Mercurial > repos > bgruening > hicexplorer_chicviewpoint
diff chicViewpoint.xml @ 8:f881c94fb3b3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
| author | iuc |
|---|---|
| date | Wed, 18 Oct 2023 10:44:35 +0000 |
| parents | dbfd2cfc0f66 |
| children |
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--- a/chicViewpoint.xml Tue Jan 10 19:01:02 2023 +0000 +++ b/chicViewpoint.xml Wed Oct 18 10:44:35 2023 +0000 @@ -8,7 +8,6 @@ <command detect_errors="exit_code"><![CDATA[ #import re - mkdir interactionFiles && #for $m in $matrix_h5_cooler_multiple: #set identifier = @ESCAPE_IDENTIFIER_M@ ln -s '$m' '$identifier' && @@ -21,46 +20,24 @@ --referencePoints '$referencePoints' --averageContactBin $averageContactBin --fixateRange $fixateRange - --decimalPlaces $decimalPlaces --threads @THREADS@ --backgroundModelFile '$backgroundModelFile' - --outputFolder interactionFiles - $writeFileNamesToFile - - #if $tar: - && cd interactionFiles - && tar -cvf ../viewpoints.tar . - && cd .. - && rm -rf interactionFiles - #end if + --outFileName interactionFiles.hdf5 ]]> </command> <inputs> <expand macro="matrix_h5_cooler_multiple_macro" /> - <param argument="--referencePoints" type="data" format='interval' label="Reference points" help="Bed file contains all reference points which should be used to create viewpoints." /> - <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="--referencePoints" type="data" format="interval" label="Reference points" help="Bed file contains all reference points which should be used to create viewpoints." /> + <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="--backgroundModelFile" type="data" format='tabular' label="Background model" help="The background file computed by chicViewpointBackgroundModel" /> - <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.' /> - <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 argument="--decimalPlaces" type="integer" value="12" label="Decimal places for output" help='Decimal places for all floating value in the output.' /> - - <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt' falsevalue="" checked="false" label="Save interaction file names (batch processing)" help="Set this parameter if you want to use the batch processing mode for the further analysis." /> - <param name='tar' type='boolean' checked="false" 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="--averageContactBin" type="integer" value="5" label="Average contacts window size" help="Average the contacts of n bins via a sliding window approach." /> + <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." /> </inputs> <outputs> - <collection name="interactionFilesCollection" type="list" label="Interaction files"> - <discover_datasets pattern="__name__" format="interval" directory="interactionFiles" /> - </collection> - <data name="interactionFileNames" from_work_dir="interactionFiles.txt" format="txt" label="${tool.name} interaction file names"> - <filter>writeFileNamesToFile</filter> - </data> - <data name="interactionFilesTar" from_work_dir="viewpoints.tar" format="tar" label="${tool.name} interaction file names tar"> - <filter>tar</filter> - </data> + <data name="interactionFileNames" from_work_dir="interactionFiles.hdf5" format="h5" label="${tool.name} interaction file" /> </outputs> <tests> <test> @@ -70,98 +47,15 @@ <param name="fixateRange" value="500000" /> <param name="rangeUpstream" value="200000" /> <param name="rangeDownstream" value="200000" /> - <param name="writeFileNamesToFile" value="True" /> - - <output_collection name="interactionFilesCollection" type="list" count="6"> - <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3" /> - <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3" /> - <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval"> - <assert_contents> - <has_text text="18895000" /> - <has_text text="chr1" /> - <has_text text="Tfap2d" /> - <has_text text="interactions" /> - <has_text text="472.0" /> - </assert_contents> - </element> - <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3" /> - <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval"> - <assert_contents> - <has_text text="14100000" /> - <has_text text="chr1" /> - <has_text text="Eya1" /> - <has_text text="interactions" /> - <has_text text="832.0" /> - </assert_contents> - </element> - <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval"> - <assert_contents> - <has_text text="4455000" /> - <has_text text="chr1" /> - <has_text text="Sox17" /> - <has_text text="interactions" /> - <has_text text="978.0" /> - <has_text text="-30000" /> - </assert_contents> - </element> - </output_collection> - <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0' /> - </test> - <test> - <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" /> - <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" /> - <param name="backgroundModelFile" value="cHi-C/background.txt" /> - <param name="fixateRange" value="500000" /> - <param name="rangeUpstream" value="200000" /> - <param name="rangeDownstream" value="200000" /> - <param name="writeFileNamesToFile" value="False" /> - <output_collection name="interactionFilesCollection" type="list" count="6"> - <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3" /> - <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3" /> - <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval"> - <assert_contents> - <has_text text="18893000" /> - <has_text text="chr1" /> - <has_text text="Tfap2d" /> - <has_text text="interactions" /> - <has_text text="472.0" /> - </assert_contents> - </element> - <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3" /> - <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval"> - <assert_contents> - <has_text text="14103000" /> - <has_text text="chr1" /> - <has_text text="Eya1" /> - <has_text text="interactions" /> - <has_text text="832.0" /> - <has_text text="-199000" /> - </assert_contents> - </element> - <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval"> - <assert_contents> - <has_text text="4455000" /> - <has_text text="chr1" /> - <has_text text="Sox17" /> - <has_text text="interactions" /> - <has_text text="978.0" /> - <has_text text="-30000" /> - </assert_contents> - </element> - </output_collection> - <!-- <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> --> - </test> - <test> - <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" /> - <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" /> - <param name="backgroundModelFile" value="cHi-C/background.txt" /> - <param name="fixateRange" value="500000" /> - <param name="rangeUpstream" value="200000" /> - <param name="rangeDownstream" value="200000" /> - <param name="writeFileNamesToFile" value="True" /> - <param name='tar' value='True' /> - <output name="interactionFilesTar" file="cHi-C/chicViewpoint/viewpoints.tar" ftype='tar' compare="sim_size" delta='40000' /> - <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0' /> + <output name="interactionFileNames" ftype="h5"> + <assert_contents> + <has_h5_attribute key="averageContactBin" value="5" /> + <has_h5_attribute key="fixateRange" value="500000" /> + <!-- <has_h5_attribute key="range" value="200000,200000" /> --> + <has_h5_attribute key="resolution" value="1000" /> + <has_h5_attribute key="type" value="interactions" /> + </assert_contents> + </output> </test> </tests> <help><![CDATA[