Mercurial > repos > marie-tremblay-metatoul > nmr_bucketing

comparison NmrBucketing_xml.xml @ 4:d61f6ceef5d6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty
author lecorguille
date Tue, 22 Nov 2016 05:22:03 -0500
parents 58679e85745f
children
comparison
equal deleted inserted replaced
3:58679e85745f 4:d61f6ceef5d6
1 <tool id="NmrBucketing" name="NMR_Bucketing" version="1.0.2"> 1 <tool id="NmrBucketing" name="NMR_Bucketing" version="1.0.3">
2 2
3 <description> Bucketing and integration of NMR Bruker raw data</description> 3 <description> Bucketing and integration of NMR Bruker raw data</description>
4 4
5 <requirements> 5 <requirements>
6 <requirement type="package" version="3.1.2">R</requirement>
7 <requirement type="package" version="1.1_4">r-batch</requirement> 6 <requirement type="package" version="1.1_4">r-batch</requirement>
8 <requirement type="package" version="1.8.8">r-pracma</requirement> 7 <requirement type="package" version="1.8.8">r-pracma</requirement>
9 </requirements> 8 </requirements>
10 9
11 <stdio> 10 <stdio>
12 <exit_code range="1:" level="fatal" /> 11 <exit_code range="1:" level="fatal" />
13 </stdio> 12 </stdio>
14 13
15 <command> 14 <command>
16 Rscript $__tool_directory__/NmrBucketing_wrapper.R 15 Rscript '$__tool_directory__/NmrBucketing_wrapper.R'
17 16
18 #if $inputs.input == "lib": 17 #if $inputs.input == "lib":
19 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library 18 library '$__app__.config.user_library_import_dir/$__user_email__/$inputs.library'
19 #elif $inputs.input == "tsv_file":
20 tsvfile '$inputs.tsv_file'
20 #elif $inputs.input == "zip_file": 21 #elif $inputs.input == "zip_file":
21 zipfile $inputs.zip_file 22 zipfile '$inputs.zip_file'
22 #end if 23 #end if
23 24
24 25
25 ## Bucket width 26 ## Bucket width
26 bucket_width $bucket_width 27 bucket_width $bucket_width
42 #end for 43 #end for
43 #end if 44 #end if
44 45
45 ## Outputs 46 ## Outputs
46 logOut log.log 47 logOut log.log
47 dataMatrixOut $dataMatrixOut 48 dataMatrixOut '$dataMatrixOut'
48 sampleOut $sampleOut 49 sampleOut '$sampleOut'
49 variableOut $variableOut 50 variableOut '$variableOut'
50 graphOut $graphOut; cat log.log 51 graphOut '$graphOut'; cat log.log
51 </command> 52 </command>
52 53
53 <inputs> 54 <inputs>
54 <conditional name="inputs"> 55 <conditional name="inputs">
55 <param name="input" type="select" label="Choose your inputs method" > 56 <param name="input" type="select" label="Choose your inputs method" >
56 <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option> 57 <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option>
58 <option value="tsv_file">Tsv file containing preprocessed spectra (from your history)</option>
57 <option value="lib" >Library directory name</option> 59 <option value="lib" >Library directory name</option>
58 </param> 60 </param>
59 <when value="zip_file"> 61 <when value="zip_file">
60 <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" /> 62 <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" />
63 </when>
64 <when value="tsv_file">
65 <param name="tsv_file" type="data" format="tabular" label="Tsv file" />
61 </when> 66 </when>
62 <when value="lib"> 67 <when value="lib">
63 <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" > 68 <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >
64 <validator type="empty_field"/> 69 <validator type="empty_field"/>
65 </param> 70 </param>
101 <data format="tabular" name="dataMatrixOut" label="${tool.name}_bucketedData" /> 106 <data format="tabular" name="dataMatrixOut" label="${tool.name}_bucketedData" />
102 <data format="pdf" name="graphOut" label="${tool.name}_spectra" > 107 <data format="pdf" name="graphOut" label="${tool.name}_spectra" >
103 <filter> graphType != "None" </filter> 108 <filter> graphType != "None" </filter>
104 </data> 109 </data>
105 </outputs> 110 </outputs>
106
107 111
108 <tests> 112 <tests>
109 <test> 113 <test>
110 <param name="inputs|input" value="zip_file" /> 114 <param name="inputs|input" value="zip_file" />
111 <param name="inputs|zip_file" value="MTBLS1.zip" ftype="zip" /> 115 <param name="inputs|zip_file" value="MTBLS1.zip" ftype="zip" />
145 Workflow position 149 Workflow position
146 ----------------- 150 -----------------
147 151
148 **Upstream tools** 152 **Upstream tools**
149 153
150 ========================= ================= ======= ========= 154 ========================= ============================ =======
151 Name output file format parameter 155 Name output file format
152 ========================= ================= ======= ========= 156 ========================= ============================ =======
153 NA NA zip NA 157 NMRAlignment NMR_Alignment_alignedSpectra tsv
154 ========================= ================= ======= ========= 158 ========================= ============================ =======
155
156 159
157 **Downstream tools** 160 **Downstream tools**
158 161
159 +---------------------------+----------------------+--------+ 162 +---------------------------+----------------------+--------+
160 | Name | Output file | Format | 163 | Name | Output file | Format |
176 +---------------------------+------------+ 179 +---------------------------+------------+
177 | Parameter : num + label | Format | 180 | Parameter : num + label | Format |
178 +===========================+============+ 181 +===========================+============+
179 | 1 : Choose your inputs | zip | 182 | 1 : Choose your inputs | zip |
180 +---------------------------+------------+ 183 +---------------------------+------------+
184 | 1 : Choose your inputs | tsv |
185 +---------------------------+------------+
181 186
182 **Choose your inputs** 187 **Choose your inputs**
183 188
184 You have two methods for your inputs: 189 You have three methods for your inputs:
185 190
186 | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). 191 | Zip file (recommended): You can put a zip file containing your inputs as raw Bruker files: myinputs.zip (containing all your conditions as sub-directories).
187 | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories. 192 | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories.
193 | Tsv file: You can put a tsv file containing your inputs as preprocessed spectra: myinputs.tsv (containing all your conditions in columns and chemical shifts in rows).
188 194
189 .. image:: ./static/images/Mth_Architecture_Repertoire_Bruker.png 195 .. image:: ./static/images/Mth_Architecture_Repertoire_Bruker.png
190 :width: 800 196 :width: 800
191 197
192 ---------- 198 ----------
273 --------------------------------------------------- 279 ---------------------------------------------------
274 280
275 Changelog/News 281 Changelog/News
276 -------------- 282 --------------
277 283
284 **Version 1.0.3 - 24/10/2016**
285
286 - ENHANCEMENT: add possibility of bucketing processed files (upstream tools)
287
278 **Version 1.0.2 - 12/08/2016** 288 **Version 1.0.2 - 12/08/2016**
279 289
280 - ENHANCEMENT: x-axis customization: add chemical shift labels 290 - ENHANCEMENT: x-axis customization: add chemical shift labels
281 291
282 **Version 1.0.1 - 04/04/2016** 292 **Version 1.0.1 - 04/04/2016**