Mercurial > repos > rjmw > dimspy_process_scans
comparison macros.xml @ 0:d129e75a31d9 draft
planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
author | rjmw |
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date | Tue, 27 Feb 2018 14:04:01 -0500 |
parents | |
children | 769165c75514 |
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-1:000000000000 | 0:d129e75a31d9 |
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1 <macros> | |
2 <xml name="requirements"> | |
3 <requirements> | |
4 <requirement type="package" version="1.1.0">dimspy</requirement> | |
5 </requirements> | |
6 </xml> | |
7 <xml name="stdio"> | |
8 <stdio> | |
9 <exit_code range="1:" /> | |
10 </stdio> | |
11 </xml> | |
12 | |
13 <token name="@HDF5_PM_TO_TXT@"> | |
14 dimspy hdf5-pm-to-txt | |
15 --input "$hdf5_file_out" | |
16 --output "$matrix_file_out" | |
17 --delimiter $delimiter | |
18 --attribute_name $hdf5_to_txt.matrix_attr | |
19 --representation-samples $hdf5_to_txt.representation_samples | |
20 </token> | |
21 | |
22 <token name="@HDF5_PM_TO_TXT_COMPREHENSIVE@"> | |
23 dimspy hdf5-pm-to-txt | |
24 --input "$hdf5_file_out" | |
25 --output "$matrix_comprehensive_file_out" | |
26 --delimiter $delimiter | |
27 --comprehensive | |
28 --attribute_name $hdf5_to_txt.matrix_attr | |
29 --representation-samples $hdf5_to_txt.representation_samples | |
30 </token> | |
31 | |
32 <xml name="hdf5_pm_to_txt"> | |
33 <section name="hdf5_to_txt" title="Show options for addtional output (*.tsv files)" expanded="False"> | |
34 <param name="standard" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Standard output?" help="Set to "yes" to produce a "standard" Peak Matrix (i.e. m/z and intensity)."/> | |
35 <param name="comprehensive" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Comprehensive output?" help="Set to "yes" to produce a Peak Matrix with additional information (e.g. m/z and intensity, rsd, missing values)."/> | |
36 <param name="representation_samples" type="select" label="Should the rows or columns represent the samples?"> | |
37 <option value="rows" selected="true">Rows</option> | |
38 <option value="columns">Columns</option> | |
39 </param> | |
40 <param name="matrix_attr" type="select" label="The Peak Matrix should contain ... values"> | |
41 <option value="intensity" selected="true">Intensity</option> | |
42 <option value="mz">m/z</option> | |
43 <option value="snr">Signal-to-noise ratio (SNR)</option> | |
44 </param> | |
45 </section> | |
46 </xml> | |
47 | |
48 <xml name="outputs_peak_intensity_matrix"> | |
49 <data name="hdf5_file_out" format="h5" label="${tool.name} on ${on_string}: Peak Intensity Matrix (HDF5 file)"/> | |
50 <data name="matrix_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix"> | |
51 <filter>hdf5_to_txt["standard"] is True</filter> | |
52 </data> | |
53 <data name="matrix_comprehensive_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix (comprehensive)" > | |
54 <filter>hdf5_to_txt["comprehensive"] is True</filter> | |
55 </data> | |
56 </xml> | |
57 | |
58 <xml name="citations"> | |
59 <citations> | |
60 <citation type="doi">10.1038/nprot.2016.156</citation> | |
61 <citation type="doi">10.1038/sdata.2014.12</citation> | |
62 <citation type="doi">10.1021/ac062446p</citation> | |
63 <citation type="doi">10.1021/ac2001803</citation> | |
64 <yield /> | |
65 </citations> | |
66 </xml> | |
67 | |
68 <token name="@example_filelist@"> | |
69 <![CDATA[ | |
70 | |
71 +-----------------+-----------+-------+------------+----------------+ | |
72 | filename | replicate | batch | classLabel | injectionOrder | | |
73 +-----------------+-----------+-------+------------+----------------+ | |
74 | sample_rep1.raw | 1 | 1 | sample | 1 | | |
75 +-----------------+-----------+-------+------------+----------------+ | |
76 | sample_rep2.raw | 2 | 1 | sample | 2 | | |
