Mercurial > repos > bgruening > hicexplorer_hicpca
diff hicPCA.xml @ 14:3b5b54ed6392 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 15:05:22 +0000 |
| parents | c435572f7cf1 |
| children | 41dbf4d162a2 |
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--- a/hicPCA.xml Fri Dec 11 21:08:56 2020 +0000 +++ b/hicPCA.xml Tue Mar 16 15:05:22 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hicpca" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_hicpca" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>compute the principal components for A / B compartment analysis</description> <macros> <token name="@BINARY@">hicPCA</token> @@ -58,8 +58,8 @@ <expand macro="chromosome_list" /> - <param name='ligation_factor' type='boolean' truevalue='--ligation_factor' label='Multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation'/> - <param name='ignoreMaskedBins' type='boolean' truevalue='--ignoreMaskedBins' label='This option removes the masked bins before the PCA is computed'/> + <param name='ligation_factor' type='boolean' truevalue='--ligation_factor' label='Multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation' /> + <param name='ignoreMaskedBins' type='boolean' truevalue='--ignoreMaskedBins' label='This option removes the masked bins before the PCA is computed' /> <conditional name="extra_track_conditional"> <param name='extra_track_selection' label='Extra track type' type='select'> @@ -68,10 +68,10 @@ <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'/> + <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='extraTrack' type='data' format='bed,bigwig' 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> @@ -79,9 +79,8 @@ </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'/> + <param argument='--pearsonMatrix' type='boolean' truevalue='--pearsonMatrix' falsevalue='' label='Return internally used Pearson matrix' /> + <param argument='--obsexpMatrix' type='boolean' truevalue='--obsexpMatrix' falsevalue='' label='Return internally used observed / expected matrix' /> </inputs> <outputs> @@ -90,7 +89,7 @@ <when input="outputFormat" value="bedgraph" format="bedgraph" /> </change_format> </data> - <data name="pca2" from_work_dir="pca2" format="bigwig" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: PC2"> + <data name="pca2" from_work_dir="pca2" format="bigwig" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: PC2"> <change_format> <when input="outputFormat" value="bedgraph" format="bedgraph" /> </change_format> @@ -99,102 +98,103 @@ <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"/> + <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"/> + <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.cool"/> + <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=""/> + <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'/> + <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.cool"/> + <param name="matrix_h5_cooler" value="small_test_matrix.cool" /> <param name="outputFormat" value="bigwig" /> <param name="ligation_factor" value="True" /> <conditional name="extra_track_conditional"> - <param name="extra_track_selection" value=""/> + <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'/> + <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.cool"/> + <param name="matrix_h5_cooler" value="small_test_matrix.cool" /> <param name="outputFormat" value="bigwig" /> <param name="ignoreMaskedBins" value="True" /> <conditional name="extra_track_conditional"> - <param name="extra_track_selection" value=""/> + <param name="extra_track_selection" value="" /> </conditional> - <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='60000'/> - <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='60000'/> + <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='60000' /> + <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='60000' /> </test> <test> - <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> + <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="extra_track_selection" value="gene_density" /> <param name="extraTrack" value="dm3_genes.bed.gz" /> </conditional> <repeat name="chromosome_list"> - <param name="chromosomes" value="chrX"/> + <param name="chromosomes" value="chrX" /> </repeat> <repeat name="chromosome_list"> - <param name="chromosomes" value="chrXHet"/> + <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'/> + <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.h5"/> + <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=""/> + <param name="extra_track_selection" value="" /> </conditional> - <param name='pearsonMatrix' value='True'/> - <param name='obsexpMatrix' value='True'/> + <param name='pearsonMatrix' value='True' /> + <param name='obsexpMatrix' value='True' /> <repeat name="chromosome_list"> - <param name="chromosomes" value="chrX"/> + <param name="chromosomes" value="chrX" /> </repeat> <repeat name="chromosome_list"> - <param name="chromosomes" value="chrXHet"/> + <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="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'/> + <has_h5_keys keys='intervals,matrix' /> </assert_contents> </output> <output name="obsexp_outfile" ftype="h5"> <assert_contents> - <has_h5_keys keys='intervals,matrix'/> + <has_h5_keys keys='intervals,matrix' /> </assert_contents> </output> </test> </tests> <help><![CDATA[ + Principal component analysis ============================ @@ -229,6 +229,6 @@ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html .. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369 -]]></help> +]]> </help> <expand macro="citations" /> </tool>