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comparison FCSGateTrans.xml @ 2:66a54e77aa33 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf"
author azomics
date Mon, 06 Jul 2020 19:39:35 -0400
parents c28c2e680bf5
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1:c28c2e680bf5 2:66a54e77aa33
1 <tool id="fcs_gate_trans_convert" name="Transform FCS data" version="1.2+galaxy0"> 1 <tool id="fcs_gate_trans_convert" name="Transform FCS data" version="1.2+galaxy1" profile="18.01">
2 <description>with optional compensation and automated gating with flowDensity.</description> 2 <description>with optional compensation and automated gating with flowDensity.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.10.0">bioconductor-flowdensity</requirement> 4 <requirement type="package" version="1.10.0">bioconductor-flowdensity</requirement>
5 <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
5 </requirements> 6 </requirements>
6 <stdio> 7 <stdio>
7 <exit_code range="2:" level="fatal" description="See stderr for more details." /> 8 <exit_code range="1:" level="fatal" description="See stderr for more details." />
8 </stdio> 9 </stdio>
9 <command><![CDATA[ 10 <command><![CDATA[
10 Rscript $__tool_directory__/FCSGateTrans.R '${input}' '${output}' $comp '${outformat}' '${graph}' '${report}' '${transform.trans_method}' 11 Rscript $__tool_directory__/FCSGateTrans.R '${input}' '${output}' $comp '${outformat}'
12 #if $gate
13 '${graph}' '${report}'
14 #else
15 'None' 'None'
16 #end if
17 '${transform.trans_method}'
11 #if $transform.trans_method == "arcsinh" 18 #if $transform.trans_method == "arcsinh"
12 $transform.scaling_factor 19 $transform.scaling_factor
13 #else if $transform.trans_method == "logicle" 20 #else if $transform.trans_method == "logicle"
14 $transform.w $transform.t $transform.m 21 $transform.w $transform.t $transform.m
15 #end if 22 #end if
37 </param> 44 </param>
38 <param name="m" type="float" value="4.5" label="Full width of the transformed display m for logicle transform:" help="m is expressed in asymptotic decades and should be positive. The default value is 4.5 ."> 45 <param name="m" type="float" value="4.5" label="Full width of the transformed display m for logicle transform:" help="m is expressed in asymptotic decades and should be positive. The default value is 4.5 .">
39 </param> 46 </param>
40 </when> 47 </when>
41 </conditional> 48 </conditional>
42 <param name="gate" type="select" label="Automatically gate debris?">
43 <option value="FALSE">No, thank you</option>
44 <option value="TRUE">Yes, please</option>
45 </param>
46 <param name="gate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Automatically gate debris?"/> 49 <param name="gate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Automatically gate debris?"/>
47 <param name="outformat" type="select" label="Output Format"> 50 <param name="outformat" type="select" label="Output Format">
48 <option value="flowtext">Text File</option> 51 <option value="flowtext">Text File</option>
49 <option value="FCS">FCS 3.0</option> 52 <option value="FCS">FCS 3.0</option>
50 <option value="flowFrame">R Data, flowFrame</option> 53 <option value="flowFrame">R Data, flowFrame</option>
65 </data> 68 </data>
66 </outputs> 69 </outputs>
67 <tests> 70 <tests>
68 <test> 71 <test>
69 <param name="input" value="testfcs1.fcs"/> 72 <param name="input" value="testfcs1.fcs"/>
73 <param name="comp" value="FALSE"/>
74 <param name="gate" value="FALSE"/>
75 <param name="outformat" value="flowtext"/>
76 <param name="trans_method" value="fcstrans"/>
77 <output name="output" file="nocomp.flowtext"/>
78 </test>
79 <test>
80 <param name="input" value="testfcs1.fcs"/>
81 <param name="comp" value="FALSE"/>
82 <param name="gate" value="FALSE"/>
83 <param name="outformat" value="flowtext"/>
84 <param name="trans_method" value="None"/>
85 <output name="output" file="notrans.flowtext"/>
86 </test>
87 <test>
88 <param name="input" value="testfcs1.fcs"/>
89 <param name="comp" value="FALSE"/>
90 <param name="gate" value="FALSE"/>
91 <param name="outformat" value="flowtext"/>
92 <param name="trans_method" value="arcsinh"/>
93 <param name="scaling_factor" value="150"/>
94 <output name="output" file="arcsinh150.flowtext"/>
95 </test>
96 <test>
97 <param name="input" value="testfcs1.fcs"/>
98 <param name="comp" value="TRUE"/>
99 <param name="gate" value="TRUE"/>
100 <param name="outformat" value="flowtext"/>
101 <param name="trans_method" value="fcstrans"/>
102 <output name="output" file="withcomp.flowtext"/>
103 </test>
104 <test>
105 <param name="input" value="testfcs1.fcs"/>
106 <param name="comp" value="TRUE"/>
107 <param name="gate" value="FALSE"/>
108 <param name="outformat" value="flowtext"/>
109 <param name="trans_method" value="logicle_auto"/>
110 <output name="output" file="log_auto.flowtext"/>
111 </test>
112 <test>
113 <param name="input" value="testfcs1.fcs"/>
114 <param name="comp" value="TRUE"/>
115 <param name="gate" value="FALSE"/>
116 <param name="outformat" value="flowtext"/>
117 <param name="trans_method" value="logicle"/>
118 <param name="w" value="0.4"/>
119 <param name="t" value="10000"/>
120 <param name="m" value="4.5"/>
121 <output name="output" file="logicle.flowtext"/>
122 </test>
123 <test>
124 <param name="input" value="testfcs1.fcs"/>
125 <param name="comp" value="TRUE"/>
126 <param name="gate" value="TRUE"/>
127 <param name="outformat" value="flowtext"/>
128 <param name="trans_method" value="fcstrans"/>
129 <output name="output" file="withcomp.flowtext"/>
130 <output name="graph" file="graph.png" compare="sim_size"/>
131 <output name="report" file="report.txt"/>
132 </test>
133 <test>
134 <param name="input" value="testfcs1.fcs"/>
70 <param name="comp" value="TRUE"/> 135 <param name="comp" value="TRUE"/>
71 <param name="gate" value="FALSE"/> 136 <param name="gate" value="FALSE"/>
72 <param name="outformat" value="FCS"/> 137 <param name="outformat" value="FCS"/>
73 <param name="trans_method" value="fcstrans"/> 138 <param name="trans_method" value="fcstrans"/>
74 <output name="output" file="comp_gated.fcs" compare="sim_size"/> 139 <output name="output" file="comp_gated.fcs" compare="sim_size"/>
87 152
88 ----- 153 -----
89 154
90 **Input files** 155 **Input files**
91 156
92 This tool uses FCS files as input and files are processed serially. Users choose to automatically gate cellular debris, and/or compensate the data. 157 This tool uses FCS files as input and files are processed serially. Users choose which transformation algorithm to apply, and whether to automatically gate cellular debris, and/or compensate the data.
93 158
94 **Output files** 159 **Output files**
95 160
96 Output is tab-separated text containing transformed fluorescence intensity values for each marker. 161 Output is a table of fluorescence intensity values for each marker, as a text file, FCS3.0 or R Object (flowFrame).
97 If the option is selected, a FCS file (format FCS3.0) is generated.
98 162
99 **Gating output** 163 **Gating output**
100 164
101 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. 165 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. Please check to make sure the gating is doing what you think it should be doing.
102 166
103 ----- 167 -----
104 168
105 Compensation will be implemented according to the spillover matrix included in the FCS files (if available). 169 Compensation will be implemented according to the spillover matrix included in the FCS files (if available).
106 170