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comparison FCSMergeDownsample.xml @ 0:8e568997abda draft

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit 2fe0269eaff92916ca51729a7ca8d2017f65f89f"
author azomics
date Mon, 22 Jun 2020 20:35:09 -0400
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1 <tool id="fcs_merge_downsample" name="Merge and downsample" version="1.0+galaxy1">
2 <description>FCS files with FlowSOM</description>
3 <requirements>
4 <requirement type="package" version="1.18.0">bioconductor-flowsom</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="10" level="fatal" description="One or more FCS files is not valid. See stderr for more details." />
8 <exit_code range="11" level="fatal" description="Please provide a numeric value [0,1] for the downsampling factor." />
9 <exit_code range="12" level="fatal" description="There are inconsistencies in marker names between FCS files." />
10 </stdio>
11 <command><![CDATA[
12 FCSMergeDownsample.R '${output_file}' '${outformat}' '${factorDS}'
13 #for $f in $input
14 '${f}'
15 #end for
16 ]]>
17 </command>
18 <inputs>
19 <param format="fcs" name="input" type="data_collection" collection_type="list" label="FCS files Collection"/>
20 <param name="factorDS" type="text" label="Downsample by:" value="i.e.:0.1 or 10%" optional="true" help="By default 0.1"/>
21 <param name="outformat" type="select" label="Output Format">
22 <option value="flowFrame">R Data, flowFrame</option>
23 <option value="FCS">FCS 3.0</option>
24 </param>
25 </inputs>
26 <outputs>
27 <data format="flowframe" name="output_file" label="Merged FCS from ${input.name} in ${outformat}">
28 <change_format>
29 <when input="outformat" value="FCS" format="fcs" />
30 </change_format>
31 </data>
32 </outputs>
33 <tests>
34 <test>
35 <param name="input">
36 <collection type="list">
37 <element name="input1.fcs" value="input1.fcs"/>
38 <element name="input2.fcs" value="input2.fcs"/>
39 <element name="input3.fcs" value="input3.fcs"/>
40 </collection>
41 </param>
42 <param name="factorDS" value=".8"/>
43 <param name="outformat" value="flowFrame"/>
44 <output name="output_file" file="merge1.flowframe" compare="sim_size" delta="1000000"/>
45 </test>
46 <test>
47 <param name="input">
48 <collection type="list">
49 <element name="input1.fcs" value="input1.fcs"/>
50 <element name="input2.fcs" value="input2.fcs"/>
51 <element name="input3.fcs" value="input3.fcs"/>
52 </collection>
53 </param>
54 <param name="factorDS" value="i.e.:0.1 or 10%"/>
55 <param name="outformat" value="FCS"/>
56 <output name="output_file" file="merge2.fcs" compare="sim_size" delta="1000000"/>
57 </test>
58 </tests>
59 <help><![CDATA[
60 Merge and downsample using FlowSOM
61 -------------------
62
63 This tool merges and downsamples multiple FCS files into one flowframe or FCS file using FlowSOM.
64
65 **Input files**
66
67 This tool requires a collection of FCS files as input.
68
69 .. class:: warningmark
70
71 Input files **MUST** have the same markers *and* channels. The following tools in the FCS Files tool section can help harmonize channels and/or markers in the FCS files collection:
72
73 - Get list of markers or channels in FCS files.
74 - Edit markers or channels in FCS files
75
76 **Downsampling**
77
78 By default, files are downsampled to 10% of the total number of events across input files. If a downsampling factor is provided, each file in the input dataset collection will be downsampled randomly without replacement as follows:
79
80 - If n is between 0 and 1, the size of the output will be n times that of the input files.
81 - If n is between 1 and 100, the size of the output will be n% that of the input files.
82
83 .. class:: infomark
84
85 Downsampling is implemented such that each file will contribute an equal number of event to the aggregate.
86
87 .. class:: warningmark
88
89 At this time, up-sampling is not supported. If the number provided is greater than 100, the tool will exit.
90
91 **Output file**
92
93 The output file contains an aggregation of events from the input files provided all are valid FCS files. If a downsampling factor is provided, the corresponding proportion of each input file ONLY will be read in. Output can be provided in FCS format or in a RData object containing a flowFrame.
94
95 .. class:: infomark
96
97 The output generated contains data for all markers present in the original files. No information is added, or removed.
98
99 -----
100
101 **Example**
102
103 *File1*: 20K events::
104
105 Marker1 Marker2 Marker3 ...
106 34 45 12 ...
107 33 65 10 ...
108 87 26 76 ...
109 24 56 32 ...
110 95 83 53 ...
111 ... ... ... ...
112
113 *File2*: 20K events::
114
115 Marker1 Marker2 Marker3 ...
116 19 62 98 ...
117 12 36 58 ...
118 41 42 68 ...
119 76 74 53 ...
120 62 34 45 ...
121 ... ... ... ...
122
123 *Output*: 4K events::
124
125 Marker1 Marker2 Marker3 ...
126 34 45 12 ...
127 87 26 76 ...
128 12 36 58 ...
129 62 34 45 ...
130 ... ... ... ...
131
132 .. class:: infomark
133
134 With a downsampling factor of 0.5: 20K events::
135
136 Marker1 Marker2 Marker3 ...
137 34 45 12 ...
138 24 56 32 ...
139 95 83 53 ...
140 19 62 98 ...
141 12 36 58 ...
142 62 34 45 ...
143 ... ... ... ...
144 ]]>
145 </help>
146 <citations>
147 <citation type="doi">10.1002/cyto.a.22625</citation>
148 </citations>
149 </tool>