Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix
diff hicCorrectMatrix.xml @ 14:bccd04d7e35d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
| author | iuc |
|---|---|
| date | Mon, 09 Dec 2019 10:25:15 +0000 |
| parents | a33c2124979f |
| children | 3bd060bcefed |
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--- a/hicCorrectMatrix.xml Sat Jun 09 15:02:36 2018 -0400 +++ b/hicCorrectMatrix.xml Mon Dec 09 10:25:15 2019 +0000 @@ -6,58 +6,56 @@ </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - - hicCorrectMatrix + ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' && + + @BINARY@ $mode.mode_selector - --matrix '$matrix_h5_cooler' + --matrix 'matrix.$matrix_h5_cooler.ext' ## special: --chromosomes is optional, but if given needs at least one argument - #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomes ]) + #set chroms = ' '.join([ '\'' + str($var.chromosome) + '\'' for $var in $chromosomes ]) #if chroms - --chromosomes "$chroms" + --chromosomes $chroms #end if #if $mode.mode_selector == 'correct': - - --iterNum $mode.iterNum - --outFileName matrix.$mode.outputFormat + #if $mode.correctionMethod.correctionMethod_selector == 'ice': + --correctionMethod ICE + --iterNum $mode.correctionMethod.iterNum + - #if $mode.filterThreshold_low and $mode.filterThreshold_large: - --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large - #end if + #if $mode.correctionMethod.filterThreshold_low and $mode.correctionMethod.filterThreshold_large: + --filterThreshold $mode.correctionMethod.filterThreshold_low $mode.correctionMethod.filterThreshold_large + #end if - #if $mode.inflationCutoff: - --inflationCutoff $mode.inflationCutoff - #end if + #if $mode.correctionMethod.inflationCutoff: + --inflationCutoff $mode.correctionMethod.inflationCutoff + #end if - #if $mode.transCutoff: - --transCutoff $mode.transCutoff - #end if + #if $mode.correctionMethod.transCutoff: + --transCutoff $mode.correctionMethod.transCutoff + #end if - #if $mode.sequencedCountCutoff: - --sequencedCountCutoff $mode.sequencedCountCutoff + #if $mode.correctionMethod.sequencedCountCutoff: + --sequencedCountCutoff $mode.correctionMethod.sequencedCountCutoff + #end if + + $mode.correctionMethod.skipDiagonal + $mode.correctionMethod.perchr + #else: + --correctionMethod KR #end if - - $mode.skipDiagonal - $mode.perchr - - #elif $mode.mode_selector == 'merge_failed': + --outFileName matrix.$matrix_h5_cooler.ext + #elif $mode.mode_selector == 'diagnostic_plot': --plotName diagnostic_plot.png - --outMatrixFile corrected_matrix.npz.h5 + ##--outMatrixFile corrected_matrix.npz.h5 #if $mode.xMax: --xMax $mode.xMax #end if - #if $mode.filterThreshold_low and $mode.filterThreshold_large: - --filterThreshold '$mode.filterThreshold_low' '$mode.filterThreshold_large' - #end if - #else: - --plotName diagnostic_plot.png - #if $mode.xMax: - --xMax $mode.xMax - #end if + $mode.perchr #end if #if $mode.mode_selector == 'correct': - && mv matrix.$mode.outputFormat matrix + && mv matrix.$matrix_h5_cooler.ext matrix #end if ]]> </command> @@ -70,35 +68,44 @@ </param> <when value="diagnostic_plot"> <expand macro="xMax" /> + <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" + label="Compute statistics for each chromosome separately" /> </when> <when value="correct"> - <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500" - label="Number of iterations" /> + <conditional name='correctionMethod'> + <param name='correctionMethod_selector' type='select' label='Correction method'> + <option value='ice'>Iterative_correction (Imakaev)</option> + <option value='kr'>Knights-Ruiz</option> + </param> - <param argument="--inflationCutoff" name="inflationCutoff" type="float" optional="true" - label="Inflation cutoff" value="" - help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction. - For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction."/> + <when value='ice'> + <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500" + label="Number of iterations" /> - <param argument="--transCutoff" name="transCutoff" type="float" optional="true" - label="Trans region cutoff" value="" - help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05."/> + <param argument="--inflationCutoff" name="inflationCutoff" type="float" optional="true" + label="Inflation cutoff" value="" + help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction. + For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction."/> - <param argument="--sequencedCountCutoff" name="sequencedCountCutoff" optional="true" type="float" - label="Sequenced count cutoff" - help="Each bin receives a value indicating the fraction that is covered by reads. - A cutoff of 0.5 will discard all those bins that have less than half of the bin covered."/> + <param argument="--transCutoff" name="transCutoff" type="float" optional="true" + label="Trans region cutoff" value="" + help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05."