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comparison macros.xml @ 1:2e7d47c0b027 draft

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"planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
author malex
date Mon, 08 Mar 2021 22:04:06 +0000
parents
children caba07f41453
comparison
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0:b54326490b4d 1:2e7d47c0b027
1 <?xml version="1.0" ?>
2 <macros>
3 <token name="@WRAPPER_VERSION@">21.3.4.2</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@WRAPPER_VERSION@">secimtools</requirement>
7 <yield/>
8 </requirements>
9 </xml> <xml name="citations">
10 <citations>
11 <citation type="bibtex">@ARTICLE{Kirpich17secimtools,
12 author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
13 title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
14 journal = {BMC Bioinformatics},
15 year = {in press}
16 }</citation>
17 </citations>
18 </xml>
19
20 <token name="@TIP_AND_WARNING@">
21 **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
22
23 **WARNINGS:**
24
25 (1) SampleIDs in the wide data that have no matching name in the design file, as well as sampleIDs in the design file that have no matching name in the data, will be excluded from the analysis.
26 (2) This script automatically removes spaces and special characters from strings.
27 (3) If a compound/feature name starts with a number it will prepend an '_'.
28 (4) Input names are case sensitive and must match exactly (e.g use 'Feature' not 'feature').
29 </token>
30 <token name="@WIDE@">
31 **Wide Formatted Dataset**
32
33 A wide formatted dataset that contains measurements for each sample:
34
35 +---------+---------+---------+---------+-----+
36 | Feature | sample1 | sample2 | sample3 | ... |
37 +=========+=========+=========+=========+=====+
38 | one | 10 | 20 | 10 | ... |
39 +---------+---------+---------+---------+-----+
40 | two | 5 | 22 | 30 | ... |
41 +---------+---------+---------+---------+-----+
42 | three | 30 | 27 | 2 | ... |
43 +---------+---------+---------+---------+-----+
44 | four | 32 | 17 | 8 | ... |
45 +---------+---------+---------+---------+-----+
46 | ... | ... | ... | ... | ... |
47 +---------+---------+---------+---------+-----+
48
49 **NOTE:** The 'Feature' column defines the rows within a wide formatted dataset.
50 </token>
51 <token name="@METADATA@">
52 **Design File**
53
54 A Design file relating samples to various groups/treatment:
55
56 +----------+--------+
57 | sampleID | group |
58 +==========+========+
59 | sample1 | g1 |
60 +----------+--------+
61 | sample2 | g1 |
62 +----------+--------+
63 | sample3 | g1 |
64 +----------+--------+
65 | sample4 | g2 |
66 +----------+--------+
67 | sample5 | g2 |
68 +----------+--------+
69 | sample6 | g2 |
70 +----------+--------+
71 | ... | ... |
72 +----------+--------+
73
74 **NOTE:** You must have a column named **sampleID** and the values in this column must match the column names in the wide dataset.
75 </token>
76 <token name="@DF@">
77 **Design File**
78
79 A Design file relating samples to various groups/treatment:
80
81 +----------+--------+
82 | sampleID | group |
83 +==========+========+
84 | sample1 | g1 |
85 +----------+--------+
86 | sample2 | g1 |
87 +----------+--------+
88 | sample3 | g1 |
89 +----------+--------+
90 | sample4 | g2 |
91 +----------+--------+
92 | sample5 | g2 |
93 +----------+--------+
94 | sample6 | g2 |
95 +----------+--------+
96 | ... | ... |
97 +----------+--------+
98
99 **NOTE:** You must have a column named **sampleID** and the values in this column must match
100 the column names in the long dataset.
101 </token>
102 <token name="@LONG@">
103 **Long Dataset:**
104
105 A dataset in long/stacked format that contains measurements for each sample:
106
107 +----------+----------+------------+
108 | Feature | sampleID | Peak Height|
109 +==========+==========+============+
110 | One | 1 | 10 |
111 +----------+----------+------------+
112 | One | 2 | 5 |
113 +----------+----------+------------+
114 | One | 3 | 30 |
115 +----------+----------+------------+
116 | Two | 1 | 20 |
117 +----------+----------+------------+
118 | Two | 2 | 22 |
119 +----------+----------+------------+
120 | Two | 3 | 27 |
121 +----------+----------+------------+
122 | ... | ... | ... |
123 +----------+----------+------------+
124
125 </token>
126 <token name="@FLAGS@">
127 **Flag File:**
128
129 A wide formated dataset that contains flags for each sample or feature:
130
131 +----------+---------+---------+---------+-----+
132 | Feature | flag_A | flag_B | flag_C | ... |
133 +==========+=========+=========+=========+=====+
134 | one | 0 | 0 | 0 | ... |
135 +----------+---------+---------+---------+-----+
136 | two | 0 | 1 | 1 | ... |
137 +----------+---------+---------+---------+-----+
138 | three | 0 | 1 | 0 | ... |
139 +----------+---------+---------+---------+-----+
140 | four | 1 | 0 | 0 | ... |
141 +----------+---------+---------+---------+-----+
142 | ... | ... | ... | ... | ... |
143 +----------+---------+---------+---------+-----+
144
145 </token>
146 <token name="@MZRTFILE@">
147 **M/Z RT File:**
148
149 A wide formated dataset that contains M/Z and RT measurements for each sample:
150
151 +----------+--------+----------------+
152 | sampleID | M/Z | Retention Time |
153 +==========+========+================+
154 | sample1 | 0.1556 | 0.253618769 |
155 +----------+--------+----------------+
156 | sample2 | 0.1675 | 0.327658519 |
157 +----------+--------+----------------+
158 | sample3 | 0.1341 | 0.156587769 |
159 +----------+--------+----------------+
160 | sample4 | 0.2341 | 0.153658165 |
161 +----------+--------+----------------+
162 | sample5 | 0.4557 | 0.315765787 |
163 +----------+--------+----------------+
164 | sample6 | 0.1879 | 0.253655765 |
165 +----------+--------+----------------+
166 | ... | ... | ... |
167 +----------+--------+----------------+
168
169 </token>
170 <token name="@GROUP_OPTIONAL@">
171 **Group/Treatment [Optional]**
172
173 - Name of the column in your Design File that contains group classifications.
174 </token>
175 <token name="@GROUP@">
176 **Group/Treatment**
177
178 - Name of the column in your Design File that contains group classifications.
179 </token>
180 <token name="@UNIQID@">
181 **Unique Feature ID**
182
183 - Name of the column in your Wide Dataset that has unique Feature IDs.
184 </token>
185 <token name="@RUNORDER@">
186 **Run Order ID**
187
188 - The column name in your Design file that contains the order samples were run.
189 </token>
190 <token name="@RUNORDER_OPTIONAL@">
191 **Run Order ID [Optional]**
192
193 - The column name in your Design file that contains the order samples were run.
194 </token>
195 </macros>