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annotate FCSflowAI.xml @ 1:34397a84faf1 draft

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
author azomics
date Tue, 23 Jun 2020 18:34:02 -0400
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children fab7c5deeb65
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34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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1 <tool id="flowAI" name="flowAI" version="1.0+galaxy0">
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2 <description> automatic quality control</description>
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3 <requirements>
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4 <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
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5 <requirement type="package" version="1.2.9">bioconductor-flowai</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="2:" level="fatal" description="See stderr for more details." />
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9 </stdio>
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10 <command><![CDATA[
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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11 Rscript $__tool_directory__/FCSflowAI.R '${input}' '${remove}' $alphaFR $chremFS $outFS $penFS '${sideFM}' '${full_rep}' $highfcs $lowfcs $qcfcs
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param format="fcs" name="input" type="data" label="FCS file"/>
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16 <param name="remove" type="select" label="Remove low quality cells from:">
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17 <option value="all">Flow rate, Signal acquisition and Dynamic range</option>
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18 <option value="FR_FS">Flow rate and Signal acquisition</option>
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19 <option value="FR_FM">Flow rate and Dynamic range</option>
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20 <option value="FS_FM">Signal acquisition and Dynamic range</option>
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21 <option value="FR">Flow rate</option>
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22 <option value="FS">Signal acquisition</option>
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23 <option value="FM">Dynamic range</option>
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24 </param>
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25 <param name="alphaFR" type="float" label="Significance threshold for flow rate check:" value="0.01"/>
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26 <param name="chremFS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Do you want to exclude the FSC and SSC parameters from the signal acquisition check?" help="The FSC and SSC parameters will not be taken into account for analysis but will not be removed."/>
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27 <param name="outFS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Do you want to remove outliers before the signal acquisition check?"/>
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28 <param name="penFS" type="integer" label="Stringency of signal acquisition check (higher tolerance with higher values):" value="200"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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29 <param name="sideFM" type="select" label="Include in dynamic range check:">
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30 <option value="both">Both limits</option>
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31 <option value="upper">Upper limit only</option>
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32 <option value="lower">Lower limit only</option>
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33 </param>
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34 <param name="highQ_FCS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Create FCS file with only high quality events?"/>
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35 <param name="lowQ_FCS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Create FCS file with only low quality events?"/>
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36 <param name="QC_FCS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Create FCS file with an additional parameter where low quality events have values higher than 10,000?"/>
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37 </inputs>
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38 <outputs>
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39 <data format="html" name="full_rep" label="QC of ${input.name}">
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40 </data>
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41 <data format="fcs" name="highfcs" label="High quality events only from ${input.name}">
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42 <filter>(highQ_FCS)</filter>
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43 </data>
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44 <data format="fcs" name="lowfcs" label="Low quality events only from ${input.name}">
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45 <filter>(lowQ_FCS)</filter>
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46 </data>
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47 <data format="fcs" name="qcfcs" label="All events (low quality event marked up) from ${input.name}">
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48 <filter>(QC_FCS)</filter>
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49 </data>
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="input" value="input.fcs"/>
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54 <param name="remove" value="all"/>
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55 <param name="alphaFR" value="0.01"/>
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56 <param name="chremFS" value="TRUE"/>
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57 <param name="outFS" value="FALSE"/>
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58 <param name="penFS" value="200"/>
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59 <param name="sideFM" value="both"/>
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60 <param name="highQ_FCS" value="TRUE"/>
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61 <param name="lowQ_FCS" value="FALSE"/>
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62 <param name="QC_FCS" value="FALSE"/>
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63 <output name="full_rep" file="std/QCreport.html" compare="sim_size"/>
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64 <output name="highfcs" file="std/hqdata.fcs" compare="sim_size"/>
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65 </test>
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66 <test>
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67 <param name="input" value="input.fcs"/>
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68 <param name="remove" value="all"/>
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69 <param name="alphaFR" value="0.01"/>
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70 <param name="chremFS" value="TRUE"/>
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71 <param name="outFS" value="FALSE"/>
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72 <param name="penFS" value="200"/>
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73 <param name="sideFM" value="both"/>
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74 <param name="highQ_FCS" value="TRUE"/>
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75 <param name="lowQ_FCS" value="TRUE"/>
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76 <param name="QC_FCS" value="TRUE"/>
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77 <output name="full_rep" file="std/QCreport.html" compare="sim_size"/>
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78 <output name="highfcs" file="std/hqdata.fcs" compare="sim_size"/>
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79 <output name="lowfcs" file="std/lqdata.fcs" compare="sim_size"/>
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80 <output name="qcfcs" file="std/alldata.fcs" compare="sim_size"/>
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81 </test>
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82 <test>
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83 <param name="input" value="input.fcs"/>
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84 <param name="remove" value="all"/>
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85 <param name="alphaFR" value="0.01"/>
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86 <param name="chremFS" value="TRUE"/>
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87 <param name="outFS" value="TRUE"/>
