comparison asics_xml.xml @ 4:0ff2d9211ebe draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/nmr_annotation commit 3791815505685d0038e392a702860843fe1d443e
author marie-tremblay-metatoul
date Fri, 21 Sep 2018 07:42:53 -0400
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3:9b45c0a33573 4:0ff2d9211ebe
1 <tool id="NmrAnnotation" name="NMR_Annotation" version="3.0.0">
2
3 <description> Annotation of complex mixture NMR spectra and metabolite proportion estimation </description>
4
5 <requirements>
6 <requirement type="package" version="1.1_4">r-batch</requirement>
7 <requirement type="package" version="1.0.1">r-asics</requirement>
8 </requirements>
9
10 <stdio>
11 <exit_code range="1:" level="fatal" />
12 </stdio>
13
14 <command><![CDATA[
15 ## Wrapper
16 Rscript '$__tool_directory__/asics_wrapper.R' standards '$__tool_directory__/Library.Rdata'
17
18 ## Bruker files
19 zipfile '$zip_file'
20
21 ## Exclusion zone
22 zone_exclusion_choices.choice ${zone_exclusion_choices.choice}
23 #if str($zone_exclusion_choices.choice) == 'yes':
24 #for $i in $zone_exclusion_choices.conditions:
25 zone_exclusion_left ${i.zone_exclusion_left}
26 zone_exclusion_right ${i.zone_exclusion_right}
27 #end for
28 #end if
29
30 ## Maximal shift (spectrum alignement)
31 shift $shift
32
33 ## Graphical zone
34 zone_graphical_choices.choice ${zone_graphical_choices.choice}
35 #if str($zone_graphical_choices.choice) == 'yes':
36 #for $i in $zone_graphical_choices.conditions:
37 zone_graphical_left ${i.zone_graphical_left}
38 zone_graphical_right ${i.zone_graphical_right}
39 #end for
40 #end if
41
42 ## Outputs
43 logOut '$logOut'
44 proportionEstimation '$proportionEstimation'
45 graphOut '$graphOut'
46 ]]></command>
47
48 <inputs>
49 <param name="zip_file" type="data" format="no_unzip.zip, zip" label="Zip file" />
50
51 <conditional name="zone_exclusion_choices">
52 <param name="choice" type="select" label="Exclusion zone(s)" help="Choose if you want to exclude particular zone(s)" >
53 <option value="yes" > yes </option>
54 <option value="no" selected="true"> no </option>
55 </param>
56 <when value="yes">
57 <repeat name="conditions" title="exclusion zones">
58 <param name="zone_exclusion_left" label="Left exclusion zone border" type="float" value="10.0" />
59 <param name="zone_exclusion_right" label="Right exclusion zone border" type="float" value="10.0" />
60 </repeat>
61 </when>
62 <when value="no" />
63 </conditional>
64
65 <param name="shift" type="float" value="0.01" help="Maximal allowed shift for spectra alignment. Default value is 0.01 ppm" />
66
67 <conditional name="zone_graphical_choices">
68 <param name="choice" type="select" label="Graphical zone(s)" help="Choose if you want to display particular zone(s)" >
69 <option value="yes" > yes </option>
70 <option value="no" selected="true"> no </option>
71 </param>
72 <when value="yes">
73 <repeat name="conditions" title="grapical zones">
74 <param name="zone_graphical_left" label="Left graphical zone border" type="float" value="10.0" />
75 <param name="zone_graphical_right" label="Right graphical zone border" type="float" value="10.0" />
76 </repeat>
77 </when>
78 <when value="no" />
79 </conditional>
80 </inputs>
81
82 <outputs>
83 <data format="txt" name="logOut" label="${tool.name}_log" />
84 <data format="tabular" name="proportionEstimation" label="${tool.name}_proportionEstimation" />
85 <data format="pdf" name="graphOut" label="${tool.name}_graph" />
86 </outputs>
87
88 <tests>
89 <test>
90 <param name="zip_file" value="ADG_007.zip" ftype="zip" />
91 <output name="proportionEstimation" value="MTBLS1_177_NMR_Annotation_proportionEstimation.tabular" />
92 <output name="graphOut" value="MTBLS1_177_NMR_Annotation.pdf" compare="sim_size" delta="300" />
93 </test>
94 </tests>
95