/> - <param argument="--skipDiagonal" name="skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false" - label="Skip diagonal counts"/> + <param argument="--sequencedCountCutoff" name="sequencedCountCutoff" optional="true" type="float" + label="Sequenced count cutoff" + help="Each bin receives a value indicating the fraction that is covered by reads. + A cutoff of 0.5 will discard all those bins that have less than half of the bin covered."/> - <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" - label="Normalize each chromosome separately" /> - <expand macro="filterThreshold" /> - <param name='outputFormat' type='select' label="Output file format"> - <option value='h5'>HiCExplorer format</option> - <option value="cool">cool</option> - </param> + <param argument="--skipDiagonal" name="skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false" + label="Skip diagonal counts"/> + + <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" + label="Normalize each chromosome separately" /> + <expand macro="filterThreshold" /> + </when> + <when value='kr'> + </when> + </conditional> </when> </conditional> @@ -112,9 +119,9 @@ </inputs> <outputs> - <data name="outFileName" from_work_dir="matrix" format="h5"> + <data name="outFileName" from_work_dir="matrix" format="cool"> <change_format> - <when input="mode.outputFormat" value="cool" format="cool" /> + <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/> </change_format> <filter>mode['mode_selector'] == "correct"</filter> @@ -130,16 +137,63 @@ <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> <param name="mode_selector" value="correct"/> + <param name='correctionMethod_selector' value='ice'/> <repeat name="chromosomes"> <param name="chromosome" value="chrUextra"/> </repeat> <repeat name="chromosomes"> <param name="chromosome" value="chr3LHet"/> </repeat> - <param name='outputFormat' value='h5'/> <param name='filterThreshold_low' value='-2.0' /> <param name='filterThreshold_large' value='4' /> - <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/> + <output name="outFileName" ftype="h5"> + <assert_contents> + <has_h5_keys keys='correction_factors,intervals,matrix,nan_bins'/> + </assert_contents> + </output> + </test> + <test> + <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> + + <param name="mode_selector" value="correct"/> + <param name='correctionMethod_selector' value='kr'/> + + <output name="outFileName" ftype="h5"> + <assert_contents> + <has_h5_keys keys='correction_factors,intervals,matrix'/> + </assert_contents> + </output> + </test> + <test> + <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> + + <param name="mode_selector" value="correct"/> + <param name='correctionMethod_selector' value='kr'/> + + <output name="outFileName" ftype="cool"> + <assert_contents> + <has_h5_keys keys='bins,chroms,indexes,pixels'/> + </assert_contents> + </output> + </test> + <test> + <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> + + <param name="mode_selector" value="correct"/> + <param name='correctionMethod_selector' value='ice'/> + <repeat name="chromosomes"> + <param name="chromosome" value="chrUextra"/> + </repeat> + <repeat name="chromosomes"> + <param name="chromosome" value="chr3LHet"/> + </repeat> + <param name='filterThreshold_low' value='-2.0' /> + <param name='filterThreshold_large' value='4' /> + <output name="outFileName" ftype="h5"> + <assert_contents> + <has_h5_keys keys='correction_factors,intervals,matrix,nan_bins'/> + </assert_contents> + </output> </test> <test> <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> @@ -150,7 +204,7 @@ <repeat name="chromosomes"> <param name="chromosome" value="chr3LHet"/> </repeat> - <output name="diagnostic_plot" file="diagnostic_plot.png" ftype="png" compare="sim_size"/> + <output name="diagnostic_plot" file="hicCorrectMatrix/diagnostic_plot.png" ftype="png" compare="sim_size"/> </test> </tests> <help><![CDATA[ @@ -211,7 +265,7 @@ Correct _______ -Run the iterative correction and outputs the corrected matrix. This matrix can then be used with all downstream analysis tools such as ``hicPlotMatrix``, ``hicPlotTADs``, ``hicPlotViewpoint``, ``hicAggregateContacts`` for **visualization of Hi-C data**, ``hicCorrelate``, ``hicPlotDistVsCounts``, ``hicTransform``, ``hicFindTADs``, ``hicPCA`` **for data and scores computation on Hi-C data**. +Run the iterative correction and outputs the corrected matrix. This matrix can then be used with all downstream analysis tools such as ``hicPlotMatrix``, ``pyGenomeTracks``, ``hicPlotViewpoint``, ``hicAggregateContacts`` for **visualization of Hi-C data**, ``hicCorrelate``, ``hicPlotDistVsCounts``, ``hicTransform``, ``hicFindTADs``, ``hicPCA`` **for data and scores computation on Hi-C data**. It is noteworthy that ``hicSumMatrices`` and ``hicMergeMatrixBins`` **must be performed on uncorrected matrices**.