annotate edgeR_Design_from_Expression_Matrix.xml @ 4:5d38abf7e4b6 draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit e42aebc7a9b64744919668cb9a856b5df8a61387

<?xml version="1.0" encoding="UTF-8"?>
<tool id="design_from_expression_matrix" name="edgeR: Design- from Expression matrix" version="1.0.0.a">
    <description>Create design- from an expression matrix</description>
    
    <macros>
        <import>edgeR_macros.xml</import>
    </macros>
    
    <requirements>
        <requirement type="package" version="1.0.0">design_matrix_creator</requirement>
    </requirements>
    
    <command>
        design_matrix_creator
            -c $expression_matrix
            
            #set $unique_columns = []
            #for $factor in $treatments:
                #for $level in $factor.rep_factorLevel:
                    #for $val in $level.factorIndex.value:
                        #if str($val) not in $unique_columns:
                            #set $unique_columns = $unique_columns + [str($val)]
                        #end if
                    #end for
                #end for
            #end for
            
            #set $unique_columns = " ".join(unique_columns)
            -s $unique_columns
            
            -t
            #for $factor in $treatments:
                #set $factor_str = str($factor.name).encode('base64').replace('\n','')
                
                #for $level in $factor.rep_factorLevel:
                    #set $factor_str = $factor_str+":"+str($level.factorLevel).encode('base64').replace('\n','')+":"+",".join([str(x).strip() for x in $level.factorIndex.value])
                #end for
                
                $factor_str
            #end for
            
            #if $choose_blocking.choice == "true"
                -b
                #for blocking in $choose_blocking.blocking_repeat:
                    #set $blocking_str = str($blocking.blocking_name).encode('base64').replace('\n','')
                    
                    #for $block_iter in $blocking.block:
                        #set $block_str = ",".join([str(x).strip() for x in $block_iter.block_index.value])
                        #set $blocking_str = $blocking_str+":"+$block_str
                    #end for
                    
                    $blocking_str
                #end for
            #end if
            
             -o $design_matrix
    </command>
    
    <inputs>
        <param format="tabular" name="expression_matrix" type="data" label="Expression matrix (read counts)" help="You can create a count matrix with the tool" />
        
        <repeat name="treatments" title="Factor/Condition" min="1">
            <param name="name" type="text" value="FactorName" label="Specify a name for the factor / condition" help="e.g. 'Tumor vs. Normal', 'Timepoint' or 'DiseaseState'. Field must be non-numerical, preferably only letters!!" />
            <repeat name="rep_factorLevel" title="Factor level" min="1">
                <param name="factorLevel" type="text" value="FactorLevel" label="Specify a condition" help="e.g. Tumor or Normal; Treated, untreaded or placebo. Field must be non-numerical, preferably only letters!!" />
                <param name="factorIndex" numerical="false" use_header_names="true" label="Select columns that are associated with this factor level" type="data_column" data_ref="expression_matrix" multiple="true" size="120" display="checkboxes">
                    <validator type="no_options" message="Please select at least one column." />
                </param>
            </repeat>
        </repeat>
        
        <conditional name="choose_blocking">
            <param name="choice" type="select" label="Define blocking (paired or grouped samples)" help="e.g. to remove batch effects" >
                <option value="false">No</option>
                <option value="true">Yes</option>
            </param>
            <when value="false" />
            <when value="true">
                <repeat name="blocking_repeat" title="Blocking condition" min="1">
                    <param name="blocking_name" type="text" value="" label="Specify a name for a blocking condition" help="e.g.'Patients' or 'Batches'" />
                    <repeat name="block" title="Block" min="2">
                        <param name="block_index" label="Select columns that are associated with this factor level" type="data_column" data_ref="expression_matrix" numerical="True" multiple="true" use_header_names="true" size="120" display="checkboxes">
                            <validator type="no_options" message="Please select at least one column." />
                        </param>
                    </repeat>
                </repeat>
            </when>
        </conditional>
    </inputs>
    
    <outputs>
        <data format="tabular" name="design_matrix" label="Design matrix" />
    </outputs>
    
    <tests>
        <test>
            <param name="expression_matrix" value="GSE51403/GSE51403_expression_matrix_full.txt" />
            
            <!-- <repeat name="treatments"> -->
                <param name="treatments_0|name" value="Treatment" />
                <!-- <repeat name="rep_factorLevel"> -->
                    <param name="treatments_0|rep_factorLevel_0|factorLevel" value="Control" />
                    <param name="treatments_0|rep_factorLevel_0|factorIndex" value="2,3,4,5,6,7,8" />
                <!-- </repeat> -->
                <!-- <repeat name="rep_factorLevel"> -->
                    <param name="treatments_0|rep_factorLevel_1|factorLevel" value="E2" />
                    <param name="treatments_0|rep_factorLevel_1|factorIndex" value="9,10,11,12,13,14,15" />
                <!-- </repeat> -->
            <!-- </repeat> -->
            
            <conditional name="choose_blocking">
                <param value="false" />
            </conditional>
            
            <output name="design_matrix" file="GSE51403/GSE51403_design_matrix_full_depth.txt" />
        </test>
    </tests>
    
    <help>
edgeR: Design- from Expression matrix
#####################################

Overview
--------

Create a design matrix by selecting the desired patients from an expression matrix.

Input
-----

@CONTACT@
    </help>
    
    <expand macro="citations" />
</tool>