diff chicSignificantInteractions.xml @ 8:640e0e45518a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 10:52:55 +0000
parents 6001400eed99
children
line wrap: on
line diff
--- a/chicSignificantInteractions.xml	Tue Jan 10 18:50:07 2023 +0000
+++ b/chicSignificantInteractions.xml	Wed Oct 18 10:52:55 2023 +0000
@@ -7,37 +7,11 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         #import re
-
-        mkdir interactionFiles &&
-        mkdir targetFolder &&
-        mkdir significantFilesFolder &&
-
-        #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
+      
+        @BINARY@
     
-        #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
-                --computeSampleNumber $batchmode_conditional.computeSampleNumber
-            #else:
-                --interactionFile '$batchmode_conditional.interactionFilesOrderFile'
-                --interactionFileFolder interactionFiles
-                --batchMode
-                --targetFileList targetListFile.txt
-                --writeFileNamesToFile significantFiles.txt
-                --computeSampleNumber $batchmode_conditional.computeSampleNumber
-            #end if
-
+            --interactionFile '$interactionFile'
+    
             --pValue $pvalue
 
             #if $filter_conditional.filter_selector == 'optionXfold':
@@ -47,280 +21,84 @@
 
             #end if
             --backgroundModelFile '$backgroundModelFile'
-            --resolution $resolution
             --peakInteractionsThreshold $peakInteractionsThreshold
             --range $rangeUpstream $rangeDownstream
-            --targetFolder targetFolder
-            --outputFolder significantFilesFolder
+            --combinationMode $mode_selector
+            --outFileNameSignificant significant.hdf5
+            --outFileNameTarget target.hdf5
             $truncateZeroPvalues
             --fixateRange $fixateRange
-            -suffix significant_interactions.txt
             --threads @THREADS@
 
-            #if $tar:
-                && cd targetFolder
-                && tar -cvf ../targetFolder.tar *
-                && cd ..
-                && rm -rf targetFolder
-
-                && cd significantFilesFolder
-                && tar -cvf ../significantFilesFolder.tar *
-                && cd ..
-                && rm -rf significantFilesFolder
-
-            #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" />
-                <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files." />
-            </when>
-            <when value="optionSinglemode">
-                <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files." />
-            </when>
-        </conditional>
-        <param name='pvalue' type="float" value='0.05' label="P-value of interaction to be accepted as significant" />
+        <param name="interactionFile" type="data" format="h5" label="The interaction data file created by chicViewpoint" />
+
+        <param name="pvalue" type="float" value="0.05" label="P-value of interaction to be accepted as significant" />
         <conditional name="filter_conditional">
             <param name="filter_selector" type="select" label="List of chromosomes or a BED file containg regions">
                 <option value="optionXfold">x-fold over mean background</option>
                 <option value="optionLoosePvalue" selected="True">Loose p-value (NB background)</option>
             </param>
             <when value="optionXfold">
-                <param name='xfold' type="float" value='2.0' label="X-fold over mean background to be accepted." help='Filter x-fold over background. Used to merge neighboring bins with a broader peak but
-                                                    less significant interactions to one peak with high significance. Used only for pValue option.' />
+                <param name="xfold" type="float" value="2.0" label="X-fold over mean background to be accepted." help="Filter x-fold over background. 
+                    Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance. Used only for pValue option." />
             </when>
             <when value="optionLoosePvalue">
-                <param name='loosePvalue' type="float" value='0.3' label="Loose p-value" help='loose p-value threshold value to filter target regions in a first round.
+                <param name="loosePvalue" type="float" value="0.3" label="Loose p-value" help="loose p-value threshold value to filter target regions in a first round.
                     Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance.
