Mercurial > repos > iuc > raceid_filtnormconf

annotate raceid_filtnormconf.xml @ 10:8b917923f7d4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
author iuc
date Tue, 05 Nov 2024 16:33:25 +0000
parents c891d8b33ede
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1 <tool id="raceid_filtnormconf" name="Initial processing using RaceID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of single-cell RNA data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>macros_cheetah.xml</import>
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6 </macros>
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7 <expand macro="bio_tools"/>
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8 <expand macro="requirements" />
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9 <expand macro="version_command_config" prog="cluster.R" cheetah="FILTNORM_CHEETAH" out="2&#62; '$outlog' &#62; /dev/null" />
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10 <inputs>
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11 <param name="intable" type="data" format="tabular" label="Count Matrix" />
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12 <section name="filt" title="Filtering" expanded="true" >
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13 <param name="mintotal" type="integer" min="1" value="3000" label="Min Transcripts" help="The minimum total transcripts required. Cells with less than mintotal transcripts are filtered out." />
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14 <param name="minexpr" type="integer" min="1" value="5" label="Min Expression" help="The minimum required transcript counts of a gene in the minimum number of cells (below)" />
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15 <param name="minnumber" type="integer" min="1" value="5" label="Min Cells" help="The minumum number of cells for gene expression to be counted" />
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16 <param name="hist_geq_one" type="boolean" checked="false" label="Count filtered features greater than or equal to 1" help="By default features are counted if they are above zero, but RaceID adds 0.1 to all counts after normalisation to create a non-zero dataset." />
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17 <expand macro="use_defaults_no" >
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18 <param name="knn" type="integer" min="0" value="10" label="K-nearest-neighbours" help="Number of nearest neighbors used to infer corresponding cell types in different batches" />
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19 <param name="CGenes" type="text" optional="true" label="CGenes" help="Filter out genes with correlated expression for cell type inference" >
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20 <expand macro="sanitize_string_vector" />
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21 </param>
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22 <param name="FGenes" type="text" optional="true" label="FGenes" help="Explicitly filter out genes for cell type inference" >
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23 <expand macro="sanitize_string_vector" />
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24 </param>
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25 <param name="LBatch_regexes" type="text" optional="true" label="Batch Regex" help="List of regexes to capture experimental batches for batch effect correction" >
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26 <expand macro="sanitize_string_vector" />
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27 </param>
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28 <param name="ccor" type="float" value="0.4" label="CCor" help="Correlation coefficient used as a threshold for determining correlated genes" />
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29 <param name="bmode" type="select" label="Batch Mode" help="Method to regress out batch effects" >
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30 <option value="RaceID" selected="true" >RaceID</option>
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31 <!-- <option value="scran">SCRAN</option> -->
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32 </param>
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33 <conditional name="ccc" >
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34 <param name="use" type="select" label="Perform Cell-cycle correction?" >
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35 <option value="yes" >Yes</option>
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36 <option value="no" selected="true" >No</option>
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37 </param>
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38 <when value="no" />
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39 <when value="yes" >
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40 <param name="vset" type="text" optional="true" label="List of Gene Sets" >
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41 <expand macro="sanitize_string_vector" />
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42 </param>
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43 <param name="pvalue" type="float" value="0.01" min="0" max="1" label="P-value Cutoff" help="P-value cutoff for determining enriched components" />
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44 <param name="quant" type="float" value="0.01" min="0" max="1" label="Quantification Fraction" help="Upper and lower fraction of gene loadings use for determining enriched components" />
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45 <param name="ncomp" type="integer" min="0" optional="true" label="Number of components to use" help="If left blank, the maximum number of components are used" /><!-- 0 = NULL -->
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46 <param name="dimr" type="boolean" value="true" label="Derive Components from saturation criterion" />
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47 <param name="mode" type="select" label="Type of Component Analysis" help="If ICA is selected, ensure that the number of components value above is sufficiently high" >
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48 <option value="pca" selected="true">PCA</option>
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49 <option value="ica">ICA</option>
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50 </param>
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51 <param name="logscale" type="boolean" value="false" label="Log-transform data prior to PCA or ICA" help="" />
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52 </when>
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53 </conditional>
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54 </expand>
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55 </section>
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56 </inputs>
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57 <outputs>
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58 <data name="outtable" format="tabular" label="${tool.name} on ${on_string}: Normalised Matrix" />
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59 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
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60 <data name="outrdat" format="rds" label="${tool.name} on ${on_string}: RDS" />
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61 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Metrics" />
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62 </outputs>
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63 <tests>
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64 <test expect_num_outputs="4">
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65 <!-- This is a file with a single word 'test', which prompts the scripts to use the test intestinalData in the library -->
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66 <param name="intable" value="use.intestinal" />
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67 <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" />
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68 <output name="outlog" value="intestinal.filter.log" />
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69 <output name="outtable" >
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70 <assert_contents>
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71 <has_n_columns n="288" />
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72 <has_text_matching expression="Amdhd2\s0\.000" />
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73 <has_text_matching expression="Ammecr1(\s0\s0)+" />
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74 </assert_contents>
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75 </output>
0
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76 </test>
4
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77 <test expect_num_outputs="4">
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78 <!-- defaults, feeding in a matrix with reduced filtering -->
