata" value="out_findclust.rds"/> | 65 <param name="input" ftype="rdata" value="out_findclust.rds"/> |
48 <output name="output" ftype="rdata" value="out_runtsne.rds" compare="sim_size"/> | 66 <output name="rds_seurat_file" ftype="rdata" value="out_runtsne.rds" compare="sim_size"/> |
49 </test> | 67 </test> |
50 </tests> | 68 </tests> |
51 <help><![CDATA[ | 69 <help><![CDATA[ |
52 .. class:: infomark | 70 .. class:: infomark |
53 | 71 |
56 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. | 74 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. |
57 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and | 75 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and |
58 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse | 76 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse |
59 types of single cell data. | 77 types of single cell data. |
60 | 78 |
61 Run t-SNE dimensionality reduction on selected features. Has the option of | 79 Run t-SNE dimensionality reduction on selected features. Has the option of running |
62 running in a reduced dimensional space (i.e. spectral tSNE, recommended), | 80 in a reduced dimensional space (i.e. spectral tSNE, recommended), or |
63 or running based on a set of genes. For details about stored TSNE calculation | 81 running based on a set of genes. |
64 parameters, see standard output of the tool. | |
65 | 82 |
66 ----- | 83 ----- |
67 | 84 |
68 **Inputs** | 85 **Inputs** |
69 | 86 |