-                    Used only for pValue option.' />
+                    Used only for pValue option." />
             </when>
         </conditional>
-        <param argument="--backgroundModelFile" type="data" format='tabular' label="Background model" help="The background file computed by chicViewpointBackgroundModel" />
-        <param argument="--peakInteractionsThreshold" type="integer" value="5" label="Minimum interactions" help='The minimum number of interactions a detected peaks needs to have to be considered.' />
-        <param argument="--resolution" type="integer" value="1000" label="Bin resolution of the used data" help='Resolution of the bin in genomic units. Values are usually e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution.
-            This value is used to merge neighboring bins.' />
-        <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
-        <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
-        <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.' />
-        <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one." help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision." />
-        <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." />
+
+        <param argument="--backgroundModelFile" type="data" format="tabular" label="Background model" help="The background file computed by chicViewpointBackgroundModel" />
+        <param argument="--peakInteractionsThreshold" type="integer" value="5" label="Minimum interactions" help="The minimum number of interactions a detected peaks needs to have to be considered." />
+
+        <param name="mode_selector" type="select" label="Process matrices independently or combine always two (for differential analysis preparation)">
+                <option value="dual">Dual</option>
+                <option value="single" selected="True">Single</option>
+        </param>
+        <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." />
+        <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." />
+        <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help="Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin." />
+        <param name="truncateZeroPvalues" type="boolean" truevalue="--truncateZeroPvalues" falsevalue="" checked="false" label="Truncate zeros by setting them to one." help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision." />
     </inputs>
+
     <outputs>
-        <collection name="significantFilesCollection" type="list" label="Significant files">
-            <discover_datasets pattern="__name__" format="interval" directory="significantFilesFolder" />
-        </collection>
-        <collection name="targetFilesCollection" type="list" label="Target files">
-            <discover_datasets pattern="__name__" format="interval" directory="targetFolder" />
-        </collection>
-        <data name="significantFileNames" from_work_dir="significantFiles.txt" format="txt" label="${tool.name} significant file names">
-            <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
-        </data>
-        <data name="targetFileNames" from_work_dir="targetListFile.txt" format="txt" label="${tool.name} target file names">
-            <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
-        </data>
-        <data name="targetFolderTar" from_work_dir="targetFolder.tar" format="tar" label="Target files tar">
-            <filter>tar</filter>
-        </data>
-        <data name="significantFilesFolderTar" from_work_dir="significantFilesFolder.tar" format="tar" label="Significant files tar">
-            <filter>tar</filter>
-        </data>
+        <data name="significantFile" from_work_dir="significant.hdf5" format="h5" label="${tool.name} significant file" />
+        <data name="targetFile" from_work_dir="target.hdf5" format="h5" label="${tool.name} target file" />
     </outputs>
     <tests>
         <test>
-            <conditional name="tar_input_conditional">
-                <param name="tar_input_selector" value='interval_input' />
-                <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" />
-            </conditional>
-            <conditional name="batchmode_conditional">
-                <param name="batchmode_selector" value='optionBatchmode' />
-                <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
-                <param name="computeSampleNumber" value='2' />
-            </conditional>
-            <param name="pvalue" value='0.2' />
+            <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" />
+            <param name="pvalue" value="0.2" />
 
