annotate ReadFids_xml.xml @ 2:5e64657b4fe5 draft

planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e

<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>