annotate checkformat_config.xml @ 1:e194eec8e70c draft

planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f

<tool id="checkFormat" name="Check Format" version="2.0.4">
  <description>Checks the formats of the dataMatrix, sampleMetadata, and variableMetadata files</description>
  
  <requirements>
    <requirement type="package" version="3.2.2">R</requirement>
    <requirement type="package">r-batch</requirement>
  </requirements>

  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>
  
  <command><![CDATA[
  Rscript $__tool_directory__/checkformat_wrapper.R
  dataMatrix_in "$dataMatrix_in"
  sampleMetadata_in "$sampleMetadata_in"
  variableMetadata_in "$variableMetadata_in"
  
  information "$information"
  ]]></command>    
  
  <inputs>
    <param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
    <param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" />
    <param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" />
  </inputs>
  
  <outputs>
    <data name="information" label="${tool.name}_information.txt" format="txt"/>
  </outputs>
  
  <tests>
    <test>
      <param name="dataMatrix_in" value="input-dataMatrix.tsv"/>
      <param name="sampleMetadata_in" value="input-sampleMetadata.tsv"/>
      <param name="variableMetadata_in" value="input-variableMetadata.tsv"/>
      <output name="information" file="output-information.txt" lines_diff="4"/>  
    </test>
  </tests>
  
  <help>
    
.. class:: infomark
    
**Author** Etienne Thevenot (W4M Core Development Team, MetaboHUB Paris, CEA)
    
---------------------------------------------------
    
.. class:: infomark
    
**Tool updates**
    
See the **NEWS** section at the bottom of this page
    
---------------------------------------------------
    
========================
Check Format
========================
    
-----------
Description
-----------
    
| Checks the format (row and column names) of the dataMatrix, sampleMetadata and variableMetadata tables
    
    
-----------------
Workflow position
-----------------
    
.. image:: ./static/images/checkFormat_workflowPositionImage.png
:width: 600
    
    
    
-----------
Input files
-----------
 
+----------------------------+---------+
| Parameter : num + label    |  Format |
+============================+=========+
| 1 : Data matrix file       | tabular |
+----------------------------+---------+
| 2 : Sample metadata file   | tabular |
+----------------------------+---------+
| 3 : Variable metadata file | tabular |
+----------------------------+---------+
    
|
| **Required formats for the dataMatrix, sampleMetadata, and variableMetadata files are**
| **described in the HowTo entitled 'Format Data For Postprocessing' available on the**
| **main page of Workflow4Metabolomics.org**
|
    
------------
Output files
------------
    
information.txt
| Text file with all messages when error(s) in formats are detected
|
    
---------------------------------------------------
    
---------------
Working example
---------------
    
.. class:: infomark
  
See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-complete**, **W4M00002_mtbls2**, or **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
    
---------------------------------------------------
    
----
NEWS
----

CHANGES IN VERSION 2.0.4
========================

INTERNAL MODIFICATIONS

Minor internal modifications
    
CHANGES IN VERSION 2.0.2
========================
    
INTERNAL MODIFICATIONS
    
Test for R code
Planemo running validation
Planemo installing validation
Travis automated testing
Toolshed export
    
  </help>
  
  <citations>
    <citation type="bibtex">@Article{Thevenot2015,
    Title                    = {Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses},
    Author                   = {Thévenot, Etienne A. and Roux, Aurélie and Xu, Ying and Ezan, Eric and Junot, Christophe},
    Journal                  = {Journal of Proteome Research},
    Year                     = {2015},
    Note                     = {PMID: 26088811},
    Number                   = {8},
    Pages                    = {3322-3335},
    Volume                   = {14},
    
    Doi                      = {10.1021/acs.jproteome.5b00354},
    Url                      = {http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354}
    }</citation>
    <citation type="doi">10.1093/bioinformatics/btu813</citation>
  </citations>