96 <help><![CDATA[
97
98 .. class:: infomark
99
100 **Authors** Marie Tremblay-Franco (marie.tremblay-franco@inra.fr), Patrick Tardivel (patrick.tardivel@inra.fr), RĂ©mi Servien (remi.servien@inra.fr) and Gaelle Lefort (gaelle.lefort@inra.fr)
101
102 .. class:: infomark
103
104 **Please cite**
105
106 Tardivel P., Servien R. and Concordet D. Non asymptotic active set properties of lasso-type estimators in small-dimension (submitted)
107 Tardivel P., Servien R., Canlet C., Tremblay-Franco M., Debrauwer L. and Concordet D. ASICS: an automatic method for identification and quantification of metabolites in NMR 1D 1H spectra (in preparation)
108
109 ---------------------------------------------------
110
111 ==============
112 NMR Annotation
113 ==============
114
115 -----------
116 Description
117 -----------
118
119 ASICS, based on a strong statistical theory, handles automatically the metabolite identification and quantification
120
121 -----------------
122 Workflow position
123 -----------------
124
125 **Upstream tools**
126
127 ========================= ================= ======= =========
128 Name output file format parameter
129 ========================= ================= ======= =========
130 NA NA NA NA
131 ========================= ================= ======= =========
132
133
134 **Downstream tools**
135
136 ========================= ================= ======= =========
137 Name output file format parameter
138 ========================= ================= ======= =========
139 NA NA NA NA
140 ========================= ================= ======= =========
141
142
143
144 -----------
145 Input files
146 -----------
147
148 +---------------------------+------------+
149 | Parameter : num + label | Format |
150 +===========================+============+
151 | 1 : Choose your inputs | zip |
152 +---------------------------+------------+
153
154 **Choose your inputs**
155
156 You have two methods for your inputs:
157
158 | Zip file : You can put a zip file containing one condition (sample): myinputs.zip.
159
160 .. image:: ./static/images/Mth_Architecture_Repertoire_Bruker.png
161
162 ----------
163 Parameters
164 ----------
165
166 Exclusion zone(s)
167 | Spectral regions to exclude, water, solvent or contaminant resonances
168 | If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible,
169 | If NO: no zone to exclude
170 | Default value is NO
171 |
172
173 Left exclusion zone
174 | Upper boundary of exclusion zone
175
176
177 Right exclusion zone
178 | Lower boundary of exclusion zone
179
180 | *Notes:*
181 | - these parameters can be used several times using the "Add new exclusion zones" button
182
183
184 Shift
185 | Maximum variation of the chemical shift (due to experimental conditions) of a peak of a fixed metabolite allowed in the warping function
186
187
188 Graphical zone(s)
189 | Spectral regions to display
190 | If YES: parameters **Lower graphical zone** and **Upper graphical zone** are visible,
191 | If NO: no zone to display
192 | Default value is NO
193
194
195 ------------
196 Output files
197 ------------
198
199 proportionEstimation.tsv
200 | tabular output
201 | Array with p rows (corresponding to the identified metabolites) and 1 column containing the estimated relative intensities
202
203
204 spectra.pdf
205 | pdf output
206 | Graphical chart of real and estimated spectrum (whole spectral width and zooms depending on exclusion zone(s))
207
208
209
210 ---------------------------------------------------
211
212 -------
213 Example
214 -------
215
216 .. image:: ./static/images/NmrAnnotation_ASICS.png
217
218
219 ]]></help>
220
221 <citations>
222 <citation type="doi">10.1007/s11306-017-1244-5</citation>
223 <citation type="doi">10.1093/bioinformatics/btu813</citation>
224 </citations>
225
226 </tool>