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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 80069808371b58f45da0c8133c27d67ac1a5b448"
author computational-metabolomics
date Wed, 17 Feb 2021 10:44:07 +0000
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1 <tool id="dimspy_merge_peaklists" name="Merge peaklists" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
2 <description> produced by the tools 'Process scans (and SIM-Stitch)' or 'Replicate filter'</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 <![CDATA[
9 dimspy merge-peaklists
10 #for $fn in $hdf5_files_in
11 --input '$fn'
12 #end for
13
14 #if $multilist
15 --output .
16 #else
17 --output '$hdf5_file_out'
18 #end if
19
20 #if $filelist
21 --filelist '$filelist'
22 #end if
23 ]]>
24 </command>
25 <inputs>
26 <param name="hdf5_files_in" type="data" multiple="true" format="h5" min="2" label="Peaklist to merge" help="Select a minimum of two hdf5 files" argument="--input" />
27 <param name="multilist" type="boolean" checked="false" label="Create multiple merged peaklists?"
28 help="Based on a 'multilist' column in the filelist text file, divide the peaklists into different lists
29 e.g. [pl1 pl2], [pl3, pl4] can be converted to 2 new lists:
30 [pl1, pl3] [pl2, pl4]"/>
31 <param type="data" format="tsv,tabular" optional="true" label="Filelist"
32 help="A table containing metadata for each experimental sample. See help section below for more details." argument="--filelist" />
33 </inputs>
34 <outputs>
35 <collection name="multiple_merged" type="list" label="${tool.name} on ${on_string}: Peaklists (HDF5)">
36 <filter>multilist</filter>
37 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.hdf5" format="h5" directory="." visible="false" />
38 </collection>
39 <data name="hdf5_file_out" format="h5" label="${tool.name} on ${on_string}: Peaklists (HDF5 file)">
40 <filter>multilist is False</filter>
41 </data>
42 </outputs>
43 <tests>
44 <test>
45 <!-- Merge (no filelist) -->
46 <param name="hdf5_files_in" value="pls.h5,pls_QC18.h5" ftype="h5" />
47 <output name="hdf5_file_out" value="merged_01.h5" ftype="h5" compare="sim_size" />
48 </test>
49 <test>
50 <!-- Merge (with filelist) -->
51 <param name="hdf5_files_in" value="pls.h5,pls_QC18.h5" ftype="h5" />
52 <param name="filelist" value="filelist_merge.txt" ftype="tsv"/>
53 <output name="hdf5_file_out" value="merged_02.h5" ftype="h5" compare="sim_size" />
54 </test>
55 <test>
56 <!-- Merge (multilist) -->
57 <param name="hdf5_files_in" value="pls.h5,pls_QC18.h5" ftype="h5" />
58 <param name="filelist" value="filelist_multilist_merge.txt" ftype="tsv"/>
59 <param name="multilist" value="true"/>
60 <output_collection name="multiple_merged" type="list">
61 <element name="merged_peaklist_001" file="merged_peaklist_001.h5" ftype="h5" compare="sim_size" />
62 <element name="merged_peaklist_002" file="merged_peaklist_002.h5" ftype="h5" compare="sim_size" />
63 <element name="merged_peaklist_003" file="merged_peaklist_003.h5" ftype="h5" compare="sim_size" />
64 </output_collection>
65 </test>
66
67 </tests>
68 <help>
69 ---------------
70 Merge Peaklists
71 ---------------
72
73 ..
74
75 -----------------------------------
76
77 Description
78 -----------
79
80 This tool allows users to extract and export specific peaklists from one or more .hdf5, to one or more .hdf5 files. If more-than one .hdf5 file is exported, users can control which subset of peaklists are exported to which .hdf5 file.
81
82
83 -----------------------------------
84
85 Parameters
86 ----------
87
88 |
89
90 **Peaklist to merge** (REQUIRED; minimally requires two .hdf5 files) - selection menu from which the user must select two or more .hdf5 files from the active Galaxy history.
