Mercurial > repos > bgruening > hicexplorer_hicpca
diff hicPCA.xml @ 8:b4b8343dd681 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
| author | bgruening |
|---|---|
| date | Mon, 16 Dec 2019 14:33:42 -0500 |
| parents | ebb9b94138c1 |
| children | 3ed8e85f4f4c |
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--- a/hicPCA.xml Mon Dec 16 08:36:03 2019 -0500 +++ b/hicPCA.xml Mon Dec 16 14:33:42 2019 -0500 @@ -6,14 +6,42 @@ </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ + ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' && + @BINARY@ --matrix 'matrix.$matrix_h5_cooler.ext' - hicPCA --matrix '$matrix_h5_cooler' + @CHROMOSOME_LIST@ --outputFileName pca1.$outputFormat pca2.$outputFormat --format $outputFormat + #if $norm: + $norm + #end if + + #if $extra_track_conditional.extra_track_selection == 'gene_density': + --extraTrack '$extra_track_conditional.extraTrack' + #elif $extra_track_conditional.extra_track_selection == 'histon_mark': + --extraTrack '$extra_track_conditional.extraTrack' + --histonMarkType '$extra_track_conditional.histonMarkType' + #end if + + #if $pearsonMatrix: + --pearsonMatrix pearson.$matrix_h5_cooler.ext + #end if + + #if $obsexpMatrix: + --obsexpMatrix obsexp.$matrix_h5_cooler.ext + #end if + && mv pca1.$outputFormat pca1 && mv pca2.$outputFormat pca2 + #if $pearsonMatrix: + && mv pearson.$matrix_h5_cooler.ext pearson + #end if + + #if $obsexpMatrix: + && mv obsexp.$matrix_h5_cooler.ext obsexp + #end if ]]> </command> @@ -24,11 +52,35 @@ <option value="bedgraph">bedgraph</option> </param> + <expand macro="chromosome_list" /> + + <param name='norm' type='boolean' truevalue='--norm' label='Use different expected value computation'/> + + <conditional name="extra_track_conditional"> + <param name='extra_track_selection' label='Extra track type' type='select'> + <option value='' selected='true'>No track</option> + <option value='gene_density'>Gene density</option> + <option value='histon_mark'>Histon mark coverage</option> + </param> + <when value='gene_density' > + <param name='extraTrack' type='data' format='bed' label='Correlate PCA with e.g. gene density or histon marks to flip sign'/> + </when> + <when value='histon_mark'> + <param name='extraTrack' type='data' format='bed' label='Correlate PCA with e.g. gene density or histon marks to flip sign'/> + <param name='histonMarkType' type='select' label="Histon mark type"> + <option value='active' selected="true">active</option> + <option value="inactive">inactive</option> + </param> + </when> + <when value='' /> + </conditional> + + <param name='pearsonMatrix' type='boolean' truevalue='--pearsonMatrix' falsevalue='' label='Return internally used Pearson matrix'/> + <param name='obsexpMatrix' type='boolean' truevalue='--obsexpMatrix' falsevalue='' label='Return internally used observed / expected matrix'/> + </inputs> <outputs> - <data name="pca1" from_work_dir="pca1" format="bigwig" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: PC1"> - <filter>outputFormat == 'bigwig'</filter> <change_format> <when input="outputFormat" value="bedgraph" format="bedgraph" /> </change_format> @@ -39,21 +91,79 @@ </change_format> </data> - + <data name="pearson_outfile" from_work_dir="pearson" format="cool"> + <filter>pearsonMatrix</filter> + <change_format> + <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/> + </change_format> + </data> + <data name="obsexp_outfile" from_work_dir="obsexp" format="cool"> + <filter>obsexpMatrix</filter> + <change_format> + <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/> + </change_format> + </data> </outputs> <tests> <test> - <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/> - <param name="outputFormat" value="bedgraph" /> - <output name="pca1" file="pca1.bedgraph" ftype="bedgraph" compare="sim_size"/> - <output name="pca2" file="pca2.bedgraph" ftype="bedgraph" compare="sim_size"/> + <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> + <param name="outputFormat" value="bigwig" /> + <conditional name="extra_track_conditional"> + <param name="extra_track_selection" value=""/> + </conditional> + + <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/> + <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/> + </test> + <test> + <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> + <param name="outputFormat" value="bigwig" /> + <conditional name="extra_track_conditional"> + <param name="extra_track_selection" value="gene_density"/> + <param name="extraTrack" value="dm3_genes.bed.gz" /> + </conditional> + + <repeat name="chromosome_list"> + <param name="chromosomes" value="chrX"/> + </repeat> + <repeat name="chromosome_list"> + <param name="chromosomes" value="chrXHet"/> + </repeat> + + <output name="pca1" file="hicPCA/pca1_test2.bw" ftype="bigwig" compare="sim_size" delta='40000'/> + <output name="pca2" file="hicPCA/pca2_test2.bw" ftype="bigwig" compare="sim_size" delta='40000'/> </test> <test> - <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/> + <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> <param name="outputFormat" value="bigwig" /> - <output name="pca1" file="pca1.bw" ftype="bigwig" compare="sim_size"/> - <output name="pca2" file="pca2.bw" ftype="bigwig" compare="sim_size"/> + <conditional name="extra_track_conditional"> + <param name="extra_track_selection" value=""/> + </conditional> + <param name='norm' value='True'/> + <param name='pearsonMatrix' value='True'/> + <param name='obsexpMatrix' value='True'/> + + <repeat name="chromosome_list"> + <param name="chromosomes" value="chrX"/> + </repeat> + <repeat name="chromosome_list"> + <param name="chromosomes" value="chrXHet"/> + </repeat> + + <output name="pca1" file="hicPCA/pca1_test3.bw" ftype="bigwig" compare="sim_size" delta='40000'/> + <output name="pca2" file="hicPCA/pca2_test3.bw" ftype="bigwig" compare="sim_size" delta='40000'/> + + <output name="pearson_outfile" ftype="h5"> + <assert_contents> + <has_h5_keys keys='intervals,matrix'/> + </assert_contents> + </output> + <output name="obsexp_outfile" ftype="h5"> + <assert_contents> + <has_h5_keys keys='intervals,matrix'/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[ @@ -78,7 +188,7 @@ Output ------ -Two files are outputed by **hicPCA**, one with the first (pca1) and one with the second (pca2) eigenvector as bigwig or bedgraph. These files can be plotted alongside Hi-C heatmaps, gene density or external datasets such as open chromatin or histone marks enrichment using ``hicPlotTADs`` or ``hicPlotMatrix``. +Two files are outputed by **hicPCA**, one with the first (pca1) and one with the second (pca2) eigenvector as bigwig or bedgraph. These files can be plotted alongside Hi-C heatmaps, gene density or external datasets such as open chromatin or histone marks enrichment using ``pyGenomeTracks`` or ``hicPlotMatrix``. For example, below you can find a ``hicPlotMatrix`` of the Pearson correlation matrix derived from a contact matrix for chromosome 6 in mouse computed with ``hicTransform`` (which is part of A/B compartments computation). The optional data track at the bottom shows the first eigenvector for A/B compartment obtained using **hicPCA**.