77 +-----------------+-----------+-------+------------+----------------+ | |
78 | sample_rep3.raw | 3 | 1 | sample | 3 | | |
79 +-----------------+-----------+-------+------------+----------------+ | |
80 | sample_rep4.raw | 4 | 1 | sample | 4 | | |
81 +-----------------+-----------+-------+------------+----------------+ | |
82 | blank_rep1.raw | 1 | 1 | blank | 5 | | |
83 +-----------------+-----------+-------+------------+----------------+ | |
84 | blank_rep2.raw | 2 | 1 | blank | 6 | | |
85 +-----------------+-----------+-------+------------+----------------+ | |
86 | blank_rep3.raw | 3 | 1 | blank | 7 | | |
87 +-----------------+-----------+-------+------------+----------------+ | |
88 | blank_rep4.raw | 4 | 1 | blank | 8 | | |
89 +-----------------+-----------+-------+------------+----------------+ | |
90 | ... | ... | ... | ... | ... | | |
91 +-----------------+-----------+-------+------------+----------------+ | |
92 | |
93 ]]> | |
94 </token> | |
95 | |
96 | |
97 <token name="@help_options_addtional_output@"> | |
98 | | |
99 | **Show options for additonal output(s)** (OPTIONAL) | |
100 | | |
101 | |
102 **\A. Standard output** (default = "No") | |
103 | |
104 Boolean toggle where selection of: | |
105 | |
106 - "Yes" will generate a .txt formatted Peak Matrix (i.e. m/z and intensity). | |
107 - "No" will prevent the creation of a .txt formatted Peak Matrix. | |
108 | |
109 **\B. Comprehensive output** (default = "No") | |
110 | |
111 Boolean toggle where selection of: | |
112 | |
113 - "Yes" generates a Peak Matrix containing the m/z, intensity, missing values and other metrics associated with the aligned peaks. | |
114 - "No" will prevent the creation of a .txt formatted comprehensive Peak Matrix.. | |
115 | |
116 **\C. Should rows or columns represent the samples?** (default = "rows") | |
117 | |
118 Binary toggle (default = "rows") where selection of: | |
119 | |
120 - "rows" puts sample information in to the rows and m/z values (for aligned mass spectral peaks) in to columns of any output Peak Matrix. | |
121 - "columns" puts sample information in the columns and m/z values (for aligned mass spectral peaks) in to the rows of any output Peak Matrix. | |
122 | |
123 **\D. The Peak Matrix should contain ... values** | |
124 | |
125 Use this option to define which metric is inserted in to the cells of the output Peak Matrix. | |
126 | |
127 - "Intensity" writes the absolute peak intensity to the Peak Matrix. | |
128 - "m/z" writes the m/z value to the Peak Matrix. | |
129 - "Signal-to-noise ratio (SNR)" writes the signal-to-noise ratio to the Peak Matrix. | |
130 | |
131 Output file(s) | |
132 -------------- | |
133 | |
134 | A HDF5 file containing a Peak Matrix | |
135 | | |
136 | **OPTIONAL** | |
137 | A (standard and/or comprehenstive) Peak Matrix comprising samples on one axis and m/z values on the perpendicular axis | |
138 | | |
139 | |
140 - Tab-delimited text file containing a numeric data matrix, with . as decimal, and NA for missing values. | |
141 - File only created if user toggles "Standard output" and/or "Comprehensive output" to "Yes" | |
142 - By default, samples are in rows and peaks are in columns. Altering the "Should rows or columns represent samples" toggle will transpose this matrix. | |
143 | |
144 </token> | |
145 | |
146 <token name="@github_developers_contributors@"> | |
147 Github respository (source code) | |
148 -------------------------------- | |
149 | |
150 https://github.com/computational-metabolomics/dimspy-galaxy/ | |
151 | |
152 Developers and contributors | |
153 --------------------------- | |
154 | |
155 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)** | |
156 - **Martin R. Jones (m.r.jones.1@bham.ac.uk) - University of Birmingham (UK)** | |
157 - **Thomas Lawson (tnl495@bham.ac.uk) - University of Birmingham (UK)** | |
158 | |
159 | | |
160 </token> | |
161 | |
162 </macros> |