Mercurial > repos > marie-tremblay-metatoul > nmr_alignment
comparison nmr_alignement/NmrAlignment_xml.xml @ 2:908e1345d7ca draft
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| author | marie-tremblay-metatoul |
|---|---|
| date | Fri, 31 Mar 2017 09:56:39 -0400 |
| parents | 58eecef626da |
| children | f3ec6799c435 |
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| 1:58eecef626da | 2:908e1345d7ca |
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| 1 <tool id="NmrAlignment" name="NMR spectra alignment" version="2.0.1"> | 1 <tool id="NmrAlignment" name="NMR spectra alignment" version="2.0.2"> |
| 2 <description>based on the Cluster-based Peak Alignment (CluPA) algorithm</description> | 2 <description>based on the Cluster-based Peak Alignment (CluPA) algorithm</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="3.1.2">R</requirement> | 4 <requirement type="package" version="3.1.2">R</requirement> |
| 5 <requirement type="package" version="1.1_4">r-batch</requirement> | 5 <requirement type="package" version="1.1_4">r-batch</requirement> |
| 6 <requirement type="package" version="1.2.1">r-speaq</requirement> | 6 <requirement type="package" version="1.2.1">r-speaq</requirement> |
| 13 Rscript '$__tool_directory__/NmrAlignment_wrapper.R' | 13 Rscript '$__tool_directory__/NmrAlignment_wrapper.R' |
| 14 | 14 |
| 15 ## File input | 15 ## File input |
| 16 #if $inputs.input == "lib": | 16 #if $inputs.input == "lib": |
| 17 library '$__app__.config.user_library_import_dir/$__user_email__/$inputs.library' | 17 library '$__app__.config.user_library_import_dir/$__user_email__/$inputs.library' |
| 18 #elif $inputs.input == "tsv_file": | |
| 19 tsvfile $inputs.tsv_file | |
| 18 #elif $inputs.input == "zip_file": | 20 #elif $inputs.input == "zip_file": |
| 19 zipfile '$inputs.zip_file' | 21 zipfile '$inputs.zip_file' |
| 20 #end if | 22 #end if |
| 21 | 23 |
| 22 ## Spectra borders | 24 ## Spectra borders |
| 48 </command> | 50 </command> |
| 49 <inputs> | 51 <inputs> |
| 50 <conditional name="inputs"> | 52 <conditional name="inputs"> |
| 51 <param name="input" type="select" label="Choose your inputs method" > | 53 <param name="input" type="select" label="Choose your inputs method" > |
| 52 <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option> | 54 <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option> |
| 55 <option value="tsv_file">Tsv file containing preprocessed spectra (from your history)</option> | |
| 53 <option value="lib" >Library directory name</option> | 56 <option value="lib" >Library directory name</option> |
| 54 </param> | 57 </param> |
| 55 <when value="zip_file"> | 58 <when value="zip_file"> |
| 56 <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" /> | 59 <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" /> |
| 60 </when> | |
| 61 <when value="tsv_file"> | |
| 62 <param name="tsv_file" type="data" format="tabular" label="Tsv file" /> | |
| 57 </when> | 63 </when> |
| 58 <when value="lib"> | 64 <when value="lib"> |
| 59 <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" > | 65 <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" > |
| 60 <validator type="empty_field"/> | 66 <validator type="empty_field"/> |
| 61 </param> | 67 </param> |