Mercurial > repos > bgruening > deeptools_plot_pca
comparison deepTools_macros.xml @ 1:47bf2e1f065b draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
author | bgruening |
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date | Mon, 15 Feb 2016 10:32:55 -0500 |
parents | 7fb0a96e74c1 |
children | eae52f5abf7b |
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0:7fb0a96e74c1 | 1:47bf2e1f065b |
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70 label="Region of the genome to limit the operation to" | 70 label="Region of the genome to limit the operation to" |
71 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." /> | 71 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." /> |
72 </xml> | 72 </xml> |
73 | 73 |
74 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> | 74 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> |
75 <token name="@WRAPPER_VERSION@">2.0.1</token> | 75 <token name="@WRAPPER_VERSION@">2.1.0</token> |
76 <xml name="requirements"> | 76 <xml name="requirements"> |
77 <requirements> | 77 <requirements> |
78 <requirement type="package" version="2.7.10">python</requirement> | 78 <requirement type="package" version="2.7.10">python</requirement> |
79 <requirement type="binary">@BINARY@</requirement> | 79 <requirement type="binary">@BINARY@</requirement> |
80 <requirement type="package" version="2.0.1">deepTools</requirement> | 80 <requirement type="package" version="2.1.0">deepTools</requirement> |
81 <yield /> | 81 <yield /> |
82 </requirements> | 82 </requirements> |
83 <expand macro="stdio" /> | 83 <expand macro="stdio" /> |
84 <version_command>@BINARY@ --version</version_command> | 84 <version_command>@BINARY@ --version</version_command> |
85 </xml> | 85 </xml> |
102 <when value="no"> | 102 <when value="no"> |
103 <conditional name="clustering"> | 103 <conditional name="clustering"> |
104 <param name="clustering_options" type="select" label="Clustering algorithm"> | 104 <param name="clustering_options" type="select" label="Clustering algorithm"> |
105 <option value="none">No clustering</option> | 105 <option value="none">No clustering</option> |
106 <option value="kmeans">Kmeans clustering</option> | 106 <option value="kmeans">Kmeans clustering</option> |
107 <option value="hclust">Hierarchical clustering</option> | |
107 </param> | 108 </param> |
108 <when value="kmeans"> | 109 <when value="kmeans"> |
109 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" | 110 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" |
110 help="When this option is set, the matrix is split into clusters using the k-means algorithm. | 111 help="When this option is set, the matrix is split into clusters using the k-means algorithm. |
111 This only works for data that is not grouped, otherwise only the first group will be clustered. | 112 This only works for data that is not grouped, otherwise only the first group will be clustered. |
112 If more specific clustering methods are required it is advisable to save the underlying matrix and | 113 If more specific clustering methods are required it is advisable to save the underlying matrix and |
113 run the clustering using other software."/> | 114 run the clustering using other software."/> |
114 </when> | 115 </when> |
116 <when value="hclust"> | |
117 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute." | |
118 help="WARNING: This option causes the tool to run for a very long time! When this option is | |
119 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage. | |
120 This only works for data that is not grouped, otherwise only the first group will be clustered. | |
121 Note that you must have used the '--missingDataAsZero' option within computeMatrix! | |
122 If more specific clustering methods are required it is advisable to save the underlying matrix and | |
123 run the clustering using other software."/> | |
124 </when> | |
115 <when value="none" /> | 125 <when value="none" /> |
116 </conditional> | 126 </conditional> |
117 </when> | 127 </when> |
118 <when value="yes" /> | 128 <when value="yes" /> |
119 </conditional> | 129 </conditional> |
122 <token name="@KMEANS_CLUSTERING@"> | 132 <token name="@KMEANS_CLUSTERING@"> |
123 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': | 133 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': |
124 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': | 134 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': |
125 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: | 135 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: |
126 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans | 136 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans |
137 #end if | |
138 #end if | |
139 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust': | |
140 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0: | |
141 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust | |
127 #end if | 142 #end if |
128 #end if | 143 #end if |
129 #end if | 144 #end if |
130 </token> | 145 </token> |
131 | 146 |
291 <yield /> | 306 <yield /> |
292 </citations> | 307 </citations> |
293 </xml> | 308 </xml> |
294 | 309 |
295 <xml name="multiple_input_bams"> | 310 <xml name="multiple_input_bams"> |
311 <param argument="--bamfiles" type="data" format="bam" min="1" | |
312 label="Bam file" multiple="true" | |
313 help="The BAM file must be sorted."/> | |
314 </xml> | |
315 | |
316 <xml name="multiple_input_bams_min2"> | |
296 <param argument="--bamfiles" type="data" format="bam" min="2" | 317 <param argument="--bamfiles" type="data" format="bam" min="2" |
297 label="Bam file" multiple="true" | 318 label="Bam file" multiple="true" |
298 help="The BAM file must be sorted."/> | 319 help="The BAM file must be sorted."/> |
299 </xml> | 320 </xml> |
300 | 321 |
307 <xml name="plotTitle"> | 328 <xml name="plotTitle"> |
308 <param argument="--plotTitle" type="text" value="" size="30" optional="True" | 329 <param argument="--plotTitle" type="text" value="" size="30" optional="True" |
309 label="Title of the plot" | 330 label="Title of the plot" |
310 help="Title of the plot, to be printed on top of the generated image." /> | 331 help="Title of the plot, to be printed on top of the generated image." /> |
311 </xml> | 332 </xml> |
333 | |
312 | 334 |
313 <token name="@multiple_input_bams@"> | 335 <token name="@multiple_input_bams@"> |
314 <![CDATA[ | 336 <![CDATA[ |
315 #set files=[] | 337 #set files=[] |
316 #set labels=[] | 338 #set labels=[] |