  
  ---------------
  Working example
  ---------------
  
  
  Input files
  ===========
  
  | **To generate the "dataMatrix", "sampleMetadata" and "variableMetadata" files:**
  |   **1) copy/paste the values below in three distinct .txt files**
  |   **2) use the "Get Data" / "Upload File" in the "Tools" (left) panel from the Galaxy / ABiMS page by choosing:**
  |     **a) File Format: 'tabular'**
  |     **b) Convert spaces to tabs: 'Yes'**
  | 
  
  **dataMatrix file**::
  
  dataMatrix HU_017 HU_021 HU_027 HU_032 HU_041 HU_048 HU_049 HU_050 HU_052 HU_059 HU_060 HU_066 HU_072 HU_077 HU_090 HU_109 HU_110 HU_125 HU_126 HU_131 HU_134 HU_149 HU_150 HU_173 HU_179 HU_180 HU_182 HU_202 HU_204 HU_209
  HMDB01032 2569204.92420381 6222035.77434915 17070707.9912636 1258838.24348419 13039543.0754619 1909391.77026598 3495.09386434063 2293521.90928998 128503.275117713 81872.5276382213 8103557.56578035 149574887.036181 1544036.41049333 7103429.53933206 14138796.50382 4970265.57952158 263054.73056162 1671332.30008058 88433.1944958815 23602331.2894815 18648126.5206986 1554657.98756878 34152.3646391152 209372.71275317 33187733.370626 202438.591636003 13581070.0886437 354170.810678102 9120781.48986975 43419175.4051586
  HMDB03072 3628416.30251025 65626.9834353751 112170.118946651 3261804.34422417 42228.2787747563 343254.201250707 1958217.69317664 11983270.0435677 5932111.41638028 5511385.83359531 9154521.47755199 2632133.21209418 9500411.14556502 6551644.51726592 7204319.80891836 1273412.04795188 3260583.81592376 8932005.5351622 8340827.52597275 9256460.69197759 11217839.169041 5919262.81433556 11790077.0657915 9567977.80797097 73717.5811684739 9991787.29074293 4208098.14739633 623970.649925847 10904221.2642849 2171793.93621067
  HMDB00792 429568.609438384 3887629.50527037 1330692.11658995 1367446.73023821 844197.447472453 2948090.71886592 1614157.90566884 3740009.19379795 3292251.66531919 2310688.79492013 4404239.59008605 3043289.12780863 825736.467181043 2523241.91730649 6030501.02648005 474901.604069803 2885792.42617652 2955990.64049134 1917716.3427982 1767962.67737699 5926203.40397675 1639065.69474684 346810.763557826 1054776.22313737 2390258.27543894 1831346.37315857 1026696.36904362 7079792.50047866 4368341.01359769 3495986.87280275
  
  
  **sampleMetadata file**::
  
  sampleMetadata age ageGrp
  HU_017 41 experienced
  HU_021 34 junior
  HU_027 37 experienced
  HU_032 38 experienced
  HU_041 28 junior
  HU_048 39 experienced
  HU_049 50 senior
  HU_050 30 junior
  HU_052 51 senior
  HU_059 81 senior
  HU_060 55 senior
  HU_066 25 junior
  HU_072 47 experienced
  HU_077 27 junior
  HU_091 46 experienced
  HU_109 32 junior
  HU_110 50 senior
  HU_125 58 senior
  HU_126 45 experienced
  HU_131 42 experienced
  HU_134 48 experienced
  HU_149 35 experienced
  HU_150 49 experienced
  HU_173 55 senior
  HU_179 33 junior
  HU_180 53 senior
  HU_182 43 experienced
  HU_202 42 experienced
  HU_204 31 junior
  HU_209 17.5 junior
  
  
  **variableMetadata file**::
  
  variableMetadata name
  HMDB01032        Dehydroepiandrosterone sulfate
  HMDB03072        Quinic acid
  HMDB00792        Sebacic acid

  
</tool>