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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:10:12 +0000
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-1:000000000000 0:ec596d238781
1 <tool id="mspurity_dimspredictpuritysingle" name="msPurity.dimsPredictPuritySingle" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
2 <description>Calculate the anticipated precursor ion purity from a DIMS dataset.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 Rscript '$__tool_directory__/dimsPredictPuritySingle.R'
9 #if $mzML_data.format == 'mzML_file'
10 --mzML_file '$mzML_data.source'
11 #elif $mzML_data.format == 'library'
12 --mzML_file '$__app__.config.user_library_import_dir/$__user_email__/$mzML_data.source'
13 #elif $mzML_data.format == 'mzML_data_collection'
14 --mzML_files='
15 #for $i in $mzML_data.source
16 $i,
17 #end for
18 '
19 --galaxy_names='
20 #for $i in $mzML_data.source
21 $i.name,
22 #end for
23 '
24 --mzML_filename=' $mzML_data.mzML_filename'
25
26 #end if
27 --peaks_file='$peaks_file'
28 --out_dir='.'
29 --minoffset=$minoffset
30 --maxoffset=$maxoffset
31 --ppm=$ppm
32 --iwNorm=$iw_norm
33 --ilim=$ilim
34 #if $sim
35 --sim
36 #end if
37 #if $remove_NAs
38 --remove_nas
39 #end if
40 #if $dimspy_usage.usage == "dimspy"
41 --dimspy
42 --file_num_dimspy $dimspy_usage.file_num_dimspy
43 #end if
44 #if $isotopes.isotopes == "exclude_default":
45 --exclude_isotopes
46 #elif $isotopes.isotopes == "user"
47 --exclude_isotopes
48 --isotope_matrix = '$isotopes.im'
49 #end if
50 ]]></command>
51 <inputs>
52
53 <param argument="--peaks_file" type="data" format="tsv, tabular"
54 help="tsv or tabular file with one column containing the mz values (column header should be either
55 mz)"/>
56
57 <conditional name="mzML_data">
58 <param name="format" type="select" label="Choose the source for the dataset" >
59 <option value="mzML_file" selected="true">A single .mzML files to check purity from</option>
60 <option value="library">Library directory name (to be used with dimspy workflows) or path to
61 to an individual .mzML file</option>
62 <option value="mzML_data_collection" selected="true">A data collection of .mzML files</option>
63 </param>
64 <when value="mzML_file">
65 <param argument="--mzML_file" name="source" type="data" format="mzml" label="Single *.mzML" >
66 <validator type="empty_field" />
67 </param>
68 </when>
69 <when value="mzML_data_collection">
70 <param argument="--mzML_files" name="source" type="data_collection"
71 label="Data collection containing *.mzml files" >
72 <validator type="empty_field" />
73 </param>
74 <param argument="--mzML_filename" type="text" label="Name of file to to calculate purity from" help=""/>
75 </when>
76
77 <when value="library">
78 <param argument="--mzML_file" name="source" type="text"
79 size="40" label="Library directory containing *.mzml files (dimspy input only)
80 or path to an individual .mzML file">
81 <validator type="empty_field" />
82 </param>
83 </when>
84
85 </conditional>
86
87 <expand macro="general_params" />
88 <expand macro="offsets" />
89
90 <param argument="--ppm" type="float" label="ppm" min="0" value="10"
91 help="ppm tolerance to compare between mz values"/>
92 <param argument="--remove_NAs" type="boolean" label="Remove rows where mz value is NA or NaN?" help=""/>
93 <param argument="--sim" type="boolean" label="SIM-Stitch experiment?" help=""/>
94 <conditional name="dimspy_usage">
95 <param name="usage" type="select" label="dimspy peak matrix text file usage?">
96 <option value="no_dimspy" selected="true">dimspy not used to prepare the mz text file</option>
97 <option value="dimspy">dimspy used to prepare mz file</option>
98 </param>
99 <when value="no_dimspy">
100 </when>
101 <when value="dimspy">
102 <param argument="--file_num_dimspy" type="integer" label="File number" min="0" value="1"
103 help="Choose the file number from the dimspy matrix to use to calculate the precursor ion
104 purity metric (order based on column order). This file will then be looked for in the
105 library folder to calculate the metric.
106 "/>
107 </when>
108 </conditional>
109
110 </inputs>
111 <outputs>
112 <data name="dimsPredictPuritySingle_output" format="tsv" label="${tool.name} on ${on_string}"
113 from_work_dir="dimsPredictPuritySingle_output.tsv" />
114 </outputs>
115 <tests>
116 <test>
117 <param name="mzML_data|format" value="mzML_file" />
118 <param name="mzML_data|source" value="dimsPredictPuritySingle_full_scan.mzML" />
119 <param name="remove_NAs" value="True" />
120 <param name="dimspy_usage|usage" value="dimspy" />
121 <param name="dimspy_usage|file_num_dimspy" value="1" />
122 <param name="peaks_file" value="dimsPredictPuritySingle_input_dimspy_peakmatrix.tsv" />
123 <output name="dimsPredictPuritySingle_output" value="dimsPredictPuritySingle_output.tsv" />
124 </test>
125 </tests>
126
127
128
129 <help><![CDATA[
130
131 =============================================================
132 Calculate anticipated precursor ion purity from DI-MS dataset
133 =============================================================
134 -----------
135 Description
136 -----------
137
138 Tool to calculate the anticipated precursor ion purity of selected precursor based on a prior DI-MS dataset. The dataset
139 can either be in the form of multiple 'full scans' or a SIM-Stitch dataset. See the Bioconductor documentation for more
140 details, function msPurity::dimsPredictPurity()
141
142 --------------
143 Output example
144 --------------
145 Output consists of the mz column (along with any other columns that were in the original mz file). The median and
146 mean calculated purity. The standard deviation (sdPurity), coefficient of variation (relative standard deviation)
147 cvPurity, the standard error of the purity (sdePurity) and the median number of peaks within the isolation window
148 (medianPeakNum)
149
150 ============= ============= ============= ================ ================ ================ ================
151 mz medianPurity meanPurity sdPurity cvPurity sdePurity medianPeakNum
152 ============= ============= ============= ================ ================ ================ ================
153 50.20428 0.39 0.39 0.0007 0.19 0.0005 3
154 ------------- ------------- ------------- ---------------- ---------------- ---------------- ----------------
155 56.91206 0.01 0.01 0.0002 4.53 0.0001 12
156 ------------- ------------- ------------- ---------------- ---------------- ---------------- ----------------
157 62.02906 0.14 0.13 0.0014 22.63 0.0009 7
158 ------------- ------------- ------------- ---------------- ---------------- ---------------- ----------------
159 75.07431 0.93 0.94 0.019 37.87 0.0134 3
160 ============= ============= ============= ================ ================ ================ ================
161
162 ]]></help>
163 <expand macro="citations" />
164 </tool>