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comparison metacyto_search_clr.xml @ 0:94ac403d134a draft default tip

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"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_search_clr commit a1b796a09f6b30919a73b5ded0ce5a6378317007"
author azomics
date Wed, 28 Jul 2021 22:02:38 +0000
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1 <tool id="metacyto_search_clr" name="Guided identification of clusters" version="1.0+galaxy0" profile="18.01">
2 <description>using 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 FCS files pre-processed for MetaCyto." />
10 <exit_code range="12" level="fatal" description="Pre-processing summary doesn't match the set of FCS files." />
11 <exit_code range="13" level="fatal" description="The pre-processing summary is in the wrong format." />
12 <exit_code range="14" level="fatal" description="Please provide a cluster definition" />
13 <exit_code range="15:" />
14 </stdio>
15 <command><![CDATA[
16 Rscript --slave --vanilla '$__tool_directory__/metacyto_search_clr.R' '${summary}' 'fcs_stats' '${first_def}' '${unused}' '${cluster_list}'
17 #for $r in $cl_df
18 '${r.cluster_def}'
19 #end for
20 'FCS_FILES'
21 #for $f in $group
22 '${f}' '${f.name}'
23 #end for
24 ]]>
25 </command>
26 <inputs>
27 <param format="metacyto_summary.txt" name="summary" type="data" label="MetaCyto preprocessing summary"/>
28 <param format="fcs" name="group" type="data_collection" collection_type="list" label="FCS files Collection pre-processed for MetaCyto"/>
29 <param name="first_def" type="text" label="Cluster definition" help="i.e.:CD3+,CD4-,CD8+,CCR7+"/>
30 <repeat name="cl_df" title="Cluster">
31 <param name="cluster_def" type="text" label="Additional cluster definition" help="i.e.:CD3+,CD4-,CD8+,CCR7+"/>
32 </repeat>
33 </inputs>
34 <outputs>
35 <data format="tabular" name="unused" label="List of clusters not found in all files from ${group.name}"/>
36 <data format="metacyto_clr.txt" name="cluster_list" label="List of clusters from guided clustering analysis of ${group.name}"/>
37 <collection type="list" label="Guided cluster identification analysis in ${group.name}" name="output">
38 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="fcs_stats" format="metacyto_stats.txt" />
39 </collection>
40 </outputs>
41 <tests>
42 <test>
43 <param name="summary" value="preprocess.metacyto_summary.txt"/>
44 <param name="group">
45 <collection type="list">
46 <element name="Group1" value="Group1.fcs"/>
47 <element name="Group2" value="Group2.fcs"/>
48 </collection>
49 </param>
50 <param name="first_def" value="CD3+,CD4-,CD8+" />
51 <repeat name="cl_df">
52 <param name="cluster_def" value="CD8+,CCR7+" />
53 </repeat>
54 <output name="unused" >
55 <assert_contents>
56 <has_n_lines n="2"/>
57 </assert_contents>
58 </output>
59 <output_collection name="output">
60 <element name="Group2_cluster_stats.txt">
61 <assert_contents>
62 <has_n_lines n="9"/>
63 </assert_contents>
64 </element>
65 </output_collection>
66 </test>
67 </tests>
68 <help><![CDATA[
69 This tool uses MetaCyto to search for clusters of cells corresponding to provided gate definitions
70 --------------------------------------------------------------------------------------------------
71
72 **Input files**
73
74 This tool requires the pre-processing summary generated for MetaCyto as well as the pre-processed FCS files.
75
76 *Cluster definitions*
77
78 Please provide gate definitions as comma-separated lists of marker names, for instance "CD3+, CD4+, CD25+, Foxp3+".
79
80 **Output**
81
82 This tool generates a list of provided clusters 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.
83
84 **Example**
85
86 *Input* - Pre-Processing Summary Table
87
88 ======== =========================== =========
89 study_id antibodies filenames
90 ======== =========================== =========
91 group1 Marker1|Marker2|Marker3|... file1.fcs
92 group2 Marker1|Marker2|Marker3|... file2.fcs
93 ... ... ...
94 ======== =========================== =========
95
96
97 *Output* - Clustering Summary Tables
98
99 ========== ================ ========== ========================== ================ ======= ======= === ========
100 group_name fcs_files cluster_id label fcs_names Marker1 Marker2 ... fraction
101 ========== ================ ========== ========================== ================ ======= ======= === ========
102 group1 file1_group1.fcs cluster1 Marker1+|Marker2+|Marker3+ file1_group1.fcs 1.9815 0.2024 ... 0.373
103 group1 file2_group1.fcs cluster1 Marker1+|Marker2+|Marker3+ file2_group1.fcs 2.3739 0.3377 ... 0.26
104 ... ... ... ... ... ... ... ... ...
105 ========== ================ ========== ========================== ================ ======= ======= === ========
106 ]]>
107 </help>
108 </tool>