Mercurial > repos > computational-metabolomics > dimspy_get_peaklists

comparison get_peaklists.xml @ 0:afc9136ab094 draft

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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
author computational-metabolomics
date Sat, 11 Apr 2020 16:47:41 -0400
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-1:000000000000 0:afc9136ab094
1 <tool id="dimspy_get_peaklists" name="Get peaklists" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
2 <description> or an average peaklist from a Peak Intensity Matrix</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 <![CDATA[
9 #if $input.format == 'all'
10 dimspy get-peaklists
11 #elif $input.format == 'average'
12 dimspy get-average-peaklist
13 --name-peaklist '${input.name_peaklist}'
14 #end if
15 --input '$hdf5_file_in'
16 --output '$hdf5_file_out'
17 #if $input.to_txt
18 &&
19 dimspy hdf5-pls-to-txt
20 --input '$hdf5_file_out'
21 --output .
22 --delimiter $delimiter
23 #end if
24 #if $input.format == 'average' and $input.to_txt
25 &&
26 mv '${input.name_peaklist}.txt' '$tsv_file_out'
27 #end if
28 ]]>
29 </command>
30 <inputs>
31 <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peak Intensity Matrix (HDF5 file)" help="" />
32 <conditional name="input">
33 <param name="format" type="select" label="Get..." help="">
34 <option value="average" selected="true">Average Peaklist</option>
35 <option value="all">Multiple Peaklists (samples)</option>
36 </param>
37 <when value="average">
38 <param name="name_peaklist" argument="--name-peaklist" type="text" value="" label="Name average Peaklist" >
39 <validator type="empty_field" />
40 <validator type="regex" message="Value may include alphanumeric characters, underscores, dashes and spaces.">[A-Za-z0-9_\- ]+</validator>
41 </param>
42 <param name="to_txt" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Write Peaklists to tsv files (data collection)?" help=""/>
43 </when>
44 <when value="all">
45 <param name="to_txt" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Write Peaklists to tsv files?" help=""/>
46 </when>
47 </conditional>
48 <param name="delimiter" argument="--delimiter" type="hidden" value="tab" help=""/>
49 </inputs>
50 <outputs>
51 <data name="hdf5_file_out" format="h5" label="${tool.name} on ${on_string}: Peaklists (HDF5 file)"/>
52 <collection name="peaklists_txt" type="list" label="${tool.name} on ${on_string}: Peaklists">
53 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tsv" directory="." visible="false" />
54 <filter>input['to_txt'] is True</filter>
55 <filter>input['format'] == 'all'</filter>
56 </collection>
57 <data name="tsv_file_out" format="tsv" label="${tool.name} on ${on_string}: Average Peaklist">
58 <filter>input['to_txt'] is True</filter>
59 <filter>input['format'] == 'average'</filter>
60 </data>
61 </outputs>
62 <tests>
63 <test>
64 <param name="format" value="all"/>
65 <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
66 <param name="to_txt" value="True"/>
67 <param name="delimiter" value="tab"/>
68 <output_collection name="peaklists_txt" type="list">
69 <element name="batch04_S01_rep01_247_2_248_3_249" file="batch04_S01_rep01_247_2_248_3_249.txt" ftype="tsv"/>
70 </output_collection>
71 </test>
72 <test>
73 <param name="format" value="average"/>
74 <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
75 <param name="name_peaklist" value="batch04_S01_average"/>
76 <param name="to_txt" value="True"/>
77 <param name="delimiter" value="tab"/>
78 <output name="tsv_file_out" file="batch04_S01_average.txt" ftype="tsv"/>
79 </test>
80 </tests>
81 <help>
82 -------------
83 Get Peaklists
84 -------------
85
86 ..
87
88 --------------------------------------
89
90 Description
91 -----------
92
93 Use this tool to extract all individual peaklists, or an average of the individual peaklists, that were used in generating the input peak intensity matrix (.hdf5 format).
94
95 --------------------------------------
96
97 Parameters
98 ----------
99
100 |
101
102 **Peak Intensity Matrix (HDF5 file)** (REQUIRED) - a selection menu from which a specific peak intensity matrix (in .hdf5 format) can be selected from the active Galaxy history.
103
104 |
105
106 **Get…** (REQUIRED; default **Average peaklist**) - a selection menu with options:
107
108 - **Average peaklist** - extract an intensity-averaged (non-weighted mean average and with NA values ignored) peaklist from the input peak intensity matrix. Averaging of intensities is performed across ALL samples included in the input peak intensity matrix (.hdf5 format).
109
110 **Name average peaklist** (REQUIRED if “average peaklist” selected; default = “'') - string indicating the name to append to the exported average peaklist (if any).
111
112 - **Multiple peaklists (samples)** - extract independent peaklists from the input .hdf5 file for each of the samples used in generating the peak intensity matrix.
113
114 |
115
116 **Write peaklists to tsv files (data collection)?** (REQUIRED; default = **Yes**) - binary toggle where:
117
118 - **Yes** - corresponds to exporting peaklists(s) to the active Galaxy history in .tsv format
119
120 - **No** - corresponds to skipping the export of peaklist(s) to the active Galaxy history in .tsv format
121
122 |
123
124 **NOTE** - it is currently not possible to use the 'Write Peaklists to tsv files (data collection)?' option when selecting “Multiple Peaklists (samples)” from the “Get…” drop down menu.
125
126 |
127
128 --------------------------------------
129
130 Output file(s)
131 --------------
132
133 **Default output** - a .hdf5 file containing individual peaklists or an average peaklist.
134
135
136 **Optional output** - peaklists (data collection), or an average peaklist, in .tsv format (tab-delimited text file) comprising a numeric data matrix (“.” as decimal, and NA for missing values). Each row corresponds to a peak detected in a specific file, or in the case of an average peaklist, a peak that was detected in AT LEAST one of the study samples. There is no filtering based on a minimum fraction of samples having a measured peak intensity value for a given peak. Columns provide metrics associated with each mass spectral peak. Metrics include:
137
138 @help_columns_peaklist@
139
140 @example_peaklist@
141
142 |
143
144 --------------------------------------
145
146 @github_developers_contributors@
147 @license@
148 </help>
149 <expand macro="citations" />
150 </tool>