diff chicDifferentialTest.xml @ 0:fa6fc09ba259 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chicDifferentialTest.xml	Mon Dec 16 14:36:01 2019 -0500
@@ -0,0 +1,122 @@
+<tool id="hicexplorer_chicdifferentialtest" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <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 &&
+
+        #for $file in $interactionFiles:
+            #set identifier = @ESCAPE_IDENTIFIER_FILE@
+            ln -s '$file' 'interactionFiles/$identifier' &&
+        #end for
+
+        #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 $alpha
+            --outputFolder differentialFolder
+            --threads @THREADS@
+    ]]></command>
+    <inputs>
+        <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
+
+        <conditional name="batchmode_conditional">
+            <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
+                <option value="optionBatchmode">Batch processing</option>
+                <option value="optionSinglemode" selected="True">Single file processing</option>
+            </param>
+            <when value="optionBatchmode">
+                <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/>
+            </when>
+            <when value="optionSinglemode">              
+            </when>
+        </conditional>
+        <param name='alpha' type="float" value='2.0' label="Alpha" help='Accept all samples to significance level alpha.'/> 
+        <param name="statisticTest_selector" type="select" label="Statistical test">
+                <option value="fisher" selected="True">Fisher exact</option>
+                <option value="chi2">Chi2 contingency</option>
+        </param>    
+    </inputs>
+    <outputs>
+        <collection name="differentialFolderCollection" type="list" label="Differential test files">
+            <discover_datasets pattern="__name__" format="interval"  directory="differentialFolder" />
+        </collection>
+        <data name="rejectedFileNames" from_work_dir="rejected_H0.txt" format="txt" label="${tool.name} rejected H0">
+            <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed"/>
+            
+            <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.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed" ftype="interval" lines_diff="4"/>
+                <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed" ftype="interval" lines_diff="4"/>
+                <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed" ftype="interval" lines_diff="4"/>
+
+
+                <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed" ftype="interval" lines_diff="4"/>
+                <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed" ftype="interval" lines_diff="4"/>
+                <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed" ftype="interval" lines_diff="4"/>
+               
+                <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed" ftype="interval" lines_diff="4"/>
+                <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed" ftype="interval" lines_diff="4"/>
+                <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed" 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>
+            <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed"/>
+            
+            <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.bed" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed" ftype="interval" lines_diff="4"/>
+                <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed" ftype="interval" lines_diff="4"/>
+                <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed" ftype="interval" lines_diff="4"/>
+            </output_collection>
+        </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. For this either Fisher's test or chi2 contingency test can be used.
+The files that are accepted 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>