Mercurial > repos > iuc > schicexplorer_schicplotconsensusmatrices
comparison scHicPlotConsensusMatrices.xml @ 1:259899fbb6ae draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
| author | iuc |
|---|---|
| date | Tue, 10 Mar 2020 15:09:29 -0400 |
| parents | 1a1e085c352e |
| children | 95b1216e1e70 |
comparison
equal
deleted
inserted
replaced
| 0:1a1e085c352e | 1:259899fbb6ae |
|---|---|
| 6 </macros> | 6 </macros> |
| 7 <expand macro="requirements" /> | 7 <expand macro="requirements" /> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 @BINARY@ | 9 @BINARY@ |
| 10 | 10 |
| 11 --matrix $matrix_mcooler | 11 --matrix $matrix_scooler |
| 12 #if $chromosomes: | 12 #if $chromosomes: |
| 13 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ]) | 13 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ]) |
| 14 --chromosomes $chromosome | 14 --chromosomes $chromosome |
| 15 #end if | 15 #end if |
| 16 | 16 |
| 26 | 26 |
| 27 && mv plot.$image_file_format plot | 27 && mv plot.$image_file_format plot |
| 28 | 28 |
| 29 ]]></command> | 29 ]]></command> |
| 30 <inputs> | 30 <inputs> |
| 31 <expand macro="matrix_mcooler_macro"/> | 31 <expand macro="matrix_scooler_macro"/> |
| 32 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> | 32 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> |
| 33 <expand macro="colormap" /> | 33 <expand macro="colormap" /> |
| 34 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/> | 34 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/> |
| 35 | 35 |
| 36 <param name="image_file_format" type="select" label="Image output format"> | 36 <param name="image_file_format" type="select" label="Image output format"> |
| 39 <option value="pdf">pdf</option> | 39 <option value="pdf">pdf</option> |
| 40 </param> | 40 </param> |
| 41 | 41 |
| 42 </inputs> | 42 </inputs> |
| 43 <outputs> | 43 <outputs> |
| 44 <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'> | 44 <data name='output_plot' from_work_dir='plot' format='png' label='Consensus matrix plot on ${on_string}'> |
| 45 <change_format> | 45 <change_format> |
| 46 <when input="image_file_format" value="svg" format="svg" /> | 46 <when input="image_file_format" value="svg" format="svg" /> |
| 47 <when input="image_file_format" value="pdf" format="pdf" /> | 47 <when input="image_file_format" value="pdf" format="pdf" /> |
| 48 </change_format> | 48 </change_format> |
| 49 </data> | 49 </data> |
| 50 </outputs> | 50 </outputs> |
| 51 <tests> | 51 <tests> |
| 52 <test> | 52 <test> |
| 53 <param name='matrix_mcooler' value='scHicConsensusMatrices/consensus_matrix.mcool' /> | 53 <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' /> |
| 54 <param name="image_file_format" value="png" /> | 54 <param name="image_file_format" value="png" /> |
| 55 <param name="dpi" value="300" /> | 55 <param name="dpi" value="300" /> |
| 56 <output name="output_plot" file="scHicPlotConsensusMatrices/plot.png" ftype="png" compare="sim_size" delta="35000"/> | 56 <output name="output_plot" file="scHicPlotConsensusMatrices/plot.png" ftype="png" compare="sim_size" delta="35000"/> |
| 57 </test> | 57 </test> |
| 58 <test> | 58 <test> |
| 59 <param name='matrix_mcooler' value='scHicConsensusMatrices/consensus_matrix.mcool' /> | 59 <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' /> |
| 60 <param name="image_file_format" value="png" /> | 60 <param name="image_file_format" value="png" /> |
| 61 <param name="dpi" value="300" /> | 61 <param name="dpi" value="300" /> |
| 62 <param name="chromosomes" value="chr1 chr2" /> | 62 <param name="chromosomes" value="chr1 chr2" /> |
| 63 | 63 |
| 64 <output name="output_plot" file="scHicPlotConsensusMatrices/plot_chr1_chr2.png" ftype="png" compare="sim_size" delta="35000"/> | 64 <output name="output_plot" file="scHicPlotConsensusMatrices/plot_chr1_chr2.png" ftype="png" compare="sim_size" delta="35000"/> |
| 68 <help><![CDATA[ | 68 <help><![CDATA[ |
| 69 | 69 |
| 70 Plot consensus matrices | 70 Plot consensus matrices |
| 71 ======================= | 71 ======================= |
| 72 | 72 |
| 73 scHicPlotConsensusMatrices plots the consensus (average) matrix of a cluster. | 73 scHicPlotConsensusMatrices plots the consensus (average) matrix of a cluster. This tool is useful to compare the single cell clusters. |
| 74 | 74 |
| 75 .. image:: $PATH_TO_IMAGES/consensus_svl_spectral.png | 75 .. image:: $PATH_TO_IMAGES/consensus_svl_spectral.png |
| 76 :width: 50% | 76 :width: 50% |
| 77 | 77 |
| 78 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ | 78 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ |