Mercurial > repos > computational-metabolomics > dimspy_merge_peaklists

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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 <macros>
2 <token name="@TOOL_VERSION@">2.0.0</token>
3 <token name="@GALAXY_TOOL_VERSION@">0</token>
4
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">dimspy</requirement>
8 </requirements>
9 </xml>
10
11
12 <token name="@HDF5_PM_TO_TXT@">
13 dimspy hdf5-pm-to-txt
14 --input '$hdf5_file_out'
15 --output '$matrix_file_out'
16 --delimiter $delimiter
17 --attribute_name $hdf5_to_txt.matrix_attr
18 --representation-samples $hdf5_to_txt.representation_samples
19 </token>
20
21 <token name="@HDF5_PM_TO_TXT_COMPREHENSIVE@">
22 dimspy hdf5-pm-to-txt
23 --input '$hdf5_file_out'
24 --output '$matrix_comprehensive_file_out'
25 --delimiter $delimiter
26 --comprehensive
27 --attribute_name $hdf5_to_txt.matrix_attr
28 --representation-samples $hdf5_to_txt.representation_samples
29 </token>
30
31 <xml name="hdf5_pm_to_txt">
32 <section name="hdf5_to_txt" title="Show options for addtional output (*.tsv files)" expanded="False">
33 <param name="standard" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Standard output?" help="Set to &quot;yes&quot; to produce a &quot;standard&quot; Peak Matrix (i.e. m/z and intensity)."/>
34 <param name="comprehensive" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Comprehensive output?" help="Set to &quot;yes&quot; to produce a Peak Matrix with additional information (e.g. m/z and intensity, rsd, missing values)."/>
35 <param name="representation_samples" type="select" label="Should the rows or columns represent the samples?" help="">
36 <option value="rows" selected="true">Rows</option>
37 <option value="columns">Columns</option>
38 </param>
39 <param name="matrix_attr" type="select" label="The Peak Matrix should contain ... values" help="">
40 <option value="intensity" selected="true">Intensity</option>
41 <option value="mz">m/z</option>
42 <option value="snr">Signal-to-noise ratio (SNR)</option>
43 </param>
44 </section>
45 </xml>
46
47 <xml name="outputs_peak_intensity_matrix">
48 <data name="hdf5_file_out" format="h5" label="${tool.name} on ${on_string}: Peak Intensity Matrix (HDF5 file)"/>
49 <data name="matrix_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix">
50 <filter>hdf5_to_txt["standard"] is True</filter>
51 </data>
52 <data name="matrix_comprehensive_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix (comprehensive)" >
53 <filter>hdf5_to_txt["comprehensive"] is True</filter>
54 </data>
55 </xml>
56
57 <xml name="citations">
58 <citations>
59 <citation type="doi">10.1038/nprot.2016.156</citation>
60 <citation type="doi">10.1038/sdata.2014.12</citation>
61 <citation type="doi">10.1021/ac062446p</citation>
62 <citation type="doi">10.1021/ac2001803</citation>
63 <yield />
64 </citations>
65 </xml>
66
67 <token name="@example_filelist@"><![CDATA[
68
69 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
70 | **filename** | **classLabel** | **replicate** | **batch** | **injectionOrder** | **[...]** |
71 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
72 | sample_rep1.raw | sample | 1 | 1 | 1 | [...] |
73 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
74 | sample_rep2.raw | sample | 2 | 1 | 2 | [...] |
75 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
76 | sample_rep3.raw | sample | 3 | 1 | 3 | [...] |
77 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
78 | sample_rep4.raw | sample | 4 | 1 | 4 | [...] |
79 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
80 | blank_rep1.raw | blank | 1 | 1 | 5 | [...] |
81 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
82 | blank_rep2.raw | blank | 2 | 1 | 6 | [...] |
83 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
84 | blank_rep3.raw | blank | 3 | 1 | 7 | [...] |
85 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
86 | blank_rep4.raw | blank | 4 | 1 | 8 | [...] |
87 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
88 | ... | ... | ... | ... | ... | [...] |
89 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
90
91 ]]></token>
92
93
94 <token name="@help_columns_peaklist@">
95
96 - **mz** - the mass-to-charge ratio of the extracted mass spectral peak
97
98 - **intensity** - the intensity of the extracted mass spectral peak
99
100 - **snr** - the signal-to-noise ratio of the extracted peak, which is defined as the ratio of the peak’s intensity value to that of the background noise intensity value
101
102 - **present** - a numeric value greater than 0 that indicates the total number of scans at least one peak was detected in a given file
103
104 - **fraction** - a proportion ranging from 0 to 1 that indicates the total number of times a peak was detected in a given scan event type, divided by the total number of occurrences of that scan event type recorded in a given file.
