Mercurial > repos > bgruening > deeptools
diff computeMatrix.xml @ 10:135f3bae5c56 draft
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author | bgruening |
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date | Sat, 14 Dec 2013 03:29:29 -0500 |
parents | c53a73b8eef9 |
children | b4c5dd45778a |
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--- a/computeMatrix.xml Tue Dec 10 12:13:18 2013 -0500 +++ b/computeMatrix.xml Sat Dec 14 03:29:29 2013 -0500 @@ -1,6 +1,7 @@ -<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0"> +<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0.2"> <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description> <expand macro="requirements" /> + <expand macro="stdio" /> <macros> <import>deepTools_macros.xml</import> </macros> @@ -116,7 +117,7 @@ <when value="reference-point"> <param name="referencePoint" type="select" label="The reference point for the plotting"> <option value="TSS" selected="true">beginning of region (e.g. TSS)</option> - <option value="TES">end of region (e.g. TES)</option> + <option value="TES">end of region (e.g. TES)</option> <option value="center">center of region</option> </param> @@ -126,19 +127,8 @@ <param name="afterRegionStartLength" type="integer" value="1000" min="1" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/> </when> </conditional> - - <conditional name="output" > - <param name="showOutputSettings" type="select" label="Show additional output options" > - <option value="no" selected="true">no</option> - <option value="yes">yes</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="saveData" type="boolean" label="Save the averages per matrix column into a text file" help="This corresponds to the underlying data used to plot a summary profile."/> - <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" help="This matrix can easily be loaded into R or other programs."/> - <param name="saveSortedRegions" type="boolean" label="Save the regions after skiping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> - </when> - </conditional> + + <expand macro="graphic_output_settings" /> <conditional name="advancedOpt" > <param name="showAdvancedOpt" type="select" label="Show advanced options" > @@ -183,32 +173,8 @@ </inputs> <outputs> - <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix"> - </data> - <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> - <filter> - (( - output['showOutputSettings'] == 'yes' and - output['saveData'] is True - )) - </filter> - </data> - <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> - <filter> - (( - output['showOutputSettings'] == 'yes' and - output['saveMatrix'] is True - )) - </filter> - </data> - <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> - <filter> - (( - output['showOutputSettings'] == 'yes' and - output['saveSortedRegions'] is True - )) - </filter> - </data> + <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix" /> + <expand macro="output_graphic_outputs" /> </outputs> <!-- computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1