             <conditional name="filter_conditional">
-                <param name="filter_selector" value='optionLoosePvalue' />
-                <param name="loosePvalue" value='0.5' />
+                <param name="filter_selector" value="optionLoosePvalue" />
+                <param name="loosePvalue" value="0.5" />
             </conditional>
-
+            <param name="mode_selector" value="dual" />
             <param name="backgroundModelFile" value="cHi-C/background.txt" />
             <param name="rangeUpstream" value="200000" />
             <param name="rangeDownstream" value="200000" />
 
-            <output_collection name="significantFilesCollection" type="list" count="6">
-                <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval">
-                    <assert_contents>
-                        <has_text text="4480000" />
-                        <has_text text="chr1" />
-                        <has_text text="Sox17" />
-                        <has_text text="810.0" />
-                        <has_text text="interactions" />
-                    </assert_contents>
-                </element>
-                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval">
-                    <assert_contents>
-                        <has_text text="14274000" />
-                        <has_text text="chr1" />
-                        <has_text text="Eya1" />
-                        <has_text text="interactions" />
-                    </assert_contents>
-                </element>
-                <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval" lines_diff="4" />
-                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval">
-                    <assert_contents>
-                        <has_text text="4480000" />
-                        <has_text text="chr1" />
-                        <has_text text="Sox17" />
-                        <has_text text="interactions" />
-                        <has_text text="93000" />
-                        <has_text text="978.0" />
-                    </assert_contents>
-                </element>
-                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval" lines_diff="4" />
-                <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval">
-                    <assert_contents>
-                        <has_text text="19077000" />
-                        <has_text text="chr1" />
-                        <has_text text="Tfap2d" />
-                        <has_text text="interactions" />
-                        <has_text text="-15000" />
-                    </assert_contents>
-                </element>
-            </output_collection>
-            <output_collection name="targetFilesCollection" type="list" count="3">
-                <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt" ftype="interval">
-                    <assert_contents>
-                        <has_text text="4555000" />
-                        <has_text text="chr1" />
-                        <has_text text="p-value" />
-                        <has_text text="interactions" />
-                    </assert_contents>
-                </element>
-                <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4" />
-                <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt" ftype="interval">
-                    <assert_contents>
-                        <has_text text="19143000" />
-                        <has_text text="chr1" />
-                        <has_text text="p-value" />
-                        <has_text text="19150000" />
-                    </assert_contents>
-                </element>
-            </output_collection>
-            <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" />
-            <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" />
-        </test>
-        <test>
-            <conditional name="tar_input_conditional">
-                <param name="tar_input_selector" value='interval_input' />
-                <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" />
-            </conditional>
-            <conditional name="batchmode_conditional">
-                <param name="batchmode_selector" value='optionSinglemode' />
-                <param name="computeSampleNumber" value="1" />
-            </conditional>
-            <param name="pvalue" value='0.2' />
-
-            <conditional name="filter_conditional">
-                <param name="filter_selector" value='optionXfold' />
-                <param name="xfold" value='1.5' />
-            </conditional>
+            <output name="significantFile" ftype="h5">
+                <assert_contents>
+                    <has_h5_attribute key="combinationMode" value="dual" />
+                    <has_h5_attribute key="mode_preselection" value="loosePValue" />
+                    <has_h5_attribute key="type" value="significant" />
+                </assert_contents>
+            </output>
 
-            <param name="backgroundModelFile" value="cHi-C/background.txt" />
-            <param name="rangeUpstream" value="200000" />
-            <param name="rangeDownstream" value="200000" />
-
-            <output_collection name="significantFilesCollection" type="list" count="2">
-                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt" ftype="interval" lines_diff="4" />
-                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval">
-                    <assert_contents>
-                        <has_text text="14295000" />
-                        <has_text text="chr1" />
-                        <has_text text="Eya1" />
-                        <has_text text="interactions" />
-                    </assert_contents>
-                </element>
-            </output_collection>
-            <output_collection name="targetFilesCollection" type="list" count="2">
-                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4" />
-                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4" />
-            </output_collection>
+            <output name="targetFile" ftype="h5">
+                <assert_contents>
+                     <has_h5_attribute key="combinationMode" value="dual" />
+                    <has_h5_attribute key="mode_preselection" value="loosePValue" />
+                    <has_h5_attribute key="type" value="target" />
+                </assert_contents>
+            </output>
         </test>
-
-        <test>
-            <conditional name="tar_input_conditional">
-                <param name="tar_input_selector" value='interval_input' />
-                <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" />
-            </conditional>
-            <conditional name="batchmode_conditional">
-                <param name="batchmode_selector" value='optionBatchmode' />
-                <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
-                <param name="computeSampleNumber" value='2' />
-            </conditional>
-            <param name="pvalue" value='0.2' />
-
-            <conditional name="filter_conditional">
-                <param name="filter_selector" value='optionLoosePvalue' />
-                <param name="loosePvalue" value='0.5' />
-            </conditional>
-
-            <param name="backgroundModelFile" value="cHi-C/background.txt" />
-            <param name="rangeUpstream" value="200000" />
-            <param name="rangeDownstream" value="200000" />
-
-            <param name='tar' value='True' />
-
-            <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
-            <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
-            <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" />
-            <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" />
-        </test>
-
-        <test>
-            <conditional name="tar_input_conditional">
-                <param name="tar_input_selector" value='tar_input' />
-                <param name="interactionFiles" value="cHi-C/chicViewpoint/viewpoints.tar" />
-            </conditional>
-            <conditional name="batchmode_conditional">
-                <param name="batchmode_selector" value='optionBatchmode' />
-                <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
-                <param name="computeSampleNumber" value='2' />
-            </conditional>
-            <param name="pvalue" value='0.2' />
-
-            <conditional name="filter_conditional">
-                <param name="filter_selector" value='optionLoosePvalue' />
-                <param name="loosePvalue" value='0.5' />
-            </conditional>
-
-            <param name="backgroundModelFile" value="cHi-C/background.txt" />
-            <param name="rangeUpstream" value="200000" />
-            <param name="rangeDownstream" value="200000" />
-
-            <param name='tar' value='True' />
-
-            <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
-            <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
-
-            <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000' />
-            <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000' />
-        </test>
+      
     </tests>
     <help><![CDATA[