Mercurial > repos > bgruening > deeptools_bam_coverage

comparison deepTools_macros.xml @ 1:36f655a04a57 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
author bgruening
date Mon, 15 Feb 2016 10:27:58 -0500
parents 19a6007845cc
children 10e697ec9bfb
comparison
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0:19a6007845cc 1:36f655a04a57
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=[]