Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix
diff hicCorrectMatrix.xml @ 15:3bd060bcefed draft
"planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 91a0182476a7fc26be7bef1677790518c4e88348-dirty"
| author | bgruening |
|---|---|
| date | Mon, 16 Dec 2019 13:09:28 +0000 |
| parents | bccd04d7e35d |
| children | 9582c8c75c17 |
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--- a/hicCorrectMatrix.xml Mon Dec 09 10:25:15 2019 +0000 +++ b/hicCorrectMatrix.xml Mon Dec 16 13:09:28 2019 +0000 @@ -6,56 +6,58 @@ </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' && - - @BINARY@ + + hicCorrectMatrix $mode.mode_selector - --matrix 'matrix.$matrix_h5_cooler.ext' + --matrix '$matrix_h5_cooler' ## special: --chromosomes is optional, but if given needs at least one argument - #set chroms = ' '.join([ '\'' + str($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': - #if $mode.correctionMethod.correctionMethod_selector == 'ice': - --correctionMethod ICE - --iterNum $mode.correctionMethod.iterNum - + + --iterNum $mode.iterNum + --outFileName matrix.$mode.outputFormat - #if $mode.correctionMethod.filterThreshold_low and $mode.correctionMethod.filterThreshold_large: - --filterThreshold $mode.correctionMethod.filterThreshold_low $mode.correctionMethod.filterThreshold_large - #end if + #if $mode.filterThreshold_low and $mode.filterThreshold_large: + --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large + #end if - #if $mode.correctionMethod.inflationCutoff: - --inflationCutoff $mode.correctionMethod.inflationCutoff - #end if + #if $mode.inflationCutoff: + --inflationCutoff $mode.inflationCutoff + #end if - #if $mode.correctionMethod.transCutoff: - --transCutoff $mode.correctionMethod.transCutoff - #end if - - #if $mode.correctionMethod.sequencedCountCutoff: - --sequencedCountCutoff $mode.correctionMethod.sequencedCountCutoff - #end if + #if $mode.transCutoff: + --transCutoff $mode.transCutoff + #end if - $mode.correctionMethod.skipDiagonal - $mode.correctionMethod.perchr - #else: - --correctionMethod KR + #if $mode.sequencedCountCutoff: + --sequencedCountCutoff $mode.sequencedCountCutoff #end if - --outFileName matrix.$matrix_h5_cooler.ext - #elif $mode.mode_selector == 'diagnostic_plot': + + $mode.skipDiagonal + $mode.perchr + + #elif $mode.mode_selector == 'merge_failed': --plotName diagnostic_plot.png - ##--outMatrixFile corrected_matrix.npz.h5 + --outMatrixFile corrected_matrix.npz.h5 #if $mode.xMax: --xMax $mode.xMax #end if - $mode.perchr + #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 #end if #if $mode.mode_selector == 'correct': - && mv matrix.$matrix_h5_cooler.ext matrix + && mv matrix.$mode.outputFormat matrix #end if ]]> </command> @@ -68,44 +70,35 @@ </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"> - <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="--iterNum" name="iterNum" type="integer" optional="true" value="500" + label="Number of iterations" /> - <when value='ice'> - <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500" - label="Number of iterations" /> + <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="--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="--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="--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="--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="--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="--skipDiagonal" name="skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false" + label="Skip diagonal counts"/> - <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> + <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> </when> </conditional> @@ -119,9 +112,9 @@ </inputs> <outputs> - <data name="outFileName" from_work_dir="matrix" format="cool"> + <data name="outFileName" from_work_dir="matrix" format="h5"> <change_format> - <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/> + <when input="mode.outputFormat" value="cool" format="cool" /> </change_format> <filter>mode['mode_selector'] == "correct"</filter> @@ -137,63 +130,16 @@ <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" 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> + <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/> </test> <test> <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> @@ -204,7 +150,7 @@ <repeat name="chromosomes"> <param name="chromosome" value="chr3LHet"/> </repeat> - <output name="diagnostic_plot" file="hicCorrectMatrix/diagnostic_plot.png" ftype="png" compare="sim_size"/> + <output name="diagnostic_plot" file="diagnostic_plot.png" ftype="png" compare="sim_size"/> </test> </tests> <help><![CDATA[ @@ -265,7 +211,7 @@ Correct _______ -Run the iterative correction and outputs the corrected matrix. This matrix can then be used with all downstream analysis tools such as ``hicPlotMatrix``, ``pyGenomeTracks``, ``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``, ``hicPlotTADs``, ``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**.