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comparison deepTools_macros.xml @ 28:f7712a057440 draft

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new bugfix release
author bgruening
date Wed, 02 Apr 2014 09:15:44 -0400
parents bf1b1dcdd67b
children 3a2aab18a217
comparison
equal deleted inserted replaced
27:bf1b1dcdd67b 28:f7712a057440
42 label="Region of the genome to limit the operation to" 42 label="Region of the genome to limit the operation to"
43 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"" /> 43 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"" />
44 </xml> 44 </xml>
45 45
46 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> 46 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
47 <token name="@WRAPPER_VERSION@">1.1</token>
47 <xml name="requirements"> 48 <xml name="requirements">
48 <requirements> 49 <requirements>
49 <requirement type="binary">@BINARY@</requirement> 50 <requirement type="binary">@BINARY@</requirement>
50 <requirement type="package" >samtools</requirement> 51 <requirement type="package" >samtools</requirement>
51 <requirement type="package" >deepTools</requirement> 52 <requirement type="package" >deepTools</requirement>
52 <requirement type="package" >ucsc_tools</requirement> 53 <requirement type="package" >ucsc_tools</requirement>
53 <requirement type="package" version="1.5.4_43d3b51b3c3ab71dc07f31fefe6b3492226cc217">deepTools</requirement> 54 <requirement type="package" version="1.5.8_09023018b96c23f922aa2ea553090e9df8ecf41e">deepTools</requirement>
54 <requirement type="package" version="0.1">ucsc_tools</requirement> 55 <requirement type="package" version="0.1">ucsc_tools</requirement>
55 <requirement type="package" version="1.7.1">numpy</requirement> 56 <requirement type="package" version="1.7.1">numpy</requirement>
56 <requirement type="package" version="0.7.7">pysam</requirement> 57 <requirement type="package" version="0.7.7">pysam</requirement>
57 <requirement type="package" version="0.12.0">scipy</requirement> 58 <requirement type="package" version="0.12.0">scipy</requirement>
58 <requirement type="package" version="1.2.1">matplotlib</requirement> 59 <requirement type="package" version="1.2.1">matplotlib</requirement>
62 </requirements> 63 </requirements>
63 <version_command>@BINARY@ --version</version_command> 64 <version_command>@BINARY@ --version</version_command>
64 </xml> 65 </xml>
65 66
66 <xml name="kmeans_clustering"> 67 <xml name="kmeans_clustering">
67
68 <conditional name="used_multiple_regions"> 68 <conditional name="used_multiple_regions">
69 <param name="used_multiple_regions_options" type="select" 69 <param name="used_multiple_regions_options" type="select"
70 label="Did you use multiple regions in computeMatrix?" 70 label="Did you compute the matrix with more than one groups of regions?"
71 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions."> 71 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
72 <option value="yes">Yes, I used multiple regions.</option> 72 <option value="yes">Yes, I used multiple groups of regions</option>
73 <option value="no">No, I used only one region.</option> 73 <option value="no">No, I used only one region.</option>
74 </param> 74 </param>
75 <when value="no"> 75 <when value="no">
76 <conditional name="clustering"> 76 <conditional name="clustering">
77 <param name="clustering_options" type="select" label="Clustering algorithm"> 77 <param name="clustering_options" type="select" label="Clustering algorithm">