annotate edgeR_Concatenate_Expression_Matrices.xml @ 8:31a23ae7c61e draft default tip

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/edger_with_design_matrix commit eb5cd7834861d8ddbffce974ed0ca6f1c0ecccf2

<?xml version="1.0" encoding="UTF-8"?>
<tool id="concatenate_expression_matrices" name="edgeR: Concatenate Expression Matrices" version="1.0.0.b">
    <description>Create a full expression matrix by selecting the desired columns from specific count tables</description>
    
    <macros>
        <import>edgeR_macros.xml</import>
    </macros>
    
    <command>
        #set $j = 0
        #set $paste = []
        
        #if $add_geneids.choice == "true":
            #set $filename = str($j)+".txt"
            #set paste = paste + [$filename]
            
            cut -f $add_geneids.column_geneids.value "$add_geneids.sample_geneids" > $filename ;
            #set $j += 1
        #end if
        
        #for $sample in $samples:
            ##echo "$sample.column_index"
            ##echo "$sample.column_index.value"
            
            #set $column_str = ",".join([str(x).strip() for x in $sample.column_index.value])
            #set $filename = str($j)+".txt"
            #set paste = paste + [$filename]
            
            cut -f "$column_str" "$sample.sample" > $filename ;
            #set $j += 1
        #end for
        
        #if $add_lengths.choice == "true":
            #set $filename = str($j)+".txt"
            #set paste = paste + [$filename]
            
            cut -f $add_lengths.column_lengths.value "$add_lengths.sample_lengths" > $filename ;
            #set $j += 1
        #end if
        
        #set $paste_str = " ".join([str(x).strip() for x in $paste])
        
        paste $paste_str > $expression_matrix
    </command>
    
    <inputs>
        <conditional name="add_geneids">
            <param name="choice" type="select" label="Add a gene-IDs column at the end of the file" help="Highly recommended to select!" >
                <option value="false">No</option>
                <option value="true" selected="true">Yes</option>
            </param>
            <when value="false" />
            <when value="true">
                <param name="sample_geneids" type="data" format="tabular"
                       label="Select Read-count dataset that contains a column for GeneIDs"
                       help="from featureCounts/DEXSeq-count/HTSeq-count, etc." />

                <param name="column_geneids"
                       numerical="false"
                       use_header_names="true"
                       label="Select GeneID column"
                       type="data_column"
                       data_ref="sample_geneids"
                       multiple="false">
                    <validator type="no_options" message="Please select at least one column." />
                </param>
            </when>
        </conditional>
        
        <repeat name="samples" title="Expression Table" help="E.g. a earlier concatenated table, or a HT-seq, featureCounts or DESeq-count result.">
            <param name="sample" type="data" format="tabular" label="Read-count dataset that belongs to a pair" help="from featureCounts/DEXSeq-count/HTSeq-count, etc." />
            <!-- select columns  -->
            <param name="column_index"
                   numerical="false"
                   use_header_names="true"
                   label="Select columns that are associated with this factor level"
                   type="data_column"
                   data_ref="sample"
                   multiple="true">
                <validator type="no_options" message="Please select at least one column." />
            </param>
        </repeat>
        
        <conditional name="add_lengths">
            <param name="choice" type="select" label="Add a gene-lengths column at the end of the file" help="Optional, only usefull if RPKM/FPKM calculation is desired." >
                <option value="false">No</option>
                <option value="true">Yes</option>
            </param>
            <when value="false" />
            <when value="true">
                <param name="sample_lengths" type="data" format="tabular" label="Read-count dataset that belongs to a pair" help="from featureCounts/DEXSeq-count/HTSeq-count, etc." />
                <param name="column_lengths" numerical="false" use_header_names="true" label="Select columns that are associated with this factor level" type="data_column" data_ref="sample_lengths" multiple="false" size="120">
                    <validator type="no_options" message="Please select at least one column." />
                </param>
            </when>
        </conditional>
        