105
106 - **purity** - a numeric value ranging from 0 to 1 that indicates the proportion of scans, for a given scan event type, that contained a single mass spectral peak following hierarchical clustering. A purity score less-than 1 indicates that in some proportion of scans, multiple peaks within a single scan were grouped together during the hierarchical clustering process.
107
108 - **occurrence** - a numeric value greater than 0 that indicates the total number of peaks that were observed across scans within the user-defined ppm error tolerance.
109
110 - **snr_flag** - a boolean value indicating whether to keep (“1”) or discard (“0”) a peak according to its signal-to-noise ratio value.
111
112 - **fraction_flag** - a boolean value indicating whether a peak should be kept or discarded according to the ratio of the number of scans in which it was detected, to the the number of scans in which it was not detected.
113
114 - **flags** - a boolean value indicating whether a peak should be retained or discarded based upon both its ‘snr_flag’ and ‘fraction_flag’ boolean values (if either is set to ‘0’ i.e. discard peak, then the ‘flags’ boolean should also be 0).
115
116 </token>
117
118 <token name="@example_peaklist@">
119
120
121 **Example of an processed and filtered peaklist**:
122
123
124 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
125 | mz | intensity | snr | present | fraction | rsd | occurrence | purity | snr_flag | fraction_flag | flags |
126 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
127 | 90.44000 | 4744.0 | 3.06 | 1 | 0.063 | nan | 1 | 1 | 1 | 0 | 0 |
128 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
129 | 97.07380 | 5423.6 | 3.52 | 1 | 0.063 | nan | 1 | 1 | 1 | 0 | 0 |
130 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
131 | 99.04180 | 4105.8 | 3.60 | 1 | 0.063 | nan | 1 | 1 | 1 | 0 | 0 |
132 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
133 | 99.49800 | 4775.7 | 3.05 | 1 | 0.063 | nan | 1 | 1 | 1 | 0 | 0 |
134 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
135 | 99.95020 | 5657.8 | 3.63 | 1 | 0.063 | nan | 1 | 1 | 1 | 0 | 0 |
136 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
137 | 100.40660 | 5489.5 | 3.57 | 3 | 0.188 | 14.51 | 3 | 1 | 1 | 0 | 0 |
138 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
139 | 100.8672 | 4841.18 | 3.27 | 7 | 0.4375 | 16.36 | 7 | 1 | 1 | 0 | 0 |
140 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
141 | 101.0027 | 9047.79 | 5.99 | 16 | 1 | 21.53 | 19 | 0.8125 | 1 | 1 | 1 |
142 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
143 | 101.0033 | 271893.9 | 182 | 16 | 1 | 4.17 | 16 | 1 | 1 | 1 | 1 |
144 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
145 | 101.0038 | 8738.03 | 5.9 | 14 | 0.875 | 9.71 | 14 | 1 | 1 | 1 | 1 |
146 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
147 | 101.004 | 5166.67 | 3.5 | 5 | 0.3125 | 18.02 | 6 | 0.8 | 1 | 0 | 0 |
148 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
149 | 101.0599 | 5894.69 | 3.88 | 2 | 0.125 | 15.06 | 2 | 1 | 1 | 0 | 0 |
150 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
151 | 101.2728 | 6846.28 | 4.44 | 1 | 0.0625 | nan | 1 | 1 | 1 | 0 | 0 |
152 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
153
154 </token>
155
156 <token name="@help_options_addtional_output@">
157
158 **Show options for additional output(s)** (OPTIONAL):
159
160 - **Standard output** (default = **No**) - boolean toggle where selection of:
161
162 - **No** - prevent the export of a .txt formatted peak matrix to the active Galaxy history.
163
164 - **Yes** - export a .txt formatted peak matrix to the active Galaxy history that includes only those peaks from the input peak intensity matrix that passed the filtering procedure.
165
166 - **Comprehensive output** (default = "No") - boolean toggle where selection of:
167
168 - **No** - prevents export of a .txt formatted comprehensive peak matrix.
169
170 - **Yes** - exports a .txt formatted comprehensive peak matrix to the active Galaxy history that contains the m/z, missing values and other metrics associated with all peaks included in the input peak intensity matrix, including the metric defined by the "The peak matrix should contain intensity | m/z | SNR values" parameter.
