Mercurial > repos > iuc > raceid_filtnormconf

annotate raceid_filtnormconf.xml @ 3:d55e29ac02e3 draft

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author iuc
date Mon, 15 Apr 2019 17:55:17 -0400
parents 01290f30211f
children 5d5b14dbd092
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1 <tool id="raceid_filtnormconf" name="Filtering, Normalisation, and Confounder Removal using RaceID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.3" >
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2 <description>generates 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_cluster.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <version_command><![CDATA[
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9 Rscript '$__tool_directory__/scripts/cluster.R' @GET_VERSION@
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10 ]]>
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11 </version_command>
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12
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13 <command detect_errors="exit_code"><![CDATA[
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14 #set bin = 'cluster.R'
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15 Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2> '$outlog' > /dev/null
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16 ]]></command>
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17 <configfiles>
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18 <configfile name="userconf" ><![CDATA[
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19 @STRING2VECTOR@
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21 @FILTNORM_CHEETAH@
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22 ]]>
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23 </configfile>
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24 </configfiles>
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25 <inputs>
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26 <param name="intable" type="data" format="tabular" label="Count Matrix" />
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27 <section name="filt" title="Filtering" expanded="true" >
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28 <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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29 <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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30 <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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31 <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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32 <expand macro="use_defaults_no" >
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33 <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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34 <param name="CGenes" type="text" optional="true" label="CGenes" help="Filter out genes with correlated expression for cell type inference" >
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35 <expand macro="sanitize_string_vector" />
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36 </param>
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37 <param name="FGenes" type="text" optional="true" label="FGenes" help="Explicitly filter out genes for cell type inference" >
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38 <expand macro="sanitize_string_vector" />
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39 </param>
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40 <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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41 <expand macro="sanitize_string_vector" />
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42 </param>
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43 <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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44 <param name="bmode" type="select" label="Batch Mode" help="Method to regress out batch effects" >
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45 <option value="RaceID" selected="true" >RaceID</option>
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46 <option value="scran">SCRAN</option>
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47 </param>
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48 <conditional name="ccc" >
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49 <param name="use" type="select" label="Perform Cell-cycle correction?" >
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50 <option value="yes" >Yes</option>
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51 <option value="no" selected="true" >No</option>
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52 </param>
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53 <when value="no" />
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54 <when value="yes" >
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55 <param name="vset" type="text" optional="true" label="List of Gene Sets" >
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56 <expand macro="sanitize_string_vector" />
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57 </param>
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58 <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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59 <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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60 <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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61 <param name="dimr" type="boolean" value="true" label="Derive Components from saturation criterion" />
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62 <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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63 <option value="pca" selected="true">PCA</option>
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64 <option value="ica">ICA</option>
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65 </param>
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66 <param name="logscale" type="boolean" value="false" label="Log-transform data prior to PCA or ICA" help="" />
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67 </when>
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68 </conditional>
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69 </expand>
3
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70 </section>
0
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71 </inputs>
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72 <outputs>
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73 <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
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74 <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" />
3
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75 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Metrics" />
0
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76 </outputs>
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77 <tests>
3
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78 <test expect_num_outputs="3">
0
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79 <!-- 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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80 <param name="intable" value="use.intestinal" />
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81 <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" />
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82 <output name="outlog" value="intestinal.filter.log" />
0
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83 </test>
3
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84 <test expect_num_outputs="3">
0
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85 <!-- defaults, feeding in a matrix with reduced filtering -->
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86 <param name="intable" value="matrix.tabular" />
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87 <section name="filt" >
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88 <param name="mintotal" value="1050" />
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89 <param name="minexpr" value="1" />
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90 <param name="minnumber" value="3" />
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91 </section>
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92 <output name="outrdat" value="matrix.filter.rdat" compare="sim_size" delta="300" />
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93 <output name="outpdf" value="matrix.filter.pdf" compare="sim_size" delta="10" />
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94 </test>
3
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95 <test expect_num_outputs="3">
0
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96 <!-- defaults, but manually specified. No opts, no CC. Generates identical to above -->
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97 <param name="intable" value="use.intestinal" />
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98 <section name="filt" >
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99 <param name="mintotal" value="3000" />
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100 <param name="minexpr" value="5" />
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101 <param name="minnumber" value="5" />
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102 <expand macro="test_nondef" >
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103 <param name="knn" value="10" />
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104 <param name="ccor" value="0.4" />
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105 <param name="bmode" value="RaceID" />
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106 </expand>
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107 </section>
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108 <output name="outpdf" value="intestinal.filter.pdf" compare="sim_size" delta="50" />
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109 </test>
3
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110 <test expect_num_outputs="3">
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111 <!-- defaults, but histogram adjustment -->
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112 <param name="intable" value="use.intestinal" />
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113 <section name="filt" >
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114 <param name="hist_geq_one" value="true" />
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115 </section>
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116 <output name="outpdf" value="matrix.filter.geqone.pdf" compare="sim_size" delta="10" />
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117 </test>
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118 <test expect_num_outputs="3">
0
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119 <!-- Advanced. Opts, CC used -->
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120 <param name="intable" value="use.intestinal" />
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121 <section name="filt" >
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122 <param name="mintotal" value="2000" />
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123 <param name="minexpr" value="3" />
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124 <param name="minnumber" value="2" />
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125 <expand macro="test_nondef" >
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126 <param name="knn" value="5" />
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127 <param name="ccor" value="0.5" />
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128 <param name="CGenes" value="Gga3,Ggact,Ggct" />
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129 <param name="FGenes" value="Zxdc,Zyg11a,Zyg11b,Zyx" />
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130 <param name="LBatch_regexes" value="^I5,^II5,^III5,^IV5d,^V5d" />
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131 <param name="bmode" value="scran" />
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132 <conditional name="ccc" >
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133 <param name="use" value="yes" />
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134 <param name="pvalue" value="0.05" />
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135 <param name="quant" value="0.05" />
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136 <param name="ncomp" value="3" />
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137 <param name="dimr" value="true" />
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138 <param name="mode" value="pca" />
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139 <param name="logscale" value="true" />
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140 </conditional>
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141 </expand>
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142 </section>
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143 <output name="outpdf" value="intestinal_advanced.filter.pdf" compare="sim_size" delta="150" />
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144 </test>
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145 </tests>
3
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146 <help><![CDATA[
0
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147 RaceID3
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148 =======
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149
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150 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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151
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152 This module performs filtering, normalisation, and batch effect removal in the same step.
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153
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154
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155 Example Usage: Inspecting the Aggregated Expression for a Group of Genes
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156 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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157
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158 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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159
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160 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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161
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162 We will also be interested in the cluster that contains significant expression for Apoa genes (Apoa1, Apoa1bp, Apoa2, Apoa4, Apoa5).
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163
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164 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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165
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166 * *Mode of Analysis* → **Cluster**
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167
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168 * *Count Matrix* → [input tabular]
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169
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170 * Filtering:
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171
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172 * *Use Defaults?* → **No**
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173
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174 * *Batch Regex* → "^I5,^II5,^III5,^IV5,^V5"
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176 * *FGenes* → "Lpca5,Atk2"
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178 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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180 ]]>
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181 </help>
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182 <expand macro="citations" />
0
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183 </tool>