Mercurial > repos > bgruening > hicexplorer_hicconvertformat
diff hicConvertFormat.xml @ 6:3e598b8e72e7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 15:38:11 +0000 |
| parents | 2f62a87d4017 |
| children | 2a24ce221cd7 |
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--- a/hicConvertFormat.xml Fri Dec 11 21:25:02 2020 +0000 +++ b/hicConvertFormat.xml Tue Mar 16 15:38:11 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hicconvertformat" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_hicconvertformat" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Convert between different file formats</description> <macros> <token name="@BINARY@">hicConvertFormat</token> @@ -55,49 +55,43 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - ## single to single case - #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix': #set xml_path = $outputSingleMultiple_conditional.inputFormat_conditional #if $xml_path.inputFormat_selector == 'optionCool': - ln -s "$xml_path.matrix_h5_cooler" "matrix.cool" && + ln -s '$xml_path.matrix_h5_cooler' "matrix.cool" && #end if #if $xml_path.inputFormat_selector == 'optionH5': - ln -s "$xml_path.matrix_h5_cooler" "matrix.h5" && + ln -s '$xml_path.matrix_h5_cooler' "matrix.h5" && #end if #if $xml_path.inputFormat_selector == 'optionHomer': - ln -s "$xml_path.matrixHomer" "matrix.homer" && + ln -s '$xml_path.matrixHomer' "matrix.homer" && #end if #if $xml_path.inputFormat_selector == 'optionHicpro': - ln -s "$xml_path.matrixHicpro" "matrix.hicpro" && - ln -s "$xml_path.bedHicpro" "matrix.bed" && + ln -s '$xml_path.matrixHicpro' "matrix.hicpro" && + ln -s '$xml_path.bedHicpro' "matrix.bed" && #end if #if $xml_path.inputFormat_selector == 'optionHic': - ln -s "$xml_path.matrixHic" "matrix.hic" && + ln -s '$xml_path.matrixHic' "matrix.hic" && #end if - - @BINARY@ @SINGLE_INPUT@ - --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions': && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out - #else: - && mv "matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" matrix_out + && mv 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' matrix_out #end if #end if @@ -107,27 +101,23 @@ #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option': #set xml_path = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.inputFormat_conditional #if $xml_path.inputFormat_selector == 'optionCool': - ln -s "$xml_path.matrix_h5_cooler" "matrix.cool" && + ln -s '$xml_path.matrix_h5_cooler' "matrix.cool" && #end if #if $xml_path.inputFormat_selector == 'optionH5': - ln -s "$xml_path.matrix_h5_cooler" "matrix.h5" && - + ln -s '$xml_path.matrix_h5_cooler' "matrix.h5" && #end if #if $xml_path.inputFormat_selector == 'optionHomer': - ln -s "$xml_path.matrix_h5_cooler" "matrix.homer" && - + ln -s '$xml_path.matrix_h5_cooler' "matrix.homer" && #end if #if $xml_path.inputFormat_selector == 'optionHicpro': - ln -s "$xml_path.matrix_h5_cooler" "matrix.hicpro" && - ln -s "$xml_path.bedHicpro" "matrix.bed" && - + ln -s '$xml_path.matrix_h5_cooler' "matrix.hicpro" && + ln -s '$xml_path.bedHicpro' "matrix.bed" && #end if #if $xml_path.inputFormat_selector == 'optionHic': - ln -s "$xml_path.matrix_h5_cooler" "matrix.hic" && - + ln -s '$xml_path.matrix_h5_cooler' "matrix.hic" && #end if #else: #set xml_manyToOne = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional @@ -179,12 +169,10 @@ #if $xml_path.inputFormat_selector == 'optionH5': --matrices "matrix.h5" --inputFormat h5 - #end if #if $xml_path.inputFormat_selector == 'optionHomer': --matrices "matrix.homer" --inputFormat homer - #end if #if $xml_path.inputFormat_selector == 'optionHicpro': --matrices "matrix.hicpro" @@ -206,7 +194,6 @@ --inputFormat h5 #end if - #if $xml_manyToOne.inputFormat_conditional.inputFormat_selector == 'optionHomer': --inputFormat homer #end if @@ -220,10 +207,7 @@ #end if --outFileName matrix.mcool && mv matrix.mcool matrix_out - #end if - - ]]> </command> <inputs> @@ -241,29 +225,30 @@ <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='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'/> + <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> + </param> <expand macro='convertFormat_single_macro' /> </when> <when value='manyToOne_option'> <expand macro='convertFormat_multiple_macro' /> </when> </conditional> - <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count'/> - <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column'/> + <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' /> + <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' /> </when> </conditional> </inputs> <outputs> - <data name='output_converted_matrix' from_work_dir='matrix_out' format='cool' label='Converted matrix'> <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="tsv" /> + <when input="outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector" value="ginteractions" format="tabular" /> </change_format> </data> <data name='output_converted_matrix_multi' from_work_dir='matrix_out' format='mcool' label='Converted matrix mcool'> @@ -273,84 +258,83 @@ <tests> <test> <conditional name='outputSingleMultiple_conditional'> - <param name='outputSingleMultiple_selector' value='singleMatrix'/> + <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'/> + <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'/> + <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,nan_bins' /> </assert_contents> </output> </test> <test> <conditional name='outputSingleMultiple_conditional'> - <param name='outputSingleMultiple_selector' value='singleMatrix'/> + <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'/> + <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'/> + <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'/> + <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'/> + <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'/> + <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"/> + <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'/> + <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'/> + <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'/> + <param name='outputFormat_selector' value='ginteractions' /> </conditional> </conditional> - <output name="output_converted_matrix" file="hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv" ftype="tsv" compare="sim_size" delta="40000"/> - + <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'/> + <param name='outputSingleMultiple_selector' value='multipleMatrix' /> <conditional name='resolutionOrManyToOne_conditional'> - <param name='resolutionOrManyToOne_selector' value='resolution_option'/> - <param name='resolutions' value='5000 10000 20000'/> + <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'/> + <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"> <assert_contents> - <has_h5_keys keys='resolutions'/> + <has_h5_keys keys='resolutions' /> </assert_contents> </output> </test> @@ -370,6 +354,6 @@ | 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>