171
172 - **Should rows or columns represent the samples?** (default = **rows**) - binary toggle where selection of:
173
174 - **rows** - sample information is presented in the rows and m/z values (for aligned mass spectral peaks) in the columns of any output peak matrix.
175
176 - **columns** - sample information is presented in the columns and m/z values (for aligned mass spectral peaks) in the rows of any output peak matrix.
177
178 - **The peak matrix should contain intensity | m/z | SNR values** - use this option to define which peak metric is inserted in to the cells of any optionally-output peak matrix:
179
180 - **Intensity** - writes the absolute peak intensity to the cells of the peak matrix
181
182 - **m/z** - writes the mass-to-charge ratio to the cells of the peak matrix
183
184 - **signal-to-noise ratio (SNR)** - writes the signal-to-noise ratio to the cells of the peak matrix
185
186 </token>
187
188 <token name="@help_outputs_matrix@">
189
190 **Default output** - a HDF5 file containing the aligned peak intensity matrix.
191
192 |
193
194 **Optional outputs** - the metric recorded in any optionally output peak matrix/matrices is defined using the parameter "The peak matrix should contain intensity | m/z | SNR values". By default, study samples are listed row-wise, while mass-to-charge ratios of the aligned mass spectral peaks are presented in columns (to adjust, users must adjust the "Should rows or columns represent samples" toggle to “columns”).
195
196
197 - **Standard output** - an aligned peak matrix in tab-delimited format (“.” as decimal and NA for missing values).
198
199 **Example of a standard peak intensity matrix**:
200
201 +------------+----------+----------+----------+----------+---------+
202 | mz | 96.04216 | 99.08062 | 100.0759 | 100.8672 | ... |
203 +------------+----------+----------+----------+----------+---------+
204 | QC_1 | 0 | 0 | 0 | 0 | ... |
205 +------------+----------+----------+----------+----------+---------+
206 | Blank_1 | 3342.626 | 0 | 0 | 0 | ... |
207 +------------+----------+----------+----------+----------+---------+
208 | Control_10 | 0 | 0 | 45432.2 | 0 | ... |
209 +------------+----------+----------+----------+----------+---------+
210 | Sample_2 | 0 | 3423.3 | 0 | 0 | ... |
211 +------------+----------+----------+----------+----------+---------+
212 | Control_5 | 0 | 0 | 49759 | 0 | ... |
213 +------------+----------+----------+----------+----------+---------+
214 | Control_10 | 0 | | 39890.5 | 0 | ... |
215 +------------+----------+----------+----------+----------+---------+
216 | Sample_20 | 0 | 14563.7 | 0 | 0 | ... |
217 +------------+----------+----------+----------+----------+---------+
218 | Sample_2 | 0 | 34676.4 | 0 | 0 | ... |
219 +------------+----------+----------+----------+----------+---------+
220 | Sample_14 | 0 | 13134.9 | 0 | 521.4 | ... |
221 +------------+----------+----------+----------+----------+---------+
222 | ... | ... | ... | ... | ... | ... |
223 +------------+----------+----------+----------+----------+---------+
224
225 |
226
227 - **Comprehensive output** - an aligned peak matrix, as described for the "standard output" (above), including all metadata from the "Process Scans" Filelist/samplelist and the following additional mass spectral peak metrics:
228
229 - **present** - a positive integer value (0 <![CDATA[ < ]]> value <![CDATA[ < ]]> total number of study samples in the filelist / samplelist) that indicates the total number of study samples in which a peak was detected with the specified mass-to-charge ratio, plus or minus the user-defined ppm error tolerance.
230
231 - **occurrence** - a positive integer value indicating the number of peaks that were grouped together during the alignment procedure and thus, that were used to calculate the average mass-to-charge ratio indicated for the aligned peak. A value greater than given in the “Present” metric indicates that one or more peaklists contained more-than one mass spectral peak with the specified mass-to-charge, plus or minus the user-defined ppm error tolerance.
232
233 - **purity** - a proportion ranging from 0 to 1 that indicates the number of scans in which only a single peak was detected during the peaklist alignment process. If the value in the “occurrence” metric is greater than the “present” metric, purity will be <![CDATA[ < ]]> 1. A purity <![CDATA[ < ]]> 1 means that in at least one peaklist there was more-than one mass spectral peak with the specified mass-to-charge, plus or minus the user-defined ppm error tolerance.
