Mercurial > repos > bgruening > hicexplorer_hicplotmatrix
diff hicPlotMatrix.xml @ 21:b63363075c2e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
| author | iuc |
|---|---|
| date | Wed, 18 Oct 2023 11:11:47 +0000 |
| parents | 9939786dd9c9 |
| children | 12d51d7be66f |
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--- a/hicPlotMatrix.xml Tue Jan 10 19:21:37 2023 +0000 +++ b/hicPlotMatrix.xml Wed Oct 18 11:11:47 2023 +0000 @@ -10,7 +10,7 @@ #if str($pca_conditional.pca_type) == 'bigwig': ln -s '$pca_conditional.pca_bigwig' pca.bw && #set $pca = '--bigwig pca.bw' - #elif str($pca_conditional.pca_type) == '': + #elif str($pca_conditional.pca_type) == 'no_file': #set $pca = '' #end if ln -s $matrix_h5_cooler matrix.$matrix_h5_cooler.ext && @@ -97,14 +97,19 @@ --increaseFigureHeight $increaseFigureHeight #end if - #if $loops: - --loops '$loops' + #if str($loop_conditional.loop_selector) == 'yes': + --loops $loop_conditional.loops + --loopLargeRegionsOperation $loop_conditional.loops_large_selector + #end if + + #if $tads: + --tads '$tads' #end if && mv plot.$image_file_format plot ]]> </command> <inputs> - <expand macro='matrix_h5_cooler_macro' /> + <expand macro="matrix_h5_cooler_macro" /> <param argument="--title" type="text" optional="true" label="Plot title"> <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator> @@ -132,29 +137,47 @@ <param argument="--fontSize" type="integer" optional="true" label="Font size" help="Fontsize in the plot for x and y axis." /> <param argument="--rotationX" type="integer" optional="true" label="Rotate x-labels by degree" help="Rotation in degrees for the labels of x-axis." /> <param argument="--rotationY" type="integer" optional="true" label="Rotate y-labels by degree" help="Rotation in degrees for the labels of y-axis." /> - <param argument="--increaseFigureWidth" type="float" value='0.5' optional="true" label="Increase figure width size" help="Plotting additional bigwig tracks can cause compression in x or y direction of the heatmap. Set this factor to a value unequal to 0 to correct this." /> - <param argument="--increaseFigureHeight" type="float" value='0.5' optional="true" label="Increase figure height size" help="Plotting additional bigwig tracks can cause compression in x or y direction of the heatmap. Set this factor to a value unequal to 0 to correct this." /> + <param argument="--increaseFigureWidth" type="float" value="0.5" optional="true" label="Increase figure width size" help="Plotting additional bigwig tracks can cause compression in x or y direction of the heatmap. Set this factor to a value unequal to 0 to correct this." /> + <param argument="--increaseFigureHeight" type="float" value="0.5" optional="true" label="Increase figure height size" help="Plotting additional bigwig tracks can cause compression in x or y direction of the heatmap. Set this factor to a value unequal to 0 to correct this." /> <expand macro="colormap" /> <param argument="--vMin" type="float" optional="true" label="vMin" help="Minimum value of the plotted score." /> <param argument="--vMax" type="float" optional="true" label="vMax" help="Maximum value of the plotted score." /> <conditional name="pca_conditional"> - <param name='pca_type' label='Datatype of eigenvector file' type='select'> - <option value='' selected="true">None</option> - <option value='bigwig'>bigwig</option> + <param name="pca_type" label="Datatype of eigenvector file" type="select"> + <option value="no_file" selected="true">No file</option> + <option value="bigwig">bigwig</option> </param> - <when value='' /> - <when value='bigwig'> - <param name='pca_bigwig' type="data" format="bigwig" label="Eigenvector file" /> + <when value="no_file" /> + <when value="bigwig"> + <param name="pca_bigwig" type="data" format="bigwig" label="Eigenvector file" /> <param argument="--vMinBigwig" type="float" optional="true" label="vMinBigwig" help="Minimum value of the plotted bigwig score." /> <param argument="--vMaxBigwig" type="float" optional="true" label="vMaxBigwig" help="Maximum value of the plotted bigwig score." /> - <param name='flipBigwigSign' type='boolean' optional="true" truevalue='--flipBigwigSign' falsevalue='' label='Flip the sign of the bigwig values' /> + <param name="flipBigwigSign" type="boolean" optional="true" truevalue="--flipBigwigSign" falsevalue="" label="Flip the sign of the bigwig values" /> <param