comparison checkformat_config.xml @ 3:80a38d36f946 draft

planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 5cf3f6eb62c1396ade1b068a3dd3cc2e3f827e15

2:b6a6b4cc932a

<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">r-batch</requirement>
  </requirements>

  <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)
    

    
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
-----------
 

+----------------------------+---------+
| 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

---------------------------------------------------
    
----
NEWS
----

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

INTERNAL MODIFICATIONS

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>

3:80a38d36f946

<tool id="checkFormat" name="Check Format" version="3.0.0">
  <description>Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files</description>
  
  <requirements>
    <requirement type="package">r-batch</requirement>
  </requirements>

  <command><![CDATA[
  Rscript $__tool_directory__/checkformat_wrapper.R
  dataMatrix_in "$dataMatrix_in"
  sampleMetadata_in "$sampleMetadata_in"
  variableMetadata_in "$variableMetadata_in"
  makeNameL "$makeNameL"

  dataMatrix_out "$dataMatrix_out"
  sampleMetadata_out "$sampleMetadata_out"
  variableMetadata_out "$variableMetadata_out"
  information "$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" />
    <param name="makeNameL" label="Make syntactically valid sample and variable names" type="select" help="">
      <option value="TRUE">yes</option>
      <option value="FALSE" selected="true">no</option>
    </param>
  </inputs>
  
  <outputs>
    <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
    <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
    <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
    <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"/>
      <param name="makeNameL" value="TRUE"/>
      <output name="information">
        <assert_contents>
          <has_text text="Message: Converting sample and variable names to the standard R format" />
	  <has_text text="Warning: The sample and/or variable names or orders from the input tables have been modified" />
        </assert_contents>
      </output>
    </test>
  </tests>
  
  <help><![CDATA[
    
.. class:: infomark
    
**Author** Etienne Thevenot (W4M Core Development Team, MetaboHUB Paris, CEA)
    

    
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; in case of difference of orders of the samples and/or variables between (some of) the tables, the **orders from the dataMatrix are permuted** to match those of the sampleMetadata and/or the variableMetadata; sample and variables names can also be modified to be **syntactically valid** for R by selecting the corresponding argument (e.g. an 'X' is added to names starting with a digit, blanks will be converted to '.', etc.).
    
    
-----------------
Workflow position
-----------------
    
.. image:: ./static/images/checkFormat_workflowPositionImage.png

    
-----------
Input files
-----------
 

+----------------------------+---------+
| 2 : Sample metadata file   | tabular |
+----------------------------+---------+
| 3 : Variable metadata file | tabular |
+----------------------------+---------+

| The **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 (http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToFormatDataForPostprocessing_v02.pdf)


----------
Parameters
----------
	  
Data matrix file
	| variable x sample **dataMatrix** tabular separated file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below)
	|

Sample metadata file
	| sample x metadata **sampleMetadata** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
	|
	
Variable metadata file
	| variable x metadata **variableMetadata** tabular separated file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
	|

Make syntactically valid sample and variable names
	| if set to 'yes', sample and variable names will converted to syntactically valid names with the 'make.names' R function when required (e.g. an 'X' is added to names starting with a digit, blanks will be converted to '.', etc.)
	|
  
------------
Output files
------------

dataMatrix_out.tabular
	| dataMatrix data file; may be identical to the input dataMatrix in case no renaming of sample/variable names nor re-ordering of samples/variables (see the 'information' file for the presence/absence of modifications)
	|

sampleMetadata_out.tabular
	| sampleMetadata data file; may be identical to the input sampleMetadata in case no renaming of sample names nor re-ordering of samples (see the 'information' file for the presence/absence of modifications)
	|

variableMetadata_out.tabular
	| variableMetadata data file; may be identical to the input variableMetadata in case no renaming of variable names nor re-ordering of variables (see the 'information' file for the presence/absence of modifications)
	|

information.txt
	| Text file with all messages when error(s) in formats are detected
	|
    
---------------------------------------------------
    
---------------
Working example

---------------------------------------------------
    
----
NEWS
----

CHANGES IN VERSION 3.0.0
========================

NEW FEATURES

Automated re-ordering (if necessary) of sample and/or variable names from dataMatrix based on sampleMetadata and variableMetadata

New argument to make sample and variable names syntactically valid

Output of dataMatrix, sampleMetadata, and variableMetadata files, whether they have been modified or not

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

INTERNAL MODIFICATIONS

Planemo running validation
Planemo installing validation
Travis automated testing
Toolshed export
    
  ]]></help>
  
  <citations>
    <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
    <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
    <citation type="doi">10.1093/bioinformatics/btu813</citation>
  </citations>


</tool>