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comparison seurat_macros.xml @ 0:970696a7ae0b draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"
author ebi-gxa
date Fri, 04 Mar 2022 07:28:21 +0000
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children 834f7d8e5b4c
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-1:000000000000 0:970696a7ae0b
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@VERSION@">0.3.0</token>
4 <token name="@SEURAT_VERSION@">3.2.3</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="@VERSION@">seurat-scripts</requirement>
8 </requirements>
9 </xml>
10 <xml name="version">
11 <version_command><![CDATA[
12 echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
13 ]]></version_command>
14 </xml>
15
16 <xml name="input_object_params">
17 <conditional name="input" label="Input format">
18 <param type="select" name="format" label="Choose the format of the input" help="RData, Loom or AnnData">
19 <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
20 <option value="loom">Loom</option>
21 <option value="anndata">AnnData</option>
22 <option value="rds_sce">RDS with a Single Cell Experiment object</option>
23 </param>
24 <when value="anndata">
25 <param type="data" name="anndata_file" label="AnnData file" help="The AnnData format provided by Scanpy" format="h5,h5ad"/>
26 </when>
27 <when value="loom">
28 <param type="data" name="loom_file" label="Loom file" help="Input as Loom v? file" format="h5,h5loom"/>
29 </when>
30 <when value="rds_seurat">
31 <param type="data" name="rds_seurat_file" label="RDS file" help="Input as RDS file with Seurat 3 object" format="rdata"/>
32 </when>
33 <when value="rds_sce">
34 <param type="data" name="rds_sce_file" label="RDS file" help="Input as RDS file with Single Cell Experiment object" format="rdata"/>
35 </when>
36 </conditional>
37 </xml>
38
39 <token name="@INPUT_OBJECT@">
40 #if $input.format == "anndata"
41 --input-object-file '$input.anndata_file' --input-format anndata
42 #else if $input.format == "loom"
43 --input-object-file '$input.loom_file' --input-format loom
44 #else if $input.format == "rds_seurat"
45 --input-object-file '$input.rds_seurat_file' --input-format seurat
46 #else if $input.format == "rds_sce"
47 --input-object-file '$input.rds_sce_file' --input-format singlecellexperiment
48 #end if
49 </token>
50
51 <xml name="output_object_params">
52 <param type="select" name="format" label="Choose the format of the output" help="Seurat, Single Cell Experiment or Loom">
53 <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
54 <option value="loom">Loom</option>
55 <option value="rds_sce">RDS with a Single Cell Experiment object</option>
56 </param>
57 </xml>
58
59 <xml name="output_files">
60 <data name="loom_file" from_work_dir="seurat_obj.loom" format="h5" label="${tool.name} on ${on_string}: Seurat Loom">
61 <filter>format == 'loom'</filter>
62 </data>
63 <data name="rds_seurat_file" format="rdata" label="${tool.name} on ${on_string}: Seurat RDS">
64 <filter>format == 'rds_seurat'</filter>
65 </data>
66 <data name="rds_sce_file" format="rdata" label="${tool.name} on ${on_string}: Seurat Single Cell Experiment RDS">
67 <filter>format == 'rds_sce'</filter>
68 </data>
69 </xml>
70
71 <token name="@OUTPUT_OBJECT@">
72 #if $format == "anndata"
73 --output-object-file '$anndata_file' --output-format anndata
74 #else if $format == "loom"
75 --output-object-file seurat_obj.loom --output-format loom
76 #else if $format == "rds_seurat"
77 --output-object-file '$rds_seurat_file' --output-format seurat
78 #else if $format == "rds_sce"
79 --output-object-file '$rds_sce_file' --output-format singlecellexperiment
80 #end if
81 </token>
82
83 <xml name="genes-use-input">
84 <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv,txt,tabular" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/>
85 </xml>
86 <xml name="dims-use-input">
87 <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/>
88 </xml>
89
90 <token name="@SEURAT_INTRO@"><![CDATA[
91 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
92 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
93 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
94 types of single cell data.
95 ]]></token>
96
97 <token name="@VERSION_HISTORY@"><![CDATA[
98 **Version history**
99
100 3.2.3+galaxy0: Moves to Seurat 3.2.3 and introduce convert method, improving format interconversion support.
101
102 3.1.2_0.0.8: Update metadata parsing
103
104 3.1.1_0.0.7: Exposes perplexity and enables tab input.
105
106 3.1.1_0.0.6+galaxy0: Moved to Seurat 3.
107
108 Find clusters: removed dims-use, k-param, prune-snn.
109
110 2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
111 EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(github.com/drosofff) and Lea Bellenger(github.com/bellenger-l).
112
113 0.0.1: Initial contribution. Maria Doyle (github.com/mblue9).
114 ]]></token>
115
116
117 <xml name="citations">
118 <citations>
119 <citation type="doi">10.1038/nbt.4096</citation>
120 <citation type="bibtex">
121 @misc{r-seurat-scripts.git,
122 author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team},
123 year = {2018},
124 title = {Seurat-scripts: command line interface for Seurat},
125 publisher = {GitHub},
126 journal = {GitHub repository},
127 url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
128 }
129 </citation>
130 <citation type="doi">10.1038/s41592-021-01102-w</citation>
131 </citations>
132 </xml>
133 </macros>