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88 <param name="penFS" value="200"/>
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89 <param name="sideFM" value="both"/>
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90 <param name="highQ_FCS" value="TRUE"/>
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91 <param name="lowQ_FCS" value="FALSE"/>
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92 <param name="QC_FCS" value="FALSE"/>
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93 <output name="full_rep" file="nooutliers/QCreport_nooutliers.html" compare="sim_size"/>
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94 <output name="highfcs" file="nooutliers/hqdata_nooutliers.fcs" compare="sim_size"/>
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95 </test>
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96 <test>
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97 <param name="input" value="input.fcs"/>
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98 <param name="remove" value="all"/>
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99 <param name="alphaFR" value="0.01"/>
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100 <param name="chremFS" value="FALSE"/>
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101 <param name="outFS" value="FALSE"/>
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102 <param name="penFS" value="200"/>
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103 <param name="sideFM" value="both"/>
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104 <param name="highQ_FCS" value="TRUE"/>
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105 <param name="lowQ_FCS" value="FALSE"/>
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106 <param name="QC_FCS" value="FALSE"/>
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107 <output name="full_rep" file="withsfsc/QCreport_sfsc.html" compare="sim_size"/>
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108 <output name="highfcs" file="withsfsc/hqdata_sfsc.fcs" compare="sim_size"/>
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109 </test>
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110 </tests>
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111 <help><![CDATA[
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112 This tool automatically performs quality control of flow cytometry data.
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113
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114 -----
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115
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116 **Input files**
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117
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118 • One or more FCS files.
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119
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120 **Output files**
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121
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122 • full HTML report
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123 • new FCS file containing only high quality events (default)
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124 • new FCS file containing only low quality events (optional)
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125 • original FCS file containing an additional parameter where the low quality events have a value higher than 10,000 (optional)
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126
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127
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128 The files generated will be FCS 3.0.
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129
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130 ----
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131
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132 Description of the approach
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133 '''''''''''''''''''''''''''
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134 This tool identifies anomalies from three fundamental properties of flow cytometry data:
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135
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136 - *Flow rate*. Surges and substantial shifts of the rate of the cells passing through the capillary tube are detected.
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137
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138 - *Signal acquisition*. Instability in the signal acquired for each channel are detected. In most cases it corresponds to flow rate surges and shifts.
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139
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140 - *Dynamic range*. Values recorded in the upper limit (margin events) and negative outliers are removed.
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141
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142 .. class:: infomark
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143
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144 An HTML report with informative plots is generated. Users are advised to review the report and also::
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145
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146 1. Eventually adjust the quality control parameters
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147 2. Discard the entire FCS file because of an unacceptable number of anomalies
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148 3. Program a flow cytometry maintenance because of recurrent issues
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149
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150
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151 Parameters
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152 ''''''''''
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153 Default settings work well in the majority of cases. Setting customization may be needed to address properties of unique datasets. For example, high-dimensional FCS files may perform best with more tolerant setttings for signal acquisition checks.
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154
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155 Example
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156 '''''''
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157 This section provides an example of a flowAI quality control html report with plots:
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158
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159
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160 Flow rate check: anomalies are flagged with a green circle. In this instance a surge was detected and discarded as well as a shift from the median value later in the experiment.
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161
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162 .. image:: ./static/images/flowtools/autoflowrate.png
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163
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164 Signal acquistion check: Orange background (or yellow depending on the user's computer) highlights the stable region. Signal acquistion shifts are identified on a per channel basis and the largest region containing no anomalies is retained.
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165
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166 .. image:: ./static/images/flowtools/autosignal.png
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167
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168 Dynamic range check: red and blue lines reflect the detected number of events over time. The x-axis corresponds to that of the signal acquisition plot.
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169
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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170 .. image:: ./static/images/flowtools/margins.png
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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171
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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172 ]]>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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173 </help>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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174 <citations>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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175 <citation type="doi">10.1093/bioinformatics/btw191</citation>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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176 </citations>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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177 </tool>