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"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_preprocess commit c3d761b4fca140636c3f22ef0fdbb855f3ecbdb8"
author azomics
date Sun, 25 Jul 2021 10:36:03 +0000
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1 <tool id="metacyto_preprocess" name="Pre-process samples" version="1.0+galaxy0" profile="18.01">
2 <description>for MetaCyto</description>
3 <requirements>
4 <requirement type="package" version="1.4.0">bioconductor-metacyto</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:9" />
8 <exit_code range="10" level="fatal" description="Please provide valid input FCS files." />
9 <exit_code range="11" level="fatal" description="Please provide a label for FCS files sets." />
10 <exit_code range="12" level="fatal" description="FCS files in a same group MUST have the same set of markers." />
11 <exit_code range="13" level="fatal" description="All groups needs to have different labels"/>
12 <exit_code range="14:" />
13 </stdio>
14 <command><![CDATA[
15 Rscript --slave --vanilla '$__tool_directory__/metacyto_preprocess.R'
16 '${sampling}'
17 'preprocessed_fcs'
18 '${output_file}'
19 '${excluded_param}'
20 '${g1_name}'
21 '${g1_format}'
22 '${g1_scaling_factor}'
23 #for $f in $group1
24 '${f}' '${f.name}'
25 #end for
26 #for $panel in $fcs_set
27 'new_panel'
28 '${panel.gp_name}'
29 '${panel.gp_format}'
30 '${panel.gp_scaling_factor}'
31 #for $ff in $panel.group
32 '${ff}' '${ff.name}'
33 #end for
34 #end for
35 ]]>
36 </command>
37 <inputs>
38 <param name="sampling" type="integer" label="Number of events to sample FCS files to." help="0 will use all events from input files, default value is 5000." value="5000"/>
39 <param name="excluded_param" type="text" label="Parameters to exclude from the transformation." help="By default FSC, SSC, Time and Cell Length channels are excluded. Providing markers to exclude overrides the default setting. i.e.:FSC, SSC, CD88"/>
40 <param name="g1_name" type="text" label="Label for the first set of FCS files." value="group 1"/>
41 <param format="fcs" name="group1" type="data_collection" collection_type="list" label="FCS files Collection."/>
42 <param name="g1_format" type="select" label="Assay type for the first set of FCS files." help="If files are compensated already, please select CyTOF.">
43 <option value="FCM" selected="true">Standard Flow Cytometry data</option>
44 <option value="CyTOF">CyTOF data</option>
45 </param>
46 <param name="g1_scaling_factor" type="integer" min="0" max="200" value="150" label="Scaling factor b for arcsinh transform for the first set of files." help="The default value is 150 for standard FCM data. The recommended value for CyTOF data is 5. If data is transformed already, please select 0."/>
47 <repeat name="fcs_set" title="Set of FCS files">
48 <param name="gp_name" type="text" label="Label for this set of FCS files." help="For example: group 2"/>
49 <param format="fcs" name="group" type="data_collection" collection_type="list" label="FCS files Collection."/>
50 <param name="gp_format" type="select" label="Assay type for the first set of FCS files." help="If files are compensated already, please select CyTOF.">
51 <option value="FCM" selected="true">Standard Flow Cytometry data</option>
52 <option value="CyTOF">CyTOF data</option>
53 </param>
54 <param name="gp_scaling_factor" type="integer" min="1" max="200" value="150" label="Scaling factor b for arcsinh transform for the first set of files." help="The default value is 150 for standard FCM data. The recommended value for cyTOF data is 5. If data is transformed already, please select 0."/>
55 </repeat>
56 </inputs>
57 <outputs>
58 <data format="metacyto_summary.txt" name="output_file" label="${tool.name} on ${on_string}: samples summary"/>
