Mercurial > repos > bgruening > hicexplorer_hicpca
comparison hicPCA.xml @ 9:3ed8e85f4f4c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
| author | bgruening |
|---|---|
| date | Wed, 05 Feb 2020 19:41:11 -0500 |
| parents | b4b8343dd681 |
| children | c435572f7cf1 |
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| 8:b4b8343dd681 | 9:3ed8e85f4f4c |
|---|---|
| 12 @CHROMOSOME_LIST@ | 12 @CHROMOSOME_LIST@ |
| 13 | 13 |
| 14 --outputFileName pca1.$outputFormat pca2.$outputFormat | 14 --outputFileName pca1.$outputFormat pca2.$outputFormat |
| 15 --format $outputFormat | 15 --format $outputFormat |
| 16 | 16 |
| 17 #if $norm: | 17 #if $ligation_factor: |
| 18 $norm | 18 $ligation_factor |
| 19 #end if | |
| 20 | |
| 21 #if $ignoreMaskedBins: | |
| 22 $ignoreMaskedBins | |
| 19 #end if | 23 #end if |
| 20 | 24 |
| 21 #if $extra_track_conditional.extra_track_selection == 'gene_density': | 25 #if $extra_track_conditional.extra_track_selection == 'gene_density': |
| 22 --extraTrack '$extra_track_conditional.extraTrack' | 26 --extraTrack '$extra_track_conditional.extraTrack' |
| 23 #elif $extra_track_conditional.extra_track_selection == 'histon_mark': | 27 #elif $extra_track_conditional.extra_track_selection == 'histon_mark': |
| 52 <option value="bedgraph">bedgraph</option> | 56 <option value="bedgraph">bedgraph</option> |
| 53 </param> | 57 </param> |
| 54 | 58 |
| 55 <expand macro="chromosome_list" /> | 59 <expand macro="chromosome_list" /> |
| 56 | 60 |
| 57 <param name='norm' type='boolean' truevalue='--norm' label='Use different expected value computation'/> | 61 <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'/> |
| 62 <param name='ignoreMaskedBins' type='boolean' truevalue='--ignoreMaskedBins' label='This option removes the masked bins before the PCA is computed'/> | |
| 58 | 63 |
| 59 <conditional name="extra_track_conditional"> | 64 <conditional name="extra_track_conditional"> |
| 60 <param name='extra_track_selection' label='Extra track type' type='select'> | 65 <param name='extra_track_selection' label='Extra track type' type='select'> |
| 61 <option value='' selected='true'>No track</option> | 66 <option value='' selected='true'>No track</option> |
| 62 <option value='gene_density'>Gene density</option> | 67 <option value='gene_density'>Gene density</option> |
| 114 | 119 |
| 115 <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/> | 120 <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/> |
| 116 <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/> | 121 <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/> |
| 117 </test> | 122 </test> |
| 118 <test> | 123 <test> |
| 124 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> | |
| 125 <param name="outputFormat" value="bigwig" /> | |
| 126 <param name="ligation_factor" value="True" /> | |
| 127 | |
| 128 <conditional name="extra_track_conditional"> | |
| 129 <param name="extra_track_selection" value=""/> | |
| 130 </conditional> | |
| 131 | |
| 132 <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/> | |
| 133 <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/> | |
| 134 </test> | |
| 135 <test> | |
| 136 <param name="matrix_h5_cooler" value="small_test_matrix.cool"/> | |
| 137 <param name="outputFormat" value="bigwig" /> | |
| 138 <param name="ignoreMaskedBins" value="True" /> | |
| 139 | |
| 140 <conditional name="extra_track_conditional"> | |
| 141 <param name="extra_track_selection" value=""/> | |
| 142 </conditional> | |
| 143 | |
| 144 <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='60000'/> | |
| 145 <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='60000'/> | |
| 146 </test> | |
| 147 <test> | |
| 119 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> | 148 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> |
| 120 <param name="outputFormat" value="bigwig" /> | 149 <param name="outputFormat" value="bigwig" /> |
| 121 <conditional name="extra_track_conditional"> | 150 <conditional name="extra_track_conditional"> |
| 122 <param name="extra_track_selection" value="gene_density"/> | 151 <param name="extra_track_selection" value="gene_density"/> |
| 123 <param name="extraTrack" value="dm3_genes.bed.gz" /> | 152 <param name="extraTrack" value="dm3_genes.bed.gz" /> |
| 138 | 167 |
| 139 <param name="outputFormat" value="bigwig" /> | 168 <param name="outputFormat" value="bigwig" /> |
| 140 <conditional name="extra_track_conditional"> | 169 <conditional name="extra_track_conditional"> |
| 141 <param name="extra_track_selection" value=""/> | 170 <param name="extra_track_selection" value=""/> |
| 142 </conditional> | 171 </conditional> |
| 143 <param name='norm' value='True'/> | |
| 144 <param name='pearsonMatrix' value='True'/> | 172 <param name='pearsonMatrix' value='True'/> |
| 145 <param name='obsexpMatrix' value='True'/> | 173 <param name='obsexpMatrix' value='True'/> |
| 146 | 174 |
| 147 <repeat name="chromosome_list"> | 175 <repeat name="chromosome_list"> |
| 148 <param name="chromosomes" value="chrX"/> | 176 <param name="chromosomes" value="chrX"/> |