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comparison deepTools_macros.xml @ 45:b9feca1f07f0 draft

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author bgruening
date Mon, 31 Mar 2014 17:48:50 -0400
parents c5787c91cab8
children b5abf7b4296b
comparison
equal deleted inserted replaced
44:3fc7efe86cfc 45:b9feca1f07f0
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_3268f7e1458f3a520ab6fea3039971ee9d7a6d5b">deepTools</requirement> 54 <requirement type="package" version="1.5.4_43d3b51b3c3ab71dc07f31fefe6b3492226cc217">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 use multiple regions in computeMatrix?"
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 regions.</option>
111 </xml> 111 </xml>
112 <token name="@REFERENCES@"> 112 <token name="@REFERENCES@">
113 113
114 .. class:: infomark 114 .. class:: infomark
115 115
116 For more informations, please visit the `project site`_. 116 For more information on the tools, please visit our `help site`_.
117 117
118 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com 118 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
119 119
120 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. 120 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
121 121
122 122
123 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ 123 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
124 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de 124 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
125 .. _project site: https://github.com/fidelram/deepTools/wiki/ 125 .. _help site: https://github.com/fidelram/deepTools/wiki/
126 126
127 </token> 127 </token>
128 128
129 <xml name="multiple_input_bams"> 129 <xml name="multiple_input_bams">
130 <repeat name="input_files" title="BAM files" min="2"> 130 <repeat name="input_files" title="BAM files" min="2">