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comparison metacyto_autocluster.xml @ 0:c744db871f90 draft default tip

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"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_autocluster commit 3cc1083d473530ed4f7439d590568baa51a46857"
author azomics
date Tue, 27 Jul 2021 23:00:49 +0000
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1 <tool id="metacyto_autocluster" name="Autoclustering analysis" version="1.0+galaxy0" profile="18.01">
2 <description>using MetaCyto</description>
3 <requirements>
4 <!-- <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement> -->
5 <!-- flowcore is already a dependency of MetaCyto -->
6 <requirement type="package" version="1.4.0">bioconductor-metacyto</requirement>
7 </requirements>
8 <stdio>
9 <exit_code range="1:9" />
10 <exit_code range="10" level="fatal" description="Please provide valid input FCS files." />
11 <exit_code range="11" level="fatal" description="Please provide FCS files pre-processed for MetaCyto." />
12 <exit_code range="12" level="fatal" description="Pre-processing summary doesn't match the set of FCS files." />
13 <exit_code range="13" level="fatal" description="The pre-processing summary is in the wrong format." />
14 <exit_code range="14" level="fatal" description="Please provide a cluster definition" />
15 <exit_code range="15:" />
16 </stdio>
17 <command><![CDATA[
18 Rscript --slave --vanilla '$__tool_directory__/metacyto_autocluster.R' '${summary}' '${clr_option.clustering}' '${quantile}' '${min_event}' '${ex_param}' 'fcs_stats' '${cluster_list}'
19 #if $more_cluster_def.more_def == "TRUE"
20 '${more_cluster_def.first_def}'
21 #for $r in $more_cluster_def.cl_df
22 '${r.cluster_def}'
23 #end for
24 #end if
25 'PARAM'
26 #if $clr_option.clustering == "FlowSOM"
27 '${clr_option.mcluster}' '${clr_option.xdim}' '${clr_option.ydim}' '${clr_option.seed}'
28 #end if
29 'FCS_FILES'
30 #for $f in $group
31 '${f}' '${f.name}'
32 #end for
33 '${unused}'
34 ]]>
35 </command>
36 <inputs>
37 <param format="metacyto_summary.txt" name="summary" type="data" label="MetaCyto preprocessing summary"/>
38 <param format="fcs" name="group" type="data_collection" collection_type="list" label="FCS files Collection pre-processed for MetaCyto"/>
39 <conditional name="clr_option">
40 <param name="clustering" type="select" label="Clustering algorithm to use:">
41 <option value="FlowSOM">FlowSOM</option>
42 <option value="flowHC">flowHC</option>
43 </param>
44 <when value="FlowSOM">
45 <param name="mcluster" type="integer" value="40" label="Number of expected metaclusters" help="MetaCyto authors recommend using 40, FlowSOM default is 10." />
46 <param name="xdim" type="integer" value="10" label="Grid size, width"/>
47 <param name="ydim" type="integer" value="10" label="Grid size, height" help="By default, the grid size is 10x10. The grid size specifies the number of clusters." />
48 <param name="seed" type="integer" value="42" label="Seed" help="Let's be geeks, default is set to 42." />
49 </when>
50 </conditional>
51 <param name="quantile" type="float" value="0.95" min="0.5" max="1" label="Quantile threshold" help="Minimum percent of cells in a cluster expressing more or less than the cutoff value of a marker. The default value is 0.95"/>
52 <param name="min_event" type="float" value="0.05" min="0" max="0.5" label="Minimum percent of cells in the positive and negative region after bisection" help="The default value is 0.05. Keep this factor small to avoid bisecting uni-mode distributions."/>
53 <param name="ex_param" type="text" label="Markers to exclude from clustering analysis:" 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"/>
54 <conditional name="more_cluster_def">
55 <param name="more_def" type="boolean" label="Add cluster definitions?" checked="false" truevalue="TRUE" falsevalue="FALSE" />
56 <when value="TRUE">
57 <param name="first_def" type="text" label="Additional cluster definition:" help="For example: CD3+,CD4-,CD8+,CCR7+"/>
58 <repeat name="cl_df" title="Cluster:">
