Mercurial > repos > bgruening > deeptools_compute_matrix
comparison computeMatrix.xml @ 23:f305afa8ff0d draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3cefc7d64faa53ef9a4e5984c7b275fc47cbdaaf
author | bgruening |
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date | Wed, 20 Feb 2019 08:03:23 -0500 |
parents | fb9cf9c97ec4 |
children | d9a637e83828 |
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22:a2e50c362097 | 23:f305afa8ff0d |
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22 --regionsFileName '#echo "' '".join($bed_files)#' | 22 --regionsFileName '#echo "' '".join($bed_files)#' |
23 | 23 |
24 --scoreFileName #echo ' '.join($files)# | 24 --scoreFileName #echo ' '.join($files)# |
25 | 25 |
26 --outFileName '$outFileName' | 26 --outFileName '$outFileName' |
27 --samplesLabel #echo ' '.join($labels)# | |
27 | 28 |
28 @THREADS@ | 29 @THREADS@ |
29 | 30 |
30 #if $output.showOutputSettings == "yes" | 31 #if $output.showOutputSettings == "yes" |
31 #if $output.saveMatrix: | 32 #if $output.saveMatrix: |
70 --maxThreshold $advancedOpt.maxThreshold | 71 --maxThreshold $advancedOpt.maxThreshold |
71 #end if | 72 #end if |
72 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '': | 73 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '': |
73 --scale $advancedOpt.scale | 74 --scale $advancedOpt.scale |
74 #end if | 75 #end if |
75 #if $advancedOpt.samplesLabel is not None and str($advancedOpt.samplesLabel) != '': | |
76 --samplesLabel $advancedOpt.samplesLabel | |
77 #end if | |
78 | 76 |
79 @ADVANCED_OPTS_GTF@ | 77 @ADVANCED_OPTS_GTF@ |
80 | 78 |
81 @blacklist@ | 79 @blacklist@ |
82 | 80 |
89 <param name="regionsFile" format="bed,gtf" type="data" label="Regions to plot" | 87 <param name="regionsFile" format="bed,gtf" type="data" label="Regions to plot" |
90 help="File, in BED format, containing the regions to plot."/> | 88 help="File, in BED format, containing the regions to plot."/> |
91 </repeat> | 89 </repeat> |
92 | 90 |
93 <expand macro="multiple_input_bigwigs" MIN="1" LABEL="Score file" TITLE="Score files"/> | 91 <expand macro="multiple_input_bigwigs" MIN="1" LABEL="Score file" TITLE="Score files"/> |
92 <expand macro="custom_sample_labels" /> | |
94 | 93 |
95 <conditional name="mode" > | 94 <conditional name="mode" > |
96 <param name="mode_select" type="select" | 95 <param name="mode_select" type="select" |
97 label="computeMatrix has two main output options" | 96 label="computeMatrix has two main output options" |
98 help="In the scale-regions mode, all regions in the BED file are | 97 help="In the scale-regions mode, all regions in the BED file are |
205 numeric value will be skipped. The max threshold is useful to skip those | 204 numeric value will be skipped. The max threshold is useful to skip those |
206 few regions with very high read counts (e.g. major satellites) that may | 205 few regions with very high read counts (e.g. major satellites) that may |
207 bias the average values. (--maxThreshold)"/> | 206 bias the average values. (--maxThreshold)"/> |
208 <param name="scale" type="float" optional="True" label="Scaling factor" | 207 <param name="scale" type="float" optional="True" label="Scaling factor" |
209 help="If set, all values are multiplied by this number. (--scale)"/> | 208 help="If set, all values are multiplied by this number. (--scale)"/> |
210 <param argument="--samplesLabel" type="text" size="30" | |
211 label="Labels for the samples (each bigwig)" | |
212 help="The default is to use the history item label. The sample labels should be separated by | |
213 spaces and quoted if a label itself contains a space E.g. label-1 "label 2""> | |
214 <sanitizer> | |
215 <valid initial="string.printable"> | |
216 </valid> | |
217 </sanitizer> | |
218 </param> | |
219 | 209 |
220 <expand macro="gtf_options" /> | 210 <expand macro="gtf_options" /> |
221 | 211 |
222 <expand macro="blacklist" /> | 212 <expand macro="blacklist" /> |
223 </when> | 213 </when> |