234
235 - **rsd_all** - a numeric value indicating the percent relative standard deviation (otherwise termed the percent coefficient of variation) of peak intensities for peaks aligned together using the Align Samples tool. If fewer than 2 peaks were aligned across samples, then the rsd_all column will be filled in with ‘nan’
236
237 - **blank_flag** (may be absent if "Blank filter” tool was not applied) - a boolean value where 0 = reject peak, 1 = accept peak. A peak is accepted during blank filtering if a user-defined minimum proportion of study samples had peak intensity values greater-than the product of the average of “reference” sample peak intensities and the “min_fold_change” parameter.
238
239 - **fraction_flag** (may be absent if "Sample filter” tool was not applied)- a boolean value where 0 = reject peak, 1 = accept peak. If greater-than a user-defined minimum fraction of samples (whether checked across ALL experimental classes, or within ANY of the individual experimental classes) had recorded intensity values for a given peak, then this peak is accepted, i.e. it is considered in downstream processing procedures, while rejected peaks are not.
240
241 - **flags** - a boolean value indicating whether a peak should be included (“1”) or excluded (“0”) from downstream processing procedures. Exclusion of a peak occurs if the thresholds for “relative standard deviation” and/or “minimum number of technical replicates a peak has to be present in” were not met.
242
243 |
244
245 **Example of a comprehensive peak intensity matrix**:
246
247 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
248 | mz | missing values | tags_batch | tags_replicates | tags_replicate | tags_injectionOrder | tags_classLabel | tags_untyped | 96.04216 | 99.08062 | 100.0759 | 100.8672 | ... |
249 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
250 | present* | | | | | | | | 1 | 4 | 3 | 1 | ... |
251 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
252 | occurrence* | | | | | | | | 1 | 4 | 4 | 1 | ... |
253 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
254 | purity* | | | | | | | | 1 | 1 | 1 | 1 | ... |
255 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
256 | rsd_all* | | | | | | | | nan | nan | 10.98 | nan | ... |
257 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
258 | flags* | | | | | | | | 1 | 1 | 1 | 1 | ... |
259 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
260 | QC_1 | 2901 | 1 | 2_3_4 | 2 | 2 | QC | | 0 | 0 | 0 | 0 | ... |
261 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
262 | Blank_1 | 2948 | 1 | 1_2_4 | 1 | 5 | Blank | | 3342.626 | 0 | 0 | 0 | ... |
263 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
264 | Control_10 | 2921 | 1 | 2_3_4 | 2 | 10 | Control | | 0 | 0 | 45432.2 | 0 | ... |
265 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
266 | Sample_2 | 2819 | 1 | 1_2_4 | 1 | 13 | Exposed | | 0 | 3423.3 | 0 | 0 | ... |
267 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
268 | Control_5 | 2877 | 1 | 2_3_4 | 2 | 18 | Control | | 0 | 0 | 49759 | 0 | ... |
269 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
270 | Control_10 | 2856 | 1 | 1_2_3 | 1 | 21 | Control | | 0 | | 39890.5 | 0 | ... |
271 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
272 | Sample_20 | 2855 | 1 | 1_2_4 | 1 | 25 | Exposed | | 0 | 14563.7 | 0 | 0 | ... |
273 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
274 | Sample_2 | 2814 | 1 | 1_2_4 | 1 | 29 | Exposed | | 0 | 34676.4 | 0 | 0 | ... |
275 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
276 | Sample_14 | 2870 | 1 | 1_2_3 | 1 | 33 | Exposed | | 0 | 13134.9 | 0 | 521.4 | ... |
277 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
278 | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
279 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
280
281 </token>
282
283
284 <token name="@github_developers_contributors@">
285 Github respository (source code)
286 --------------------------------
287
288 Galaxy Tool Wrappers: https://github.com/computational-metabolomics/dimspy-galaxy/
289 DIMSpy package: https://github.com/computational-metabolomics/dimspy/
290
291
292 Developers and contributors
293 ---------------------------
294
295 - Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)
296 - Martin R. Jones (m.r.jones.1@bham.ac.uk) - University of Birmingham (UK)
297 - Thomas Lawson (tnl495@bham.ac.uk) - University of Birmingham (UK)
298
299 </token>
300
301 <token name="@license@">
302 License
303 -------
304 DIMSpy is released under the GNU General Public License v3.0 (see `LICENSE file`_)
305
306 .. _`LICENSE file`: https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/LICENSE
307
308 </token>
309
310
311 </macros>