Mercurial > repos > bgruening > hicexplorer_chicviewpoint
diff chicViewpoint.xml @ 6:dbfd2cfc0f66 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 15:06:55 +0000 |
| parents | 78b70d78a596 |
| children | f881c94fb3b3 |
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--- a/chicViewpoint.xml Fri Dec 11 21:00:03 2020 +0000 +++ b/chicViewpoint.xml Tue Mar 16 15:06:55 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.1"> +<tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>computes viewpoints with the given reference points and a background model.</description> <macros> <token name="@BINARY@">chicViewpoint</token> @@ -16,7 +16,6 @@ #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ]) @BINARY@ - --matrices $m --range $rangeUpstream $rangeDownstream --referencePoints '$referencePoints' @@ -35,32 +34,26 @@ && rm -rf interactionFiles #end if - ]]></command> + ]]> </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.' /> + <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." /> + </inputs> <outputs> <collection name="interactionFilesCollection" type="list" label="Interaction files"> - <discover_datasets pattern="__name__" format="interval" directory="interactionFiles" /> + <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> @@ -71,65 +64,104 @@ </outputs> <tests> <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="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" /> <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" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/> - - <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" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/> - <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/> + <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'/> - + <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"/> - - + <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" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/> - - <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" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/> - <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/> + <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'/> - + <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" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0' /> </test> </tests> <help><![CDATA[ @@ -148,6 +180,6 @@ For more information about HiCExplorer please consider our documentation on readthedocs.io_ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html -]]></help> +]]> </help> <expand macro="citations" /> </tool>