comparison galaxy/wrappers/ArrayNormalization.xml @ 1:2762a2622e0d draft

"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"

0:708f43bda2b6

<tool name="GIANT-Normalization with APT Summarize" id="giant_aptsummarize" version="0.1.1">
  <description>Apply Affymetrix Power Tool summarize function to .CEL collection</description>
  <requirements>
    <requirement type="package" version="2.10.1">apt-probeset-summarize</requirement>
  </requirements>
  <stdio>
    <regex match="Execution halted"
           source="both"
           level="fatal"
           description="Execution halted, please contact tool developer or administrators." />
    <exit_code range="10" level="fatal" description="Error in post-treatments, see log file for more information." />
    <exit_code range="1:9" level="fatal" description="Error during apt command execution, see log file for more information." />
  </stdio>



   <command>	<![CDATA[
  ##ONLY FOR LOCAL TEST PURPOSE, COMMENT OTHERWISE
  ##set $pathToApt='/mnt/galaxy/home/galaxy/Software/ThermoFischer/apt-1.20.6-x86_64-intel-linux/bin'

    mkdir ./apt_output/;

  #if $mainCondition.arraySelection=="other":

  fi;
  printf "[INFO]End of tool script" >> $log; 
	]]>
  </command>



  <configfiles>
    <configfile name="scriptFormat">
<![CDATA[
#for $inputDataset in $inputData
        echo '${inputDataset.name}' >> ./tempColumnName.txt

#end if 

]]>
   </configfile> 
  </configfiles>



  <inputs>
    <param type="text" name="title" value="APT_toPersonalize" label="Title for output"/>

    <param type="data" name="inputData" format="cel" label=".cel collection file" optional="false" multiple="true">

    <when value="false">
    </when>
  </conditional>
  </inputs>



  <outputs>
    <data format="tabular" name="outputData" label="${title}_NormalizedData"/>
    <data format="txt" name="log" label="${title}_Log" />
  </outputs>
  


 <tests>
  <test maxseconds="3600">
  	<param name="inputData" value="./CELfiles/GSM205766.CEL,./CELfiles/GSM205767.CEL,./CELfiles/GSM205768.CEL" />
    <param name="commandLine" value="rma-gc-scale" />
    <param name="normLevel" value="core" />
    <param name="arraySelection" value="other" />
    <param name="CDFfile" value="./Mouse430_2.cdf" />
    <param name="annotationFile" value="./formatedAnnotation.csv" />
    <param name="addAnnotation" value="true" />
    <param name="keepAnnotated" value="false" />
    <param name="mergingMethod" value="mean" />
    <output name="outputData" file="./APT-summarize/expressionOutput.csv" />
    <output name="log" file="./APT-summarize/output.log" lines_diff="2" />
  </test>
</tests> 




  <help>
  <![CDATA[

1:2762a2622e0d

<tool name="GIANT-Normalization with APT Summarize" id="giant_aptsummarize" version="0.1.1">
  <description>Apply Affymetrix Power Tool summarize function to .CEL collection</description>
  <requirements>
    <requirement type="package" version="2.10.2">apt-probeset-summarize</requirement>
  </requirements>
  <stdio>
    <regex match="Execution halted"
           source="both"
           level="fatal"
           description="Execution halted, please contact tool developer or administrators." />
    <exit_code range="10" level="fatal" description="Error in post-treatments, see log file for more information." />
    <exit_code range="1:9" level="fatal" description="Error during apt command execution, see log file for more information." />
  </stdio>
  <command>	<![CDATA[
  ##only for local test, comment otherwise
  ##set $pathToApt='/mnt/galaxy/home/galaxy/Software/ThermoFischer/apt-1.20.6-x86_64-intel-linux/bin'

    mkdir ./apt_output/;

  #if $mainCondition.arraySelection=="other":

  fi;
  printf "[INFO]End of tool script" >> $log; 
	]]>
  </command>

  <configfiles>
    <configfile name="scriptFormat">
<![CDATA[
#for $inputDataset in $inputData
        echo '${inputDataset.name}' >> ./tempColumnName.txt

#end if 

]]>
   </configfile> 
  </configfiles>

  <inputs>
    <param type="text" name="title" value="APT_toPersonalize" label="Title for output"/>

    <param type="data" name="inputData" format="cel" label=".cel collection file" optional="false" multiple="true">

    <when value="false">
    </when>
  </conditional>
  </inputs>

  <outputs>
    <data format="tabular" name="outputData" label="${title}_NormalizedData"/>
    <data format="txt" name="log" label="${title}_Log" />
  </outputs>



 <tests>
  <test maxseconds="3600">
  	<param name="inputData" value="./CELfiles/GSM205766.CEL,./CELfiles/GSM205767.CEL,./CELfiles/GSM205768.CEL" />
    <param name="commandLine" value="rma-gc-scale" />
    <param name="normLevel" value="core" />
    <param name="arraySelection" value="other" />
    <param name="CDFfile" value="./APT-summarize/input/Mouse430_2.cdf" />
    <param name="annotationFile" value="./APT-summarize/input/formatedAnnotation.csv" />
    <param name="addAnnotation" value="true" />
    <param name="keepAnnotated" value="false" />
    <param name="mergingMethod" value="mean" />
    <output name="outputData" file="./APT-summarize/output/outputExpression.csv" />
    <output name="log" file="./APT-summarize/output/outputLog.txt" compare="sim_size" delta_frac="0.15" />
  </test>
 </tests> 



  <help>
  <![CDATA[