Mercurial > repos > immport-devteam > fcs_gate_trans

comparison fcs_gate_trans/FCSGateTrans.xml @ 0:78b8ab344edd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author immport-devteam
date Mon, 27 Feb 2017 12:51:24 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:78b8ab344edd
1 <tool id="fcs_gate_trans_convert" name="Automated gating, Transformation and Conversion of FCS to Text" version="1.0">
2 <description>using FlowDensity and the FCSTrans tranformation.</description>
3 <requirements>
4 <requirement type="package" version="3.3.0">r</requirement>
5 <requirement type="package" version="1.38.2">bioconductor-flowcore</requirement>
6 <requirement type="package" version="1.6.0">bioconductor-flowdensity</requirement>
7 </requirements>
8 <stdio>
9 <exit_code range="2:" level="fatal" description="See stderr for more details." />
10 </stdio>
11 <command><![CDATA[
12 Rscript --slave --vanilla $__tool_directory__/FCSGateTrans.R --args "${input}" "${output}" $comp "${fcsout}" "${graph}" "${report}" "${transform.trans_method}"
13 #if $transform.trans_method == "arcsinh"
14 $transform.scaling_factor
15 #end if
16 ]]>
17 </command>
18 <inputs>
19 <param format="fcs" name="input" type="data" label="FCS file"/>
20 <param name="comp" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Compensate?"/>
21 <conditional name="transform">
22 <param name="trans_method" type="select" label="Transformation using:" help="by default, FCSTrans">
23 <option value="logicle">FCSTrans</option>
24 <option value="arcsinh">arcsinh</option>
25 <option value="None">no transformation please.</option>
26 </param>
27 <when value="arcsinh">
28 <param name="scaling_factor" type="integer" min="1" max="200" value="150" label="Scaling factor b for arcsinh transform:" help="The default value is 150 for standard FCM data. The recommended value for cyTOF data is 5.">
29 </param>
30 </when>
31 </conditional>
32 <param name="gate" type="select" label="Automatically gate debris?">
33 <option value="FALSE">No, thank you</option>
34 <option value="TRUE">Yes, please</option>
35 </param>
36 <param name="format" type="select" label="Output FCS3.0?">
37 <option value="FALSE">No, thank you</option>
38 <option value="TRUE">Yes, please</option>
39 </param>
40 </inputs>
41 <outputs>
42 <data format="flowtext" name="output" label="FCSGateTrans on ${input.name}"/>
43 <data format="fcs" name="fcsout" label="FCSGateTrans in FCS3.0 format on ${input.name}">
44 <filter>format=="TRUE"</filter>
45 </data>
46 <data format="pdf" name="graph" label="Graphs of automated gating on ${input.name}">
47 <filter>gate=="TRUE"</filter>
48 </data>
49 <data format="txt" name="report" label="Report of automated gating on ${input.name}">
50 <filter>gate=="TRUE"</filter>
51 </data>
52 </outputs>
53 <tests>
54 <test>
55 <param name="input" value="testfcs1.fcs"/>
56 <param name="comp" value="FALSE"/>
57 <param name="gate" value="FALSE"/>
58 <param name="format" value="FALSE"/>
59 <param name="trans_method" value="logicle"/>
60 <output name="output" file="nocomp.flowtext"/>
61 </test>
62 <test>
63 <param name="input" value="testfcs1.fcs"/>
64 <param name="comp" value="FALSE"/>
65 <param name="gate" value="FALSE"/>
66 <param name="format" value="FALSE"/>
67 <param name="trans_method" value="None"/>
68 <output name="output" file="notrans.flowtext"/>
69 </test>
70 <test>
71 <param name="input" value="testfcs1.fcs"/>
72 <param name="comp" value="FALSE"/>
73 <param name="gate" value="FALSE"/>
74 <param name="format" value="FALSE"/>
75 <param name="trans_method" value="arcsinh"/>
76 <param name="scaling_factor" value="150"/>
77 <output name="output" file="arcsinh150.flowtext"/>
78 </test>
79 <test>
80 <param name="input" value="testfcs1.fcs"/>
81 <param name="comp" value="TRUE"/>
82 <param name="gate" value="FALSE"/>
83 <param name="format" value="FALSE"/>
84 <param name="trans_method" value="logicle"/>
85 <output name="output" file="withcomp.flowtext"/>
86 </test>
87 <test>
88 <param name="input" value="testfcs1.fcs"/>
89 <param name="comp" value="TRUE"/>
90 <param name="gate" value="TRUE"/>
91 <param name="format" value="FALSE"/>
92 <param name="trans_method" value="logicle"/>
93 <output name="output" file="withcomp.flowtext"/>
94 <output name="graph" file="graph.pdf" compare="sim_size"/>
95 <output name="report" file="report.txt"/>
96 </test>
97 <test>
98 <param name="input" value="testfcs1.fcs"/>
99 <param name="comp" value="TRUE"/>
100 <param name="gate" value="TRUE"/>
101 <param name="format" value="TRUE"/>
102 <param name="trans_method" value="logicle"/>
103 <output name="output" file="withcomp.flowtext"/>
104 <output name="fcsout" file="comp_gated.fcs" compare="sim_size"/>
105 <output name="graph" file="graph.pdf" compare="sim_size"/>
106 <output name="report" file="report.txt"/>
107 </test>
108 </tests>
109 <help><![CDATA[
110 This tool allows automated gating of debris using flowDensity and conversion of FCS files to text using the FCSTrans transformation.
