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comparison dimsPredictPuritySingle.xml @ 0:fc9bb7e49a3a draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
author tomnl
date Fri, 24 May 2019 09:02:25 -0400
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1 <tool id="mspurity_dimspredictpuritysingle" name="msPurity.dimsPredictPuritySingle" version="0.2.0">
2 <description>Calculate the anticipated precursor ion purity from a DIMS dataset.
3 </description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8
9 <stdio>
10 <exit_code range="1:" />
11 </stdio>
12 <command interpreter="Rscript"><![CDATA[
13 dimsPredictPuritySingle.R
14 #if $mzML_data.format == "mzML_file"
15 --mzML_file $mzML_data.source
16 #elif $mzML_data.format == "library"
17 --mzML_file $__app__.config.user_library_import_dir/$__user_email__/$mzML_data.source
18 #end if
19 --peaks_file=$peaks_file
20 --out_dir=.
21 --minOffset=$minoffset
22 --maxOffset=$maxoffset
23 --ppm=$ppm
24 --iwNorm=$iw_norm
25 --ilim=$ilim
26 #if $sim
27 --sim
28 #end if
29 #if $remove_NAs
30 --remove_nas
31 #end if
32 #if $dimspy_usage.usage == "dimspy"
33 --dimspy
34 --file_num_dimspy $dimspy_usage.file_num
35 #end if
36 #if $isotopes.isotopes == "exclude_default":
37 --exclude_isotopes
38 #elif $isotopes.isotopes == "user"
39 --exclude_isotopes
40 --isotope_matrix = $isotopes.im
41 #end if
42 ]]></command>
43 <inputs>
44
45 <param type="data" name="peaks_file" format="tsv, tabular"
46 help="tsv or tabular file with one column containing the mz values (column header should be either
47 mz)"/>
48
49 <conditional name="mzML_data">
50 <param name="format" type="select" label="Choose the source for the dataset" >
51 <option value="mzML_file" selected="true">.mzML files to check purity from</option>
52 <option value="library">Library directory name (to be used with dimspy workflows) or path to
53 to an individual .mzML file</option>
54 </param>
55 <when value="mzML_file">
56 <param name="source" type="data" format="mzml" label="Single *.mzML" argument="--mzML_file" >
57 <validator type="empty_field" />
58 </param>
59 </when>
60 <when value="library">
61 <param name="source" type="text"
62 size="40" label="Library directory containing *.mzml files
63 or path to an individual *.mzML"
64 argument="--mzML_file">
65 <validator type="empty_field" />
66 </param>
67 </when>
68 </conditional>
69
70 <expand macro="offsets" />
71 <expand macro="general_params" />
72
73
74 <param name="ppm" type="float" label="ppm" value="10"
75 help="ppm tolerance to compare between mz values"/>
76
77 <param name="minoffset" type="float" label="minoffset" value="0.5"
78 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
79 100.0 then the range would be from 999.5 to 100.0"/>
80
81 <param name="remove_NAs" type="boolean" label="Remove rows where mz value is NA or NaN?" help=""/>
82
83 <param name="sim" type="boolean" label="SIM-Stitch experiment?" help=""/>
84
85 <conditional name="dimspy_usage">
86 <param name="usage" type="select" label="dimspy peak matrix text file usage?">
87 <option value="no_dimspy" selected="true">dimspy not used to prepare the mz text file</option>
88 <option value="dimspy">dimspy used to prepare mz file</option>
89 </param>
90 <when value="no_dimspy">
91 </when>
92 <when value="dimspy">
93 <param name="file_num" type="integer" label="File number" value="1"
94 help="Choose the file number from the dimspy matrix to use to calculate the precursor ion
95 purity metric (order based on column order). This file will then be looked for in the
96 library folder to calculate the metric.
97 "/>
98 </when>
99 </conditional>
100
101 </inputs>
102 <outputs>
103 <data name="dimsPredictPuritySingle_output" format="tsv" label="${tool.name} on ${on_string}"
104 from_work_dir="dimsPredictPuritySingle_output.tsv" />
105 </outputs>
106 <tests>
107 <test>
108 <param name="mzML_data|format" value="mzML_file" />
109 <param name="mzML_data|source" value="dimsPredictPuritySingle_full_scan.mzML" />
110 <param name="remove_NAs" value="True" />
111 <param name="dimspy_usage|usage" value="dimspy" />
112 <param name="peaks_file" value="dimsPredictPuritySingle_input_dimspy_peakmatrix.tsv" />
113 <output name="dimsPredictPuritySingle_output" value="dimsPredictPuritySingle_output.tsv" />
114 </test>
115 </tests>
116
117
118
119 <help><![CDATA[
120
121 =============================================================
122 Calculate anticipated precursor ion purity from DI-MS dataset
123 =============================================================
124 -----------
125 Description
126 -----------
127
128 Tool to calculate the anticipated precursor ion purity of selected precursor based on a prior DI-MS dataset. The dataset
129 can either be in the form of multiple 'full scans' or a SIM-Stitch dataset. See the Bioconductor documentation for more
130 details, function msPurity::dimsPredictPurity()
131
132 --------------
133 Output example
134 --------------
135 Output consists of the mz column (along with any other columns that were in the original mz file). The median and
136 mean calculated purity. The standard deviation (sdPurity), coefficient of variation (relative standard deviation)
137 cvPurity, the standard error of the purity (sdePurity) and the median number of peaks within the isolation window
138 (medianPeakNum)
139
140 ============= ============= ============= ================ ================ ================ ================
141 mz medianPurity meanPurity sdPurity cvPurity sdePurity medianPeakNum
142 ============= ============= ============= ================ ================ ================ ================
143 50.20428 0.39 0.39 0.0007 0.19 0.0005 3
144 ------------- ------------- ------------- ---------------- ---------------- ---------------- ----------------
145 56.91206 0.01 0.01 0.0002 4.53 0.0001 12
146 ------------- ------------- ------------- ---------------- ---------------- ---------------- ----------------
147 62.02906 0.14 0.13 0.0014 22.63 0.0009 7
148 ------------- ------------- ------------- ---------------- ---------------- ---------------- ----------------
149 75.07431 0.93 0.94 0.019 37.87 0.0134 3
150 ============= ============= ============= ================ ================ ================ ================
151
152 ]]></help>
153 <expand macro="citations" />
154 </tool>