annotate chicDifferentialTest.xml @ 4:126abc4b03f1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"

<tool id="hicexplorer_chicdifferentialtest" name="@BINARY@" version="@WRAPPER_VERSION@.1">
    <description>computes differential interactions of viewpoints</description>
    <macros>
        <token name="@BINARY@">chicDifferentialTest</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        #import re

        mkdir interactionFiles &&
        mkdir differentialFolder &&

        #if $tar_input_conditional.tar_input_selector == 'tar_input':
            ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar && 
            tar -C interactionFiles -xvf viewpoints.tar &&
        #else:
            #for $file in $tar_input_conditional.interactionFiles:
                #set identifier = @ESCAPE_IDENTIFIER_FILE@
                                    
                ln -s '$file' 'interactionFiles/$identifier' &&
            #end for
        #end if
        #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
            #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
        #end if
        @BINARY@
            #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
                --interactionFile $interactonfileslist
            #else:
                --interactionFile $batchmode_conditional.interactionFilesOrderFile
                --interactionFileFolder interactionFiles
                --batchMode
                --rejectedFileNamesToFile rejected_H0.txt
            #end if
            --statisticTest $statisticTest_selector
            --alpha $alpha
            --outputFolder differentialFolder
            --threads @THREADS@

            #if $tar:
                && cd differentialFolder
                && tar -cvf ../differentialFolder.tar *
                && cd ..
                && rm -rf differentialFolder
            #end  if
    ]]></command>
    <inputs>
        <conditional name="tar_input_conditional">
            <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">
                <option value="tar_input">tar file</option>
                <option value="interval_input" selected="True">Interval files</option>
            </param>
            <when value="tar_input">
        <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/>
            </when>
            <when value="interval_input">
        <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
            </when>
        </conditional>

        <conditional name="batchmode_conditional">
            <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
                <option value="optionBatchmode">Batch processing</option>
                <option value="optionSinglemode" selected="True">Single file processing</option>
            </param>
            <when value="optionBatchmode">
                <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/>
            </when>
            <when value="optionSinglemode">
            </when>
        </conditional>
        <param name='alpha' type="float" value='2.0' label="Alpha" help='Accept all samples to significance level alpha.'/>
        <param name="statisticTest_selector" type="select" label="Statistical test">
                <option value="fisher" selected="True">Fisher exact</option>
                <option value="chi2">Chi2 contingency</option>
        </param>
        <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file"
                help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/>
   
    </inputs>
    <outputs>
        <collection name="differentialFolderCollection" type="list" label="Differential test files">
            <discover_datasets pattern="__name__" format="interval"  directory="differentialFolder" />
        </collection>
        <data name="rejectedFileNames" from_work_dir="rejected_H0.txt" format="txt" label="${tool.name} rejected H0">
            <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
        </data>
        <data name="differentialFolderTar" from_work_dir="differentialFolder.tar" format="tar" label="Differential test files tar.gz">
            <filter>tar</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <conditional name="tar_input_conditional">
                <param name="tar_input_selector" value='interval_input'/>
                <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt"/>
            </conditional>

            <conditional name="batchmode_conditional">
                <param name="batchmode_selector" value='optionBatchmode'/>
                <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt'/>
            </conditional>
            <param name="statisticTest_selector" value='chi2'/>
            <param name="alpha" value='0.5'/>
            <output_collection name="differentialFolderCollection" type="list" count="9">
                <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt" ftype="interval" lines_diff="4"/>
                <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt" ftype="interval" lines_diff="4"/>
                <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt" ftype="interval" lines_diff="4"/>


                <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt" ftype="interval" lines_diff="4"/>
                <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt" ftype="interval" lines_diff="4"/>
                <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt" ftype="interval" lines_diff="4"/>

                <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt" ftype="interval" lines_diff="4"/>
                <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt" ftype="interval" lines_diff="4"/>
                <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt" ftype="interval" lines_diff="4"/>

            </output_collection>

            <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" compare="sim_size" delta='40000'/>
        </test>
        <test>
            <conditional name="tar_input_conditional">
                <param name="tar_input_selector" value='interval_input'/>
                <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt"/>

            </conditional>

            <conditional name="batchmode_conditional">
                <param name="batchmode_selector" value='optionSinglemode'/>
            </conditional>
            <param name="statisticTest_selector" value='fisher'/>
            <param name="alpha" value='0.5'/>

            <output_collection name="differentialFolderCollection" type="list" count="3">
                <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt" ftype="interval" lines_diff="4"/>
                <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt" ftype="interval" lines_diff="4"/>
                <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt" ftype="interval" lines_diff="4"/>
            </output_collection>
        </test>


        <test>
            <conditional name="tar_input_conditional">
                <param name="tar_input_selector" value='interval_input'/>
                <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt"/>
            </conditional>

            <conditional name="batchmode_conditional">
                <param name="batchmode_selector" value='optionBatchmode'/>
                <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt'/>
            </conditional>
            <param name="statisticTest_selector" value='chi2'/>
            <param name="alpha" value='0.5'/>
            <param name='tar' value='True'/>

            <output name="differentialFolderTar" file="cHi-C/chicDifferentialTest/batch_mode_chi2.tar" ftype='tar' compare="sim_size" delta='40000' />

            <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" compare="sim_size" delta='40000'/>
        </test>

        <test>
            <conditional name="tar_input_conditional">
                <param name="tar_input_selector" value='tar_input'/>
                <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode.tar"/>
            </conditional>

            <conditional name="batchmode_conditional">
                <param name="batchmode_selector" value='optionBatchmode'/>
                <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt'/>
            </conditional>
            <param name="statisticTest_selector" value='chi2'/>
            <param name="alpha" value='0.5'/>
            <param name='tar' value='True'/>

            <output name="differentialFolderTar" file="cHi-C/chicDifferentialTest/batch_mode_chi2.tar" ftype='tar' compare="sim_size" delta='40000' />

            <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" compare="sim_size" delta='40000'/>
        </test>
    </tests>
    <help><![CDATA[

Differential testing of two viewpoints
======================================

chicDifferentialTest tests if two locations under consideration of the reference point have a different interaction count. Either Fisher's test or chi2 contingency test can be used.
Input files for this test can be created with `chicAggregateStatistic`. H0 is assuming the interactions are not different. Therefore the differential interaction counts are all where H0 was rejected.


For more information about HiCExplorer please consider our documentation on readthedocs.io_

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
]]></help>
    <expand macro="citations" />
</tool>