argument="--scaleFactorBigwig" type="float" optional="true" label="Scale factor for bigwig" help="Scale the bigwig values by a factor." /> - <param name='bigwigAdditionalVerticalAxis' type='boolean' optional="true" truevalue='--bigwigAdditionalVerticalAxis' falsevalue='' label='Plot an additional vertical axis.' /> + <param name="bigwigAdditionalVerticalAxis" type="boolean" optional="true" truevalue="--bigwigAdditionalVerticalAxis" falsevalue="" label="Plot an additional vertical axis." /> </when> </conditional> - <param name='loops' type="data" format="interval" optional='True' label="Add detected loops" /> + <conditional name="loop_conditional"> + <param name="loop_selector" type="select" label="Plot loops"> + <option value="yes">Yes</option> + <option value="no" selected="True">No</option> + </param> + <when value="yes"> + <param name="loops" type="data" format="interval" optional="True" label="Add detected loops" /> + <param name="loops_large_selector" label="Start bin of the loop for plotting" type="select"> + <option value="first" selected="true">First</option> + <option value="center">Center</option> + <option value="last">Last</option> + </param> + </when> + <when value="no" /> + + </conditional> + <param name="loops" type="data" format="interval" optional="True" label="Add detected loops" /> + <param name="tads" type="data" format="interval" optional="True" label="Add detected tads" /> + <param name="image_file_format" type="select" label="Image output format"> <option value="png" selected="True">png</option> <option value="svg">svg</option> @@ -174,7 +197,7 @@ <test> <param name="matrix_h5_cooler" value="small_test_matrix.h5" /> <conditional name="pca_conditional"> - <param name="pca_type" value='' /> + <param name="pca_type" value="no_file" /> </conditional> <param name="region" value="chr2L:3000000-3500000" /> <param name="region2" value="chr2L:3100000-3600000" /> @@ -189,7 +212,7 @@ <param name="matrix_h5_cooler" value="small_test_matrix.cool" /> <param name="region" value="chr2L:3000000-3500000" /> <conditional name="pca_conditional"> - <param name="pca_type" value='' /> + <param name="pca_type" value="no_file" /> </conditional> <param name="image_file_format" value="pdf" /> <param name="dpi" value="10" /> @@ -198,14 +221,14 @@ <test> <param name="matrix_h5_cooler" value="small_test_matrix.cool" /> <conditional name="pca_conditional"> - <param name="pca_type" value='bigwig' /> + <param name="pca_type" value="bigwig" /> <param name="pca_bigwig" value="hicPCA/pca1_test1.bw" /> - <param name='vMinBigwig' value='10' /> - <param name='vMaxBigwig' value='20' /> - <param name='scaleFactorBigwig' value='2000' /> - <param name='flipBigwigSign' value='True' /> + <param name="vMinBigwig" value="10" /> + <param name="vMaxBigwig" value="20" /> + <param name="scaleFactorBigwig" value="2000" /> + <param name="flipBigwigSign" value="True" /> </conditional> - <param name='colormap' value='hot' /> + <param name="colormap" value="hot" /> <param name="region" value="chr2L:3000000-3500000" /> <param name="dpi" value="10" /> @@ -240,7 +263,7 @@ Contact matrix of *Drosophila melanogaster* embryos visualized using **hicPlotMatrix**. Hi-C matrix bins were merged to a 25 kb bin size using ``hicMergeMatrixBins`` and the matrix has then been corrected using ``hicCorrectMatrix`` before plotting. -Another example is available below using Hi-C data published by `Lieberman-Aiden <https://doi.org/10.1126/science.1181369>`_ in 2009, (`GSE18199 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18199>`_). A Hi-C contact matrix has been plotted with the ``--perChr`` option and the first eigenvector (pca1) computed by ``hicPCA``. For this plot a pearson correlated matrix was used, which is computed by first creating an observed / expected matrix and then a pearson correlation matrix with ``hicTransform``. +Another example is available below using Hi-C data published by `Lieberman-Aiden <https://pubmed.ncbi.nlm.nih.gov/19815776/>`_ in 2009, (`GSE18199 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18199>`_). A Hi-C contact matrix has been plotted with the ``--perChr`` option and the first eigenvector (pca1) computed by ``hicPCA``. For this plot a pearson correlated matrix was used, which is computed by first creating an observed / expected matrix and then a pearson correlation matrix with ``hicTransform``. .. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png :width: 70 %