Mercurial > repos > marie-tremblay-metatoul > nmr_preprocessing
diff ReadFids_xml.xml @ 2:5e64657b4fe5 draft
planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
author | lecorguille |
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date | Wed, 28 Mar 2018 08:05:12 -0400 |
parents | |
children | 6e837e9352a2 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ReadFids_xml.xml Wed Mar 28 08:05:12 2018 -0400 @@ -0,0 +1,211 @@ +<tool id="NMR_Read" name="NMR_Read" version="@WRAPPER_VERSION@"> + <description> Read Bruker NMR raw files</description> + + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements" /> + + <expand macro="stdio"/> + + <command> + ## Wrapper + Rscript $__tool_directory__/ReadFids_wrapper.R + + ## File input + fidzipfile $fidzipfile + + ## Title line + title_line $title_line + + ## Subdirectories + subdirectories $subdirectories + + ## Use subdirectories names as FID names? + dirs_names $dirs_names + + ## Outputs + dataMatrix $dataMatrix + sampleMetadata $sampleMetadata + logOut $logOut + graphOut $graphOut + + </command> + + <inputs> + <param name="fidzipfile" type="data" format="no_unzip.zip" label="Bruker FID file" /> + <param name="title_line" label="Specify the line in the title file to recover the FID names (usually in pdata/1/title)" type="integer" value="1" size="100" help="Default value is line 1"/> + + <param name="subdirectories" label="Presence of subdirectories?" type="select" help="Select 'FALSE' when there is no subdirectories, 'TRUE' if there are subdirectories"> + <option value="FALSE"> FALSE </option> + <option value="TRUE"> TRUE </option> + </param> + + <param name="dirs_names" label="Use (sub)directories names as FID names?" type="select" help="Select 'TRUE' to use the subdirectories names as the FID names (instead of looking in the title file)"> + <option value="FALSE"> FALSE </option> + <option value="TRUE"> TRUE </option> + </param> + </inputs> + + <outputs> + <data format="tabular" name="dataMatrix" label="${tool.name}_dataMatrix" /> + <data format="tabular" name="sampleMetadata" label="${tool.name}_sampleMetadata" /> + <data format="txt" name="logOut" label="${tool.name}_log" /> + <data format="pdf" name="graphOut" label="${tool.name}_graph" /> + </outputs> + + + <tests> + <test> + <param name="fidzipfile" value="MTBLS1.zip" ftype="zip" /> + <param name="title_line" value="1" /> + <param name="subdirectories" value="TRUE" /> + <param name="dirs_names" value="TRUE" /> + + <output name="dataMatrix" value="NMR_ReadFids_dataMatrix.tabular" /> + </test> + </tests> + + <help> + +@HELP_AUTHORS@ + + +============= +NMR Read +============= + +----------- +Description +----------- + +Nuclear Magnetic Resonance Bruker files reading (from the PEPS-NMR R package (https://github.com/ManonMartin/PEPSNMR)) + +----------------- +Workflow position +----------------- + +**Upstream tools** + +========================= ================= ======= +Name output file format +========================= ================= ======= +NA NA NA +========================= ================= ======= + + +**Downstream tools** + ++-----------------------+--------------------------+--------+ +| Name | Output file | Format | ++=======================+==========================+========+ +|NMR_Preprocessing | dataMatrix | Tabular| ++-----------------------+--------------------------+--------+ +|NMR_Preprocessing | sampleMetadata | Tabular| ++-----------------------+--------------------------+--------+ +|NMR_Preprocessing | NMR_Read_log | TXT | ++-----------------------+--------------------------+--------+ +|NMR_Preprocessing | NMR_Read_graph | PDF | ++-----------------------+--------------------------+--------+ +|NMR_Alignement | dataMatrix | Tabular| ++-----------------------+--------------------------+--------+ +|NMR_Bucketing | dataMatrix | Tabular| ++-----------------------+--------------------------+--------+ +|Normalization | dataMatrix | Tabular| ++-----------------------+--------------------------+--------+ +|Univariate | variableMetadata | Tabular| ++-----------------------+--------------------------+--------+ +|Multivariate | sampleMetadata | Tabular| ++-----------------------+--------------------------+--------+ +| | variableMetadata | Tabular| ++-----------------------+--------------------------+--------+ + + +----------- +Input files +----------- + ++---------------------------+-----------------+ +| Parameter : num + label | Format | ++===========================+=================+ +| 1 : Choose your inputs | zip | ++---------------------------+-----------------+ + + +**Choose your inputs** + + | Zip file (recommended) of FID Bruker files: you can put a zip file containing your FID Bruker files: myinputs.zip. + + +---------- +Parameters +---------- + +FID Title line + | Line in the acqus file to find the FID title (name) + | + +subdirectories + | Organization of individual's files + | TRUE: will search inside subdirectories for FIDs and will merge them to have unique FID and info matrices. + | + +dirs_names + | Use the (sub)directories names as FID names? + | + + +------------ +Output files +------------ + +NMR_Read_dataMatrix + | tabular output + | Data matrix with n rows (samples) and p columns (time) containing the raw FIDs. + | + +NMR_Read_sampleMetadata + | tabular output + | Data matrix with n rows (samples) containing the acquisition parameters for each sample. + | + +NMR_Read_log + | Text output + | Contains warnings + | + + +NMR_Read_graph + | pdf output + | line plots of FID + | + + +Creating the zip file +----------------------- + +.. class:: warningmark you must use the 7Zip software (http://www.7-zip.org/) to zip under Windows. + +Must contain at least the following files for every sample: fid, acqu and acqus + +.. image:: ./static/images/ReadFids.png + + + +**Possible structure and parameters values:** + + +(1) use title file and presence of sub-directories: set the FID Title line, subdirectories = TRUE, dirs_names = FALSE +(2) use title file and no sub-directories: set the FID Title line, subdirectories = FALSE, dirs_names = FALSE +(3) don't use title file and presence of sub-directories: subdirectories = TRUE, dirs_names = TRUE +(4) don't use title file and no sub-directories: subdirectories = FALSE, dirs_names = TRUE + + +@HELP_CHANGELOG@ + + </help> + + <expand macro="citation" /> + +</tool>