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79 <param name="intable" value="matrix.tabular" />
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80 <section name="filt" >
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81 <param name="mintotal" value="1050" />
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82 <param name="minexpr" value="1" />
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83 <param name="minnumber" value="3" />
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84 </section>
8
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85 <output name="outrdat" value="matrix.filter.rdat" compare="sim_size" />
0
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86 <output name="outpdf" value="matrix.filter.pdf" compare="sim_size" delta="10" />
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87 </test>
4
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88 <test expect_num_outputs="4">
0
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89 <!-- defaults, but manually specified. No opts, no CC. Generates identical to above -->
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90 <param name="intable" value="use.intestinal" />
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91 <section name="filt" >
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92 <param name="mintotal" value="3000" />
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93 <param name="minexpr" value="5" />
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94 <param name="minnumber" value="5" />
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95 <expand macro="test_nondef" >
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96 <param name="knn" value="10" />
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97 <param name="ccor" value="0.4" />
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98 <param name="bmode" value="RaceID" />
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99 </expand>
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100 </section>
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101 <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" />
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102 </test>
4
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103 <test expect_num_outputs="4">
3
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104 <!-- defaults, but histogram adjustment -->
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105 <param name="intable" value="use.intestinal" />
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106 <section name="filt" >
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107 <param name="hist_geq_one" value="true" />
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108 </section>
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109 <output name="outpdf" value="matrix.filter.geqone.pdf" compare="sim_size" delta="10" />
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110 </test>
4
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111 <test expect_num_outputs="4">
0
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112 <!-- Advanced. Opts, CC used -->
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113 <param name="intable" value="use.intestinal" />
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114 <section name="filt" >
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115 <param name="mintotal" value="2000" />
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116 <param name="minexpr" value="3" />
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117 <param name="minnumber" value="2" />
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118 <expand macro="test_nondef" >
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119 <param name="knn" value="5" />
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120 <param name="ccor" value="0.5" />
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121 <param name="CGenes" value="Gga3,Ggact,Ggct" />
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122 <param name="FGenes" value="Zxdc,Zyg11a,Zyg11b,Zyx" />
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123 <param name="LBatch_regexes" value="^I5,^II5,^III5,^IV5d,^V5d" />
6
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124 <!-- <param name="bmode" value="scran" /> -->
0
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125 <conditional name="ccc" >
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126 <param name="use" value="yes" />
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127 <param name="pvalue" value="0.05" />
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128 <param name="quant" value="0.05" />
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129 <param name="ncomp" value="3" />
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130 <param name="dimr" value="true" />
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131 <param name="mode" value="pca" />
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132 <param name="logscale" value="true" />
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133 </conditional>
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134 </expand>
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135 </section>
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136 <output name="outpdf" value="intestinal_advanced.filter.pdf" compare="sim_size" delta="150" />
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137 </test>
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138 </tests>
3
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139 <help><![CDATA[
0
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140 RaceID3
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141 =======
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142
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143 RaceID is a clustering algorithm for the identification of cell types from single-cell RNA-sequencing data. It was specifically designed for the detection of rare cells which correspond to outliers in conventional clustering methods.
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144
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145 This module performs filtering, normalisation, and batch effect removal in the same step.
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146
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147
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148 Example Usage: Inspecting the Aggregated Expression for a Group of Genes
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149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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150
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151 Our cells come from 5 different batches (I5,II5,III5,IV5,V5) and are labelled to reflect this (i.e. "I5_1", "I5_2", ..., "I5_129", "II5_1", ..., "V5_236" )
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152
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153 We wish to filter out the gene Lpca5 and Atk2 which we know in advance will saturate our analysis with unwanted expression.
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154
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155 We will also be interested in the cluster that contains significant expression for Apoa genes (Apoa1, Apoa1bp, Apoa2, Apoa4, Apoa5).
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156
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157 First, we must load in our count matrix in order to correct for batch effects, filter out unwanted genes, and compute our clusters and outliers.
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158
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159 * *Mode of Analysis* → **Cluster**
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160
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161 * *Count Matrix* → [input tabular]
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162
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163 * Filtering:
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164
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165 * *Use Defaults?* → **No**
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166
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167 * *Batch Regex* → "^I5,^II5,^III5,^IV5,^V5"
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168
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169 * *FGenes* → "Lpca5,Atk2"
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170
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171 A PDF report will be generated giving metrics about the library size and number of features as histograms, and additional metrics relating to cell-cycle correction will be produced if that option has been selected.
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172
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173 ]]>
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174 </help>
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175 <expand macro="citations" />
0
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176 </tool>