59 <param name="cluster_def" type="text" label="Additional cluster definition:" help="For example: CD3+,CD4-,CD8+,CCR7+"/>
60 </repeat>
61 </when>
62 </conditional>
63 </inputs>
64 <outputs>
65 <collection type="list" label="${clr_option.clustering} autoClustering analysis on ${on_string}" name="output">
66 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="fcs_stats" format="metacyto_stats.txt" />
67 </collection>
68 <data format="tabular" name="unused" label="List of clusters not found in all files from ${on_string}"/>
69 <data format="metacyto_clr.txt" name="cluster_list" label="List of clusters from ${clr_option.clustering} autoClustering analysis of ${group.name}"/>
70 </outputs>
71 <tests>
72 <test>
73 <param name="summary" value="preprocess.metacyto_summary.txt"/>
74 <param name="group">
75 <collection type="list">
76 <element name="Group1" value="Group1.fcs"/>
77 <element name="Group2" value="Group2.fcs"/>
78 </collection>
79 </param>
80 <output name="cluster_list" ftype="metacyto_clr.txt">
81 <assert_contents>
82 <has_n_lines n="80" />
83 <has_text text="CD16-" />
84 </assert_contents>
85 </output>
86 <output name="unused" ftype="tabular">
87 <assert_contents>
88 <has_n_lines n="81" />
89 <has_text text="CD19-" />
90 </assert_contents>
91 </output>
92 </test>
93 </tests>
94 <help><![CDATA[
95 This tool uses MetaCyto to cluster events automatically from several sets of FCS files.
96 ---------------------------------------------------------------------------------------
97
98 **Input files**
99
100 This tool requires the pre-processing summary generated for MetaCyto as well as the pre-processed FCS files.
101
102 **Parameters**
103
104 *Quantile threshold*
105
106 This value represents the minimum proportion of events in a cluster that should express more (or less) than the cutoff value for a given marker. With a value of 0.8, a cluster will be labeled Marker1+ if over 80% of cells in the cluster express Marker1 at a higher level than a cutoff value determined by the clustering analysis.
107
108 *Minimum Number of events*
109
110 This value represents the minimum proportion of cells in each region after bisection. Keep this factor small to avoid bisecting uni-mode distributions.
111
112 *Markers to exclude*
113
114 Please provide a comma-separated list of the markers that should be excluded from the clustering analysis. By default, FSC, SSC, Time and Cell Length channels are excluded, but providing a list of markers overrides the default settings.
115
116 *Additional cluster definitions*
117
118 Please provide additional gate definitions as comma-separated lists of marker names, for instance "CD3+, CD4+, CD25+, Foxp3+".
119
120 *FlowSOM - Number of meta-clusters*
121
122 Please indicate the exact number of meta-clusters expected.
123
124 *FlowSOM - Grid dimension*
125
126 Please indicate the dimension of the grid for establishing the SOM. The dimension of the grid defines the number of clusters (height x width = cluster)
127
128 *FlowSOM - Seed*
129
130 Please indicate a random number to use as seed. To make your analysis reproducible, use the same seed.
131
132 **Output**
133
134 This tool generates a list of clusters identified, including optionally provided cluster definitions, as well as a table of the MFI for each marker in each cluster in each file, and proportion of each cluster in each file. A list of unused cluster definitions, if any, is also generated.
135 -----
136
137 **Example**
138
139 *Input* - Pre-Processing Summary Table::
140 study_id antibodies filenames
141 group1 Marker1|Marker2|Marker3|... file1.fcs
142 group2 Marker1|Marker2|Marker3|... file2.fcs
143 ... ... ...
144 *Output* - Clustering Summary Tables::
145 group_name fcs_files cluster_id label fcs_names Marker1 Marker2 ... fraction
146 group1 file1_group1.fcs cluster1 Marker1-|Marker2+|Marker3+ file1_group1.fcs 1.9815 0.2024 ... 0.373
147 group1 file2_group1.fcs cluster1 Marker1-|Marker2+|Marker3+ file2_group1.fcs 2.3739 0.3377 ... 0.26
148 ... ... ... ... ... ... ... ... ...
149 *Output* - Cluster List::
150 Marker1+|Marker3-
151 Marker1-|Marker2+|Marker3-
152 ...
153 ]]>
154 </help>
155 </tool>