comparison dexseq.xml @ 22:71cb8c5ae8bd draft

Uploaded

21:45022897fb7d

    <command>
    mkdir ./html_out ;
        #import json
        Rscript $__tool_directory__/dexseq.R
            -o "$dexseq_out"
            -p 12
            #set $temp_factor_names = list()
            #for $factor in $rep_factorName:
                #set $temp_factor = list()
                #for $level in $factor.rep_factorLevel:
                    #set $count_files = list()

           source="both" 
           level="fatal" 
           description="An undefined error occured, please check your intput carefully and contact your administrator." />
    </stdio>
    <inputs>
        <param name="gtf" type="data" label="GTF file created from dexseq_count tool"/>
        <repeat name="rep_factorName" title="Factor" min="1">
            <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 
                help="Only letters, numbers and underscores will be retained in this field">
                <sanitizer>
                    <valid initial="string.letters,string.digits"><add value="_" /></valid>

        <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}"/>
        <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}">
            <filter>report == True</filter>
        </data>
    </outputs>
    <code file="dexseq_helper.py" />
    <help>

.. class:: infomark

**What it does** 

22:71cb8c5ae8bd

    <command>
    mkdir ./html_out ;
        #import json
        Rscript $__tool_directory__/dexseq.R
            -o "$dexseq_out"
            -p 6
            #set $temp_factor_names = list()
            #for $factor in $rep_factorName:
                #set $temp_factor = list()
                #for $level in $factor.rep_factorLevel:
                    #set $count_files = list()

           source="both" 
           level="fatal" 
           description="An undefined error occured, please check your intput carefully and contact your administrator." />
    </stdio>
    <inputs>
        <param name="gtf" type="data" label="GTF file created from DEXSeq-Count tool"/>
        <repeat name="rep_factorName" title="Factor" min="1">
            <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 
                help="Only letters, numbers and underscores will be retained in this field">
                <sanitizer>
                    <valid initial="string.letters,string.digits"><add value="_" /></valid>

        <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}"/>
        <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}">
            <filter>report == True</filter>
        </data>
    </outputs>
    
    <code file="dexseq_helper.py" />
    <tests>
        <test>
            <param name="gtf" value="flattened.filtered.gtf" ftype="bed"/>
            <repeat name="rep_factorName">
                <param name="factorName" value="condition" ftype="bed"/>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" type="text" value="knockdown"/>
                    <param name="countsFile" ftype="tabular" value="treated1fb.txt"/>
                </repeat>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" type="text" value="knockdown"/>
                    <param name="countsFile" ftype="tabular" value="treated2fb.txt"/>
                </repeat>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" type="text" value="knockdown"/>
                    <param name="countsFile" ftype="tabular" value="treated3fb.txt"/>
                </repeat>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" type="text" value="control"/>
                    <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/>
                </repeat>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" type="text" value="control"/>
                    <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
                </repeat>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" type="text" value="control"/>
                    <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
                </repeat>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" type="text" value="control"/>
                    <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/>
                </repeat>
            </repeat>
            <repeat name="rep_factorName">
                <param name="factorName" value="libtype" ftype="bed"/>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" type="text" value="singleend"/>
                    <param name="countsFile" ftype="tabular" value="treated1fb.txt"/>
                </repeat>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" type="text" value="singleend"/>
                    <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/>
                </repeat>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" type="text" value="singleend"/>
                    <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
                </repeat>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" type="text" value="pairedend"/>
                    <param name="countsFile" ftype="tabular" value="treated2fb.txt"/>
                </repeat>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" type="text" value="pairedend"/>
                    <param name="countsFile" ftype="tabular" value="treated3fb.txt"/>
                </repeat>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" type="text" value="pairedend"/>
                    <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/>
                </repeat>
                <repeat name="rep_factorLevel">
                    <param name="factorLevel" type="text" value="pairedend"/>
                    <param name="countsFile" ftype="tabular" value="untreated4fb.txt"/>
                </repeat>
            </repeat>
            <param name="report" type="boolean" value="False"/>
            <param name="fdr_cutoff" value="0.05"/>
            <output name="dexseq_out" file="DEXSeq_result_file.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help>

.. class:: infomark

**What it does**