        <param name="remove_comment_lines" type="boolean" truevalue="true" falsevalue="false" checked="true"
               label="Automatically remove 'comment' lines starting with a '#'"
               help="Some tools (incl. featureCounts) include comment lines that are not neccesairy for downstream analyis. By enabling this function, these lines will be removed." />

    </inputs>
    
    <outputs>
        <data format="tabular" name="expression_matrix" label="Expression matrix" />
    </outputs>
    
    <tests>
        <test>
            <conditional name="add_geneids">
                <param name="choice" value="true" />
                <param name="sample_geneids" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" />
                <param name="column_geneids" value="1" />
            </conditional>
            
            <param name="samples_0|sample" value="GSE51403/GSE51403_expression_matrix_Control_1.txt" />
            <param name="samples_0|column_index" value="2" />
            
            <conditional name="add_lengths">
                <param name="choice" value="false" />
            </conditional>
            
            <param name="remove_comment_lines" value="false" />
            
            <output name="expression_matrix" file="GSE51403/GSE51403_expression_matrix_Control_1.txt" />
        </test>
        <test>
            <conditional name="add_geneids">
                <param name="choice" value="true" />
                <param name="sample_geneids" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" />
                <param name="column_geneids" value="1" />
            </conditional>
            
            <!-- <repeat name="samples"> -->
                <param name="samples_0|sample" value="GSE51403/GSE51403_expression_matrix_Control_1.txt" />
                <param name="samples_0|column_index" value="2" />
            <!-- </repeat> -->
            
            <!-- <repeat name="samples"> -->
                <param name="samples_1|sample" value="GSE51403/GSE51403_expression_matrix_Control_2.txt" />
                <param name="samples_1|column_index" value="2" />
            <!-- </repeat> -->
            
            <!-- <repeat name="samples"> -->
                <param name="samples_2|sample" value="GSE51403/GSE51403_expression_matrix_Control_3.txt" />
                <param name="samples_2|column_index" value="2" />
            <!-- </repeat> -->
            
            <!-- <repeat name="samples"> -->
                <param name="samples_3|sample" value="GSE51403/GSE51403_expression_matrix_Control_4.txt" />
                <param name="samples_3|column_index" value="2" />
            <!-- </repeat> -->
            
            <!-- <repeat name="samples"> -->
                <param name="samples_4|sample" value="GSE51403/GSE51403_expression_matrix_Control_5.txt" />
                <param name="samples_4|column_index" value="2" />
            <!-- </repeat> -->
            
            <!-- <repeat name="samples"> -->
                <param name="samples_5|sample" value="GSE51403/GSE51403_expression_matrix_Control_6.txt" />
                <param name="samples_5|column_index" value="2" />
            <!-- </repeat> -->
            
            <!-- <repeat name="samples"> -->
                <param name="samples_6|sample" value="GSE51403/GSE51403_expression_matrix_Control_7.txt" />
                <param name="samples_6|column_index" value="2" />
            <!-- </repeat> -->
            
            <!-- <repeat name="samples"> -->
                <param name="samples_7|sample" value="GSE51403/GSE51403_expression_matrix_E2.txt" />
                <param name="samples_7|column_index" value="2,3,4,5,6,7,8" />
            <!-- </repeat> -->
            
            <conditional name="add_lengths">
                <param name="choice" value="true" />
                <param name="sample_lengths" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" />
                <param name="column_lengths" value="2" />
            </conditional>
            
            <param name="remove_comment_lines" value="false" />
            
            <output name="expression_matrix" file="GSE51403/GSE51403_expression_matrix_full.txt" />
        </test>
    </tests>
    
    <help>
edgeR: Concatenate Expression Matrices
#######################################

Overview
--------

Create subsets from or combined expression matrices.

**Notes**

Make sure the tables have an identical number of columns compared to the number of headers.
If you export tables using R, make sure you set: col.names=NA. Otherwise column may be swapped during concatenation.

Input
-----

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