Mercurial > repos > bgruening > hicexplorer_hicconvertformat
diff hicConvertFormat.xml @ 8:c0737631eea1 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
| author | iuc |
|---|---|
| date | Wed, 18 Oct 2023 10:33:29 +0000 |
| parents | 2a24ce221cd7 |
| children |
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--- a/hicConvertFormat.xml Tue Jan 10 19:02:29 2023 +0000 +++ b/hicConvertFormat.xml Wed Oct 18 10:33:29 2023 +0000 @@ -39,6 +39,15 @@ --bedFileHicpro "matrix.bed" --inputFormat hicpro #end if + #if $xml_path.inputFormat_selector == 'option2Dtext': + --matrices "matrix.2Dtext" + #if $xml_path.resolutions: + #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_path.resolutions).split(" ") ]) + --resolutions $resolutions + #end if + --chromosomeSizes "chromosomeSizes.txt" + --inputFormat 2D-text + #end if #if $xml_path.inputFormat_selector == 'optionHic': --matrices "matrix.hic" #if $xml_path.resolutions: @@ -77,7 +86,12 @@ ln -s '$xml_path.matrixHicpro' "matrix.hicpro" && ln -s '$xml_path.bedHicpro' "matrix.bed" && #end if + #if $xml_path.inputFormat_selector == 'option2Dtext': + ln -s '$xml_path.matrix2Dtext' "matrix.2Dtext" && + ln -s '$xml_path.chromosomeSizes' "chromosomeSizes.txt" && + + #end if #if $xml_path.inputFormat_selector == 'optionHic': ln -s '$xml_path.matrixHic' "matrix.hic" && #end if @@ -87,6 +101,9 @@ --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' + #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'hicpro': + --bedFileHicpro intervalls.bed + #end if ### Set up links to matrices to have correct ending #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix': @@ -108,6 +125,10 @@ ln -s '$xml_path.matrix_h5_cooler' "matrix.hicpro" && ln -s '$xml_path.bedHicpro' "matrix.bed" && #end if + #if $xml_path.inputFormat_selector == 'option2Dtext': + ln -s '$xml_path.chromosomeSizes' "chromosomeSizes.txt" && + + #end if #if $xml_path.inputFormat_selector == 'optionHic': ln -s '$xml_path.matrix_h5_cooler' "matrix.hic" && #end if @@ -132,7 +153,19 @@ #end for #set $m = ' '.join([ '"%s_matrix.homer"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrixHomer) ]) #end if - #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro': + #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'option2Dtext': + #for $counter, $m in enumerate($xml_manyToOne.matrix2Dtext): + ln -s '$m' "${counter}_matrix.matrix2Dtext" && + #end for + #set $m = ' '.join([ '"%s_matrix.matrix2Dtext"' % $counter for $counter, $matrix in enumerate($xml_manyToOne.matrix2Dtext) ]) + #if $xml_manyToOne.resolutions: + #set $resolutions = ' '.join([ '"%s"' % $resolution for $resolution in str($xml_manyToOne.resolutions).split(" ") ]) + --resolutions $resolutions + #end if + --chromosomeSizes "chromosomeSizes.txt" + + #end if + #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro': #for $counter, $m in enumerate($xml_manyToOne.matrixHicpro): ln -s '$m' "${counter}_matrix.hicpro" && #end for @@ -171,6 +204,11 @@ --bedFileHicpro "matrix.bed" --inputFormat hicpro #end if + #if $xml_path.inputFormat_selector == 'option2Dtext': + --matrices "matrix.2Dtext" + --chromosomeSizes "chromosomeSizes.txt" + --inputFormat 2D-text + #end if #if $xml_path.inputFormat_selector == 'optionHic': --matrices "matrix.hic" --inputFormat hic @@ -189,7 +227,10 @@ #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHomer': --inputFormat homer #end if - + #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'option2Dtext': + + --inputFormat 2D-text + #end if #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHicpro': --inputFormat hicpro --bedFileHicpro '$bed' @@ -205,139 +246,180 @@ #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix': #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions': && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out + #else if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'hicpro': + && mv matrix.hicpro matrix_out #else: && mv 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' matrix_out #end if #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix': && mv matrix.mcool matrix_out #end if + ]]> </command> <inputs> - <conditional name="outputSingleMultiple_conditional"> <param name="outputSingleMultiple_selector" type="select" label="Choose output matrix type"> <option value="singleMatrix" selected="True">single matrix</option> <option value="multipleMatrix">multiple matrix</option> </param> - <when value='singleMatrix'> - <expand macro='convertFormat_single_macro' /> - <expand macro='convertFormat_single_output_macro' /> + <when value="singleMatrix"> + <expand macro="convertFormat_single_macro" /> + <expand macro="convertFormat_single_output_macro" /> </when> - <when value='multipleMatrix'> + <when value="multipleMatrix"> <conditional name="resolutionOrManyToOne_conditional"> <param name="resolutionOrManyToOne_selector" type="select" label="Choose input file type"> - <option value='resolution_option' >Create out of one matrix a multi matrix with diffrerent resolutions</option> - <option value='manyToOne_option'>Create out of n matrices one multi matrix</option> + <option value="resolution_option" >Create out of one matrix