Mercurial > repos > ebi-gxa > seurat_find_markers

annotate seurat_find_markers.xml @ 0:fde95fe95f15 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 11:17:29 -0400
parents
children 7895b4bb6247
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0
fde95fe95f15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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1 <tool id="seurat_find_markers" name="Seurat FindMarkers" version="2.3.1+galaxy1">
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2 <description>find markers (differentially expressed genes)</description>
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3 <macros>
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4 <import>seurat_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 seurat-find-markers.R
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11 --input-object-file '$input'
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12 --output-text-file output.txt
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14 #if $genes_use:
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15 --genes-use '$genes_use'
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16 #end if
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18 #if str($logfc_threshold):
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19 --logfc-threshold '$logfc_threshold'
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20 #end if
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22 #if str($adv.min_pct):
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23 --min-pct '$adv.min_pct'
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24 #end if
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25
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26 #if str($adv.min_diff_pct):
fde95fe95f15 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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27 --min-diff-pct '$adv.min_diff_pct'
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28 #end if
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29
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30 #if $adv.only_pos:
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31 --only-pos '$adv.only_pos'
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32 #end if
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33
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34 --test-use '$adv.test_use'
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35
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36 #if str($max_cells_per_ident):
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37 --max-cells-per-ident '$max_cells_per_ident'
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38 #end if
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39
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40 #if str($min_cells_per_gene):
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41 --min-cells-gene '$min_cells_per_gene'
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42 #end if
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43
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44 #if str($min_cells_group):
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45 --min-cells-group '$min_cells_group'
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46 #end if
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47
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48
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49 ]]></command>
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50
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51 <inputs>
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52 <param name="input" type="data" format="rdata" label="RDS object" />
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53 <expand macro="genes-use-input"/>
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54 <param name="logfc_threshold" label="LogFC logfc_threshold" optional="true" argument="--logfc-threshold" type="float" help="Limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Default is 0.25 Increasing logfc.threshold speeds up the function, but can miss weaker signals."/>
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55 <param name="max_cells_per_ident" label="Max cells per ident" optional="true" argument="--max-cells-per-ident" type="integer" help="Down sample each identity class to a max number. Default is no downsampling. Not activated by default (set to Inf)."/>
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56 <param name="min_cells_per_gene" label="Min cells per gene" optional="true" argument="--min-cells-gene" type="integer" help="Minimum number of cells expressing the gene in at least one of the two groups, currently only used for poisson and negative binomial tests."/>
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57 <param name="min_cells_group" label="Min cells in one of the groups" optional="true" argument="--min-cells-group" type="integer"/>
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58 <section name="adv" title="Advanced Options">
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59 <param name="min_pct" type="float" label="Min Pct" optional="true" help="Only test genes that are detected in a minimum fraction of min.pct cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed. Default is 0.1."/>
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60 <param name="min_diff_pct" type="float" label="Min diff Pct" optional="true" help="Only test genes that show a minimum difference in the fraction of detection between the two groups. Set to -Inf by default."/>
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61 <param name="only_pos" type="boolean" label="Only positive markers" truevalue="TRUE" falsevalue="" help="Only return positive markers (FALSE by default)."/>
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62 <param name="test_use" type="select" label="Test to use" help="">
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63 <option value="wilcox" selected="true">Wilcoxon</option>
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64 <option value="bimod">Bi-modal</option>
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65 <option value="roc">ROC</option>
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66 <option value="t">t-Test</option>
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67 <option value="tobit">tobit</option>
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68 <option value="poisson">Poisson</option>
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69 <option value="negbinom">Negative binomia</option>
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70 <option value="MAST">MAST</option>
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71 <option value="DESeq2">DESeq2</option>
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72 </param>
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73 </section>
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74 </inputs>
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75
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76 <outputs>
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77 <data name="output" format="txt" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Text file"/>
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78 </outputs>
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79
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80 <tests>
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81 <test>
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82 <param name="input" ftype="rdata" value="out_runtsne.rds"/>
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83 <output name="output" ftype="txt" value="out_findmark.txt"/>
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84 </test>
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85 </tests>
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86 <help><![CDATA[
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87 .. class:: infomark
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88
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89 **What it does**
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90
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91 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
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92 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
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93 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
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94 types of single cell data.
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95
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96 This tool finds markers (differentially expressed genes) for each of the identity classes in a dataset. It outputs a text file containing a ranked list of putative markers, and associated statistics (p-values, ROC score, etc.)
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97
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98 -----
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99
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100 **Inputs**
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101
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102 * RDS object
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103
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104 -----
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105
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106 **Outputs**
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107
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108 * Text file
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109
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110 .. _Seurat: https://www.nature.com/articles/nbt.4096
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111 .. _Satija Lab: https://satijalab.org/seurat/
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112
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113 @VERSION_HISTORY@
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114 ]]></help>
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115 <expand macro="citations" />
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116 </tool>