<commit_before><tool id="MultiPEN-feature-selection" name="Feature Selection" version="0.0.3">
    <description>Feature selection from gene expression levels and/or metabolite levels</description>
    <requirements>
        <requirement type="package" version="0.0.3">MultiPEN</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>
    <command><![CDATA[
run_MultiPEN_slurm.sh FeatureSelection ./ '$ExpressionData' '$Interactions' '$SampleClass' $lambda $optionalParameters
&&
mv MultiPEN-performance_feature-selection_lambda${lambda}.txt Performance.txt &&
mv MultiPEN-Rankings_lambda${lambda}.txt Rankings.txt &&
mv MultiPEN-vts_lambda${lambda}.txt vts.txt &&
mv MultiPEN-Rankings_lambda${lambda}_genes-higher-in-cases.txt Rankings-higherInCases.txt &&
mv MultiPEN-Rankings_lambda${lambda}_genes-higher-in-control.txt Rankings-higherInControl.txt
    ]]></command>
    <inputs>
        <param name="ExpressionData" type="data" format="tabular" label="Expression and/or levels for features (genes and/or metabolites)" help="Gene expression and/or metabolite levels" />
        <param name="Interactions" type="data" format="tabular" label="Interaction Network" help="Molecular interaction network, where every interaction is defined by three elements: the source  node (name of gene and/or metabolite), the target node (name of gene and/or metabolite) and the weight for the interaction (a real number in the range [0,1]), i.e., the confidence level. The interaction matrix is provided as a tabular file with three columns: source, target and weight, and where each row corresponds to an interaction."  />
        <param name="SampleClass" type="data" format="txt" label="SampleClass for the samples" help="Tabular file with two columns: sample and class. The sample column contains the names of all samples, which corresponds to the columns in 'ExpressionData'. The class for each sample is 1 for cases and 0 for control" />
        <param name="lambda" type="float" value="" label="Lambda for the optimisation function" help="" />
        <param name="optionalParameters" type="string" value="000.500100" label="optional parameters" help="The digits of this string represent a sequence of parameters. The following triples define the position in the string, the parameter name and its possible values (i.e., the left most value in the string states whether the log2 transform has been used or not): {1, log2 transform, [0,1]}, {2, z-scores, [0,1]}, {3 to 6, decision threshold, e.g.: 0.60}, {7 to 10, max number of iterations, e.g.: 0300 (default value is set to 0100)}. For example, the default string shown, 000.500100, states that no log 2 transformed is used, no z-scores are used, decision threshold is 0.50 and a maximum of 100 iterations are used." /><commit_msg>modified MultiPEN-feature-selectiom.xml to include string with optional parameters for log2 transform, z-scores, decision threshold, max number of iterations; optional string is also added at the end of all output file name<commit_after><tool id="MultiPEN-feature-selection" name="Feature Selection" version="0.0.3">
    <description>Feature selection from gene expression levels and/or metabolite levels</description>
    <requirements>
        <requirement type="package" version="0.0.3">MultiPEN</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>
    <command><![CDATA[
run_MultiPEN_slurm.sh FeatureSelection ./ '$ExpressionData' '$Interactions' '$SampleClass' $lambda $optionalParameters
&&
mv MultiPEN-performance_feature-selection_lambda${lambda}_${optionalParameters}.txt Performance.txt &&
mv MultiPEN-Rankings_lambda${lambda}_${optionalParameters}.txt Rankings.txt &&
mv MultiPEN-vts_lambda${lambda}_${optionalParameters}.txt vts.txt &&
mv MultiPEN-Rankings_lambda${lambda}_genes-higher-in-cases_${optionalParameters}.txt Rankings-higherInCases.txt &&
mv MultiPEN-Rankings_lambda${lambda}_genes-higher-in-control_${optionalParameters}.txt Rankings-higherInControl.txt
    ]]></command>
    <inputs>
        <param name="ExpressionData" type="data" format="tabular" label="Expression and/or levels for features (genes and/or metabolites)" help="Gene expression and/or metabolite levels" />
        <param name="Interactions" type="data" format="tabular" label="Interaction Network" help="Molecular interaction network, where every interaction is defined by three elements: the source  node (name of gene and/or metabolite), the target node (name of gene and/or metabolite) and the weight for the interaction (a real number in the range [0,1]), i.e., the confidence level. The interaction matrix is provided as a tabular file with three columns: source, target and weight, and where each row corresponds to an interaction."  />
        <param name="SampleClass" type="data" format="txt" label="SampleClass for the samples" help="Tabular file with two columns: sample and class. The sample column contains the names of all samples, which corresponds to the columns in 'ExpressionData'. The class for each sample is 1 for cases and 0 for control" />
        <param name="lambda" type="float" value="" label="Lambda for the optimisation function" help="" />
        <param name="optionalParameters" type="string" value="000.500100" label="Optional parameters" help="The digits of this string represent a sequence of parameters. The following triples define the position in the string, the parameter name and its possible values (i.e., the left most value in the string states whether the log2 transform has been used or not): {1, log2 transform, [0,1]}, {2, z-scores, [0,1]}, {3 to 6, decision threshold, e.g.: 0.60}, {7 to 10, max number of iterations, e.g.: 0300 (default value is set to 0100)}. For example, the default string shown, 000.500100, states that no log 2 transformed is used, no z-scores are used, decision threshold is 0.50 and a maximum of 100 iterations are used." />
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