a multi matrix with diffrerent resolutions</option> + <option value="manyToOne_option">Create out of n matrices one multi matrix</option> </param> - <when value='resolution_option'> - <param name='resolutions' type='text' label='To be stored resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'"> - <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator> + <when value="resolution_option"> + <param name="resolutions" type="text" label="To be stored resolutions" help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'"> + <validator type="expression" message="Only numeric characters and a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator> </param> - <expand macro='convertFormat_single_macro' /> + <expand macro="convertFormat_single_macro" /> </when> - <when value='manyToOne_option'> - <expand macro='convertFormat_multiple_macro' /> + <when value="manyToOne_option"> + <expand macro="convertFormat_multiple_macro" /> </when> </conditional> </when> </conditional> - <param name='storeAppliedCorrection' type="boolean" truevalue="--store_applied_correction" falsevalue="" label="Store applied correction factors in column count" help="Option only for cool input files" /> - <param name='enforceInteger' type="boolean" truevalue="--enforce_integer" falsevalue="" label="Enforce integer for count column" help="Option only for cool input files" /> + <param name="storeAppliedCorrection" type="boolean" truevalue="--store_applied_correction" falsevalue="" label="Store applied correction factors in column count" help="Option only for cool input files" /> + <param name="enforceInteger" type="boolean" truevalue="--enforce_integer" falsevalue="" label="Enforce integer for count column" help="Option only for cool input files" /> </inputs> <outputs> - <data name='output_converted_matrix' from_work_dir='matrix_out' format='cool' label='Converted matrix'> - <filter>outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix'</filter> + <data name="output_converted_matrix" from_work_dir="matrix_out" format="cool" label="Converted matrix in cool format"> + <filter>outputSingleMultiple_conditional['outputSingleMultiple_selector'] == 'singleMatrix'</filter> <change_format> <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="h5" format="h5" /> <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="homer" format="zip" /> <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="ginteractions" format="tabular" /> + <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="hicpro" format="tabular" /> </change_format> </data> - <data name='output_converted_matrix_multi' from_work_dir='matrix_out' format='mcool' label='Converted matrix mcool'> - <filter>outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix'</filter> + <data name="output_converted_matrix_bed" from_work_dir="intervalls.bed" format="tabular" label="Converted matrix in tabular format"> + <filter>outputSingleMultiple_conditional['outputFormat_conditional']['outputFormat_selector'] == 'hicpro'</filter> + </data> + <data name="output_converted_matrix_multi" from_work_dir="matrix_out" format="mcool" label="Converted matrix in mcool format"> + <filter>outputSingleMultiple_conditional['outputSingleMultiple_selector'] == 'multipleMatrix'</filter> </data> </outputs> <tests> - <test> - <conditional name='outputSingleMultiple_conditional'> - <param name='outputSingleMultiple_selector' value='singleMatrix' /> - <conditional name='inputFormat_conditional'> - <param name='inputFormat_selector' value='optionCool' /> - <param name='matrix_h5_cooler' value='small_test_matrix.cool' /> + <test expect_num_outputs="1"> + <conditional name="outputSingleMultiple_conditional"> + <param name="outputSingleMultiple_selector" value="singleMatrix" /> + <conditional name="inputFormat_conditional"> + <param name="inputFormat_selector" value="optionCool" /> + <param name="matrix_h5_cooler" value="small_test_matrix.cool" /> </conditional> - <conditional name='outputFormat_conditional'> - <param name='outputFormat_selector' value='h5' /> + <conditional name="outputFormat_conditional"> + <param name="outputFormat_selector" value="h5" /> + </conditional> + </conditional> + <output name="output_converted_matrix" ftype="h5"> + <assert_contents> + <has_h5_keys keys="intervals,matrix,nan_bins" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <conditional name="outputSingleMultiple_conditional"> + <param name="outputSingleMultiple_selector" value="singleMatrix" /> + <conditional name="inputFormat_conditional"> + <param name="inputFormat_selector" value="option2Dtext" /> + <param name="matrix2Dtext" value="hicConvertFormat/GSM1436265_RAD21_ENCFF002EMQ.txt" /> + <param name="resolutions" value="10000" /> + <param name="chromosomeSizes" value="hicConvertFormat/hg19.chrom.sizes" /> + </conditional> + + <conditional name="outputFormat_conditional"> + <param name="outputFormat_selector" value="h5" /> </conditional> </conditional> <output name="output_converted_matrix" ftype="h5"> <assert_contents> - <has_h5_keys keys='intervals,matrix,nan_bins' /> + <has_h5_keys keys="intervals,matrix" /> </assert_contents> </output> </test> - <test> - <conditional