Mercurial > repos > ebi-gxa > seurat_find_markers

annotate seurat_find_markers.xml @ 4:a1842dbe01cd draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:48:02 +0000
parents 4039a99ae846
children 3dd20b758756
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4039a99ae846 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit bbe3c1f7fd8489951f2d90415fe80dd5cf961ca0
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1 <tool id="seurat_find_markers" name="Seurat FindMarkers" version="@SEURAT_VERSION@+galaxy0">
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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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10
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11 @INPUT_OBJECT@
0
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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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26 #if str($adv.min_diff_pct):
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27 --min-diff-pct '$adv.min_diff_pct'
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28 #end if
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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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34 --test-use '$adv.test_use'
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36 #if str($max_cells_per_ident):
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37 --max-cells-per-ident '$max_cells_per_ident'
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38 #end if
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40 #if str($min_cells_per_gene):
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41 --min-cells-gene '$min_cells_per_gene'
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42 #end if
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44 #if str($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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51 <inputs>
1
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52 <expand macro="input_object_params"/>
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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>
1
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77 <data name="output" format="csv" from_work_dir="output.txt" label="${tool.name} on ${on_string}: Text file"/>
0
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78 </outputs>
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79
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80 <tests>
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81 <test>
4
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82 <param name="rds_seurat_file" ftype="rdata" value="cluster_seurat.rds"/>
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83 <output name="output" value="markers.csv" compare="sim_size" delta="1000000"/>
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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 This tool finds markers (differentially expressed genes) for each of the identity classes in a dataset.
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92 It outputs a text file containing a ranked list of putative markers, and associated statistics (p-values, ROC score, etc.)
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93
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94 p-value adjustment is performed using bonferroni correction based on the total
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95 number of genes in the dataset. Other correction methods are not recommended,
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96 as Seurat pre-filters genes using the arguments above, reducing the number of
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97 tests performed. Lastly, as Aaron Lun has pointed out, p-values should be
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98 interpreted cautiously, as the genes used for clustering are the same genes
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99 tested for differential expression.
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100
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101 @SEURAT_INTRO@
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102
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103 -----
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104
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105 **Inputs**
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106
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107 * RDS object
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108
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109 -----
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110
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111 **Outputs**
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112
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113 * Text file
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114
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115 .. _Seurat: https://www.nature.com/articles/nbt.4096
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116 .. _Satija Lab: https://satijalab.org/seurat/
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117
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118 @VERSION_HISTORY@
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119 ]]></help>
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120 <expand macro="citations" />
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121 </tool>