91
92 **NOTE**: if a .hdf5 file containing a peak intensity matrix is selected, then the peaklists used in generating that matrix are extracted from the file e.g. [pl1, pl2, pl3] + [pm456] = [pl1, pl2, pl3] + [pl4, pl5, pl6] = [pl1, pl2, pl3, pl4, pl5, pl6] .
93
94 |
95
96 **Create multiple merged peaklists** (REQUIRED; default = “No”) - binary toggle:
97
98 **No** - all extracted peaklists are exported to a single .hdf5 file in the active Galaxy history. Metadata associated with each peaklist is also captured in this file.
99
100 **Yes** - multiple .hdf5 files are exported to the active Galaxy history, each of which containing a user-defined subset of the extracted peaklist(s) in accordance with the “multilist” column of the input “Filelist”, e.g. using the mock filelist shown below, two .hdf5 files would be exported to history:
101
102 * The first .hdf5 file would contain peaklists from [sample_rep1.raw, sample_rep2.raw, blank1_rep1.raw and blank1_rep2.raw], i.e. all filenames associated with multilist value '1'
103
104 * The second .hdf5 file would contain peaklists from [sample_rep1.raw, sample_rep2.raw, blank_rep3.raw and blank_rep4.raw], i.e. all filenames associated with multilist value '2'
105
106 |
107
108
109 **NOTE** - if for each analysed study sample a corresponding blank sample has been analysed, then the multilist column can be used to pair these together in an output .hdf5 file. This enables sample-specific blank filtering at a later stage.
110
111
112 |
113
114 **Filelist / Samplelist** (OPTIONAL) - a selection menu from which one or more filelists can be selected.
115
116 **Mock example of a filelist** - the optional multilist column determines which peaklists are exported together in .hdf5 format.
117
118 |
119
120 +-----------------+------------+-----------+-------+----------------+-----------+-------+
121 | filename | classLabel | replicate | batch | injectionOrder | multilist | [...] |
122 +-----------------+------------+-----------+-------+----------------+-----------+-------+
123 | sample_rep1.raw | sample | 1 | 1 | 1 | 1 | [...] |
124 +-----------------+------------+-----------+-------+----------------+-----------+-------+
125 | sample_rep2.raw | sample | 2 | 1 | 2 | 1 | [...] |
126 +-----------------+------------+-----------+-------+----------------+-----------+-------+
127 | sample_rep3.raw | sample | 3 | 1 | 3 | 2 | [...] |
128 +-----------------+------------+-----------+-------+----------------+-----------+-------+
129 | sample_rep4.raw | sample | 4 | 1 | 4 | 2 | [...] |
130 +-----------------+------------+-----------+-------+----------------+-----------+-------+
131 | blank_rep1.raw | blank | 1 | 1 | 5 | 1 | [...] |
132 +-----------------+------------+-----------+-------+----------------+-----------+-------+
133 | blank_rep2.raw | blank | 2 | 1 | 6 | 1 | [...] |
134 +-----------------+------------+-----------+-------+----------------+-----------+-------+
135 | blank_rep3.raw | blank | 3 | 1 | 7 | 2 | [...] |
136 +-----------------+------------+-----------+-------+----------------+-----------+-------+
137 | blank_rep4.raw | blank | 4 | 1 | 8 | 2 | [...] |
138 +-----------------+------------+-----------+-------+----------------+-----------+-------+
139 | ... | ... | ... | ... | ... | ... | [...] |
140 +-----------------+------------+-----------+-------+----------------+-----------+-------+
141
142 |
143
144 -----------------------------------
145
146 Output file(s)
147 --------------
148
149 |
150
151 One or more .hdf5 file(s), each containing one or more peaklists.
152
153 |
154
155 -----------------------------------
156
157 @github_developers_contributors@
158
159 </help>
160 <expand macro="citations" />
161 </tool>