name='outputSingleMultiple_conditional'> - <param name='outputSingleMultiple_selector' value='singleMatrix' /> - <conditional name='inputFormat_conditional'> - <param name='inputFormat_selector' value='optionH5' /> - <param name='matrix_h5_cooler' value='small_test_matrix.h5' /> + <test expect_num_outputs="1"> + <conditional name="outputSingleMultiple_conditional"> + <param name="outputSingleMultiple_selector" value="singleMatrix" /> + <conditional name="inputFormat_conditional"> + <param name="inputFormat_selector" value="optionH5" /> + <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> </conditional> - <conditional name='outputFormat_conditional'> - <param name='outputFormat_selector' value='cool' /> + <conditional name="outputFormat_conditional"> + <param name="outputFormat_selector" value="cool" /> </conditional> </conditional> <output name="output_converted_matrix" ftype="cool"> <assert_contents> - <has_h5_keys keys='bins,chroms,indexes,pixels' /> + <has_h5_keys keys="bins,chroms,indexes,pixels" /> </assert_contents> </output> </test> - <test> - <conditional name='outputSingleMultiple_conditional'> - <param name='outputSingleMultiple_selector' value='singleMatrix' /> - <conditional name='inputFormat_conditional'> - <param name='inputFormat_selector' value='optionCool' /> - <param name='matrix_h5_cooler' value='hicConvertFormat/small_test_matrix_chr4.cool' /> + <test expect_num_outputs="1"> + <conditional name="outputSingleMultiple_conditional"> + <param name="outputSingleMultiple_selector" value="singleMatrix" /> + <conditional name="inputFormat_conditional"> + <param name="inputFormat_selector" value="optionCool" /> + <param name="matrix_h5_cooler" value="hicConvertFormat/small_test_matrix_chr4.cool" /> </conditional> - <conditional name='outputFormat_conditional'> - <param name='outputFormat_selector' value='homer' /> + <conditional name="outputFormat_conditional"> + <param name="outputFormat_selector" value="homer" /> </conditional> </conditional> <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.homer" ftype="zip" compare="sim_size" delta="40000" /> </test> - <test> - <conditional name='outputSingleMultiple_conditional'> - <param name='outputSingleMultiple_selector' value='singleMatrix' /> - <conditional name='inputFormat_conditional'> - <param name='inputFormat_selector' value='optionCool' /> - <param name='matrix_h5_cooler' value='hicConvertFormat/small_test_matrix_chr4.cool' /> + <test expect_num_outputs="1"> + <conditional name="outputSingleMultiple_conditional"> + <param name="outputSingleMultiple_selector" value="singleMatrix" /> + <conditional name="inputFormat_conditional"> + <param name="inputFormat_selector" value="optionCool" /> + <param name="matrix_h5_cooler" value="hicConvertFormat/small_test_matrix_chr4.cool" /> </conditional> - <conditional name='outputFormat_conditional'> - <param name='outputFormat_selector' value='ginteractions' /> + <conditional name="outputFormat_conditional"> + <param name="outputFormat_selector" value="ginteractions" /> </conditional> </conditional> <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv" ftype="tabular" /> </test> - <test> - <conditional name='outputSingleMultiple_conditional'> - <param name='outputSingleMultiple_selector' value='multipleMatrix' /> - <conditional name='resolutionOrManyToOne_conditional'> - <param name='resolutionOrManyToOne_selector' value='resolution_option' /> - <param name='resolutions' value='5000 10000 20000' /> - <conditional name='inputFormat_conditional'> - <param name='inputFormat_selector' value='optionH5' /> - <param name='matrix_h5_cooler' value='small_test_matrix.h5' /> + <test expect_num_outputs="2"> + <conditional name="outputSingleMultiple_conditional"> + <param name="outputSingleMultiple_selector" value="singleMatrix" /> + <conditional name="inputFormat_conditional"> + <param name="inputFormat_selector" value="optionCool" /> + <param name="matrix_h5_cooler" value="hicConvertFormat/small_test_matrix_chr4.cool" /> + </conditional> + + <conditional name="outputFormat_conditional"> + <param name="outputFormat_selector" value="hicpro" /> + </conditional> + </conditional> + <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.hicpro" ftype="tabular" /> + <output name="output_converted_matrix_bed" file="hicConvertFormat/small_test_matrix_chr4.bed" ftype="tabular" /> + </test> + <test expect_num_outputs="2"> + <conditional name="outputSingleMultiple_conditional"> + <param name="outputSingleMultiple_selector" value="multipleMatrix" /> + <conditional name="resolutionOrManyToOne_conditional"> + <param name="resolutionOrManyToOne_selector" value="resolution_option" /> + <param name="resolutions" value="5000 10000 20000" /> + <conditional name="inputFormat_conditional"> + <param name="inputFormat_selector" value="optionH5" /> + <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> </conditional> </conditional> </conditional> - <output name="output_converted_matrix" ftype="cool"> + <output name="output_converted_matrix_multi" ftype="mcool"> <assert_contents> - <has_h5_keys keys='resolutions' /> + <has_h5_keys keys="resolutions" /> </assert_contents> </output> </test>