59 <collection type="list" label="${tool.name} on ${on_string}: processed samples" name="preprocessed">
60 <discover_datasets directory="preprocessed_fcs" pattern="__name_and_ext__" ext="fcs" />
61 </collection>
62 </outputs>
63 <tests>
64 <test>
65 <param name="sampling" value="1000"/>
66 <param name="excluded_param" value="FSC-A,FSC-W,FSC-H,Time,Cell_length"/>
67 <param name="g1_name" value="SDY376"/>
68 <param name="group1">
69 <collection type="list">
70 <element name="inputflow1" value="inputflow1.fcs"/>
71 <element name="inputflow2" value="inputflow2.fcs"/>
72 <element name="inputflow3" value="inputflow3.fcs"/>
73 <element name="inputflow4" value="inputflow4.fcs"/>
74 <element name="inputflow5" value="inputflow5.fcs"/>
75 <element name="inputflow6" value="inputflow6.fcs"/>
76 </collection>
77 </param>
78 <param name="g1_format" value="FCM"/>
79 <param name="g1_scaling_factor" value="150"/>
80 <repeat name="fcs_set">
81 <param name="gp_name" value="SDY376-2"/>
82 <param name="group">
83 <collection type="list">
84 <element name="inputcytof1" value="inputcytof1.fcs"/>
85 <element name="inputcytof2" value="inputcytof2.fcs"/>
86 <element name="inputcytof3" value="inputcytof3.fcs"/>
87 <element name="inputcytof4" value="inputcytof4.fcs"/>
88 </collection>
89 </param>
90 <param name="gp_format" value="CyTOF"/>
91 <param name="gp_scaling_factor" value="8"/>
92 </repeat>
93 <output name="output_file">
94 <assert_contents>
95 <has_n_lines n="11" />
96 </assert_contents>
97 </output>
98 <output_collection name="preprocessed" type="list">
99 <element name="SDY376" ftype="fcs">
100 <assert_contents>
101 <has_text_matching expression="^FCS3.0" />
102 </assert_contents>
103 </element>
104 <element name="SDY376-2" ftype="fcs">
105 <assert_contents>
106 <has_text_matching expression="^FCS3.0" />
107 </assert_contents>
108 </element>
109 </output_collection>
110 </test>
111 </tests>
112 <help><![CDATA[
113 Pre-process samples
114 -------------------
115
116 This tool uses MetaCyto's preprocessing function to prepare sets of FCS files for a MetaCyto analysis.
117
118 **Input**
119 This tool requires one or more sets of FCS files.
120 .. class:: infomark
121 The number provided for sub-sampling corresponds to the number of events randomly sampled from each FCS files.
122 **Output**
123 This tool generates one or more FCS files containing optionally sub-sampled data from the input FCS data sets. The FCS data can optionally be compensated and/or transformed. A summary of the operations is also generated.
124 .. class:: infomark
125 This tool uses the arcsinh transformation. If you would like to use another transformation algorithm, sets of files can be prepared independantly by using the following tools:
126 - Merge and downsample FCS files with FlowSOM
127 - Transform FCS data with optional compensation and automated gating with flowDensity.
128 .. class:: warningmark
129 The workflow to use MetaCyto in R vs. ImmPort Galaxy are slightly different - please use the following tool in FCS File Tools to harmonize FCS files before MetaCyto pre-processing:
130 - Edit markers or channels in FCS files
131
132 **Example**
133
134 *File1*: 20K events::
135
136 Marker1 Marker2 Marker3 ...
137 34 45 12 ...
138 33 65 10 ...
139 87 26 76 ...
140 24 56 32 ...
141 95 83 53 ...
142 ... ... ... ...
143
144 *File2*: 20K events::
145
146 Marker1 Marker2 Marker3 ...
147 19 62 98 ...
148 12 36 58 ...
149 41 42 68 ...
150 76 74 53 ...
151 62 34 45 ...
152 ... ... ... ...
153
154 *Output*: 5K events::
155
156 Marker1 Marker2 Marker3 ...
157 34 45 12 ...
158 87 26 76 ...
159 12 36 58 ...
160 62 34 45 ...
161 ... ... ... ...
162
163 *Output* - Summary Table::
164
165 study_id antibodies filenames
166 group1 Marker1|Marker2|Marker3|... file1.fcs
167 group2 Marker1|Marker2|Marker3|... file2.fcs
168 ]]>
169 </help>
170 </tool>