111
112 -----
113
114 **Input files**
115
116 This tool uses FCS files as input and files are processed serially. Users choose to automatically gate cellular debris, and/or compensate the data.
117
118 **Output files**
119
120 Output is tab-separated text containing transformed fluorescence intensity values for each marker.
121 If the option is selected, a FCS file (format FCS3.0) is generated.
122
123 **Gating output**
124
125 Automatically gated output includes a summary of data pre- and post-gating as well as density scatter plots pre- and post- gating for each marker pair.
126
127 -----
128
129 Compensation will be implemented according to the spillover matrix included in the FCS files (if available).
130
131 -----
132
133 **Automated Gating**
134
135 Automated gating is implemented with flowDensity. Cellular debris removal uses gate coordinates calculated based on the density of the forward scatter channel only. The calculated gate is vertical and located at the largest value of either the 0.1 quantile of the FSC density or the lowest density between the first and second density peaks. Cells smaller than the threshold are removed.
136
137 .. class:: warningmark
138
139 Users should verify whether data benefit from being gated. We recommend evaluating the number of events and scatter plots pre- and post-gating.
140
141 -----
142
143 **Example**
144
145 *Output text file*::
146
147 Forward Scatter Side Scatter Marker1 Marker2 Marker3 Marker4
148 449 157 551 129 169 292
149 894 1023 199 277 320 227
150 262 73 437 69 0 146
151 340 115 509 268 0 74
152
153 *Gating summary*::
154
155 =========================
156 == BEFORE GATING ==
157 =========================
158 events parameters
159 203584 13
160 FSC-A FSC-H SSC-A SSC-H APC-A APC-H7-A FITC-A PerCP-Cy5-5-A V450-A V500-A PE-A PE-Cy7-A Time
161 Min. 0 78 0 0.0 0 0.0 0 0 0 0 0.0 0 0
162 1st Qu. 869 769 544 514.0 940 0.0 1023 826 978 1104 358.8 913 4182
163 Median 1234 1081 754 704.0 1750 31.0 1247 1614 1971 1505 1612.0 1791 8392
164 Mean 1304 1108 1002 863.6 1629 812.8 1329 1597 1694 1765 1376.0 1813 8536
165 3rd Qu. 1675 1474 1240 1087.0 2326 1573.0 1629 2565 2326 2640 2261.0 2782 12760
166 Max. 4095 4061 4095 4012.0 4096 4086.0 4094 4022 4091 4096 4093.0 4096 17740
167
168 =========================
169 == AFTER GATING ==
170 =========================
171 events parameters
172 171547 13
173 FSC-A FSC-H SSC-A SSC-H APC-A APC-H7-A FITC-A PerCP-Cy5-5-A V450-A V500-A PE-A PE-Cy7-A Time
174 Min. 403 219 1.0 4.0 0 0.0 0 0 0 0 0 0 0
175 1st Qu. 949 849 599.0 565.0 979 0.0 1063 943 1203 1119 444 1060 4182
176 Median 1348 1170 782.0 730.0 1809 0.0 1258 1717 2082 1493 1785 1883 8358
177 Mean 1353 1177 989.2 885.9 1642 779.4 1330 1678 1778 1753 1458 1873 8504
178 3rd Qu. 1670 1475 1204.0 1076.0 2322 1559.0 1591 2623 2345 2630 2289 2808 12700
179 Max. 2953 2406 4055.0 3329.0 4069 4080.0 3498 3868 3612 4076 4093 3764 17730
180
181 *Gating plots*:
182
183 .. image:: static/images/flowdensity.png
184 ]]>
185 </help>
186 <citations>
187 <citation type="doi">10.1002/cyto.a.22037</citation>
188 <citation type="doi">10.1093/bioinformatics/btu677</citation>
189 <citation type="doi">10.1186/1471-2105-10-106</citation>
190 </citations>
191 </tool>