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comparison ideas.xml @ 93:0c2cf49dfb58 draft

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Uploaded
author greg
date Tue, 29 Aug 2017 13:05:25 -0400
parents 6f8af8e816d0
children 7d9af0d824ad
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92:917ad9574312 93:0c2cf49dfb58
82 -minerr $minerr 82 -minerr $minerr
83 #end if 83 #end if
84 #if str($maxerr) != "0.0": 84 #if str($maxerr) != "0.0":
85 -maxerr $maxerr 85 -maxerr $maxerr
86 #end if 86 #end if
87 -rseed 1234 87 -rseed $rseed
88 -thread \${GALAXY_SLOTS:-4} 88 -thread \${GALAXY_SLOTS:-4}
89 #if str($save_ideas_log) == "yes": 89 #if str($save_ideas_log) == "yes":
90 > $output_log 90 > $output_log
91 #else: 91 #else:
92 > /dev/null 92 > /dev/null
148 <validator type="unspecified_build"/> 148 <validator type="unspecified_build"/>
149 </param> 149 </param>
150 </repeat> 150 </repeat>
151 </when> 151 </when>
152 </conditional> 152 </conditional>
153 <param argument="-rseed" type="integer" value="1234" min="0" max="1000000" label="Seed for IDEAS model initialization" help="Zero value generates a random seed"/>
153 <conditional name="specify_genomic_window_cond"> 154 <conditional name="specify_genomic_window_cond">
154 <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data"> 155 <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data">
155 <option value="no" selected="true">No</option> 156 <option value="no" selected="true">No</option>
156 <option value="yes">Yes</option> 157 <option value="yes">Yes</option>
157 </param> 158 </param>
245 246
246 ----- 247 -----
247 248
248 **Options** 249 **Options**
249 250
250 * **Select input type** - select a data matrix file produced in a previous run or one or more Bam or Bigwig datasets.
251 * **Set cell type and epigenetic factor names by** - cell type and epigenetic factor names can be set manually or by extracting them from the names of the selected input datasets. The latter case requires all selected datasets to have names that contain a "-" character. 251 * **Set cell type and epigenetic factor names by** - cell type and epigenetic factor names can be set manually or by extracting them from the names of the selected input datasets. The latter case requires all selected datasets to have names that contain a "-" character.
252 252
253 * **BAM or BigWig files** - select one or more Bam or Bigwig files from yhour history, making sure that the name of every selected input include a "-" character. 253 * **BAM or BigWig files** - select one or more Bam or Bigwig files from your history, making sure that the name of every selected input include a "-" character (e.g., e001-h3k4me3.bigwig).
254 * **Cell type, Epigenetic factor and Input** - manually select any number of inputs, setting the cell type and epigenetic factor name for each. The combination of "cell type name" and "epigenetic factor name" must be unique for each input. For example, if you have replicate data you may want to specify the cell name as "cell_rep1", "cell_rep2", etc and the factor name as "factor_rep1", "factor_rep2", etc. 254 * **Cell type, Epigenetic factor and Input** - manually select any number of inputs, setting the cell type and epigenetic factor name for each. The combination of "cell type name" and "epigenetic factor name" must be unique for each input. For example, if you have replicate data you may want to specify the cell name as "cell_rep1", "cell_rep2", etc and the factor name as "factor_rep1", "factor_rep2", etc.
255 255
256 * **Cell type name** - cell type name 256 * **Cell type name** - cell type name
257 * **Epigenetic factor name** - epigenetic factor name 257 * **Epigenetic factor name** - epigenetic factor name
258 * **BAM or BigWig file** - BAM or BigWig file 258 * **BAM or BigWig file** - BAM or BigWig file
259 259
260 * **Seed for IDEAS model initialization** - enter an integer to be used as the seed for the IDEAS model initialization.
260 * **Select Bed file that defines genomic windows on which to process the data** - if "No" is selected, IDEAS will run whole genome segmentation. If "Yes" is selected, IDEAS will segment genomes in the unit of the windows defined by the bed file. This file can be in BED3, BED4 or BED5 format, but only the first three columns (chr posst posed) will be used. 261 * **Select Bed file that defines genomic windows on which to process the data** - if "No" is selected, IDEAS will run whole genome segmentation. If "Yes" is selected, IDEAS will segment genomes in the unit of the windows defined by the bed file. This file can be in BED3, BED4 or BED5 format, but only the first three columns (chr posst posed) will be used.
261 262
262 * **Window size in base pairs** - Window size in base pairs (if "No" is selected) 263 * **Window size in base pairs** - Window size in base pairs (if "No" is selected)
263 * **Restrict processing to specified chromosomes** - If "Yes" is selected, processing will be restricted to specified chromosomes 264 * **Restrict processing to specified chromosomes** - If "Yes" is selected, processing will be restricted to specified chromosomes
264 265