Mercurial > repos > bgruening > deeptools

comparison deepTools_macros.xml @ 29:3a2aab18a217 draft

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author bgruening
date Tue, 16 Sep 2014 13:46:05 -0400
parents f7712a057440
children 5231f398d784
comparison
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28:f7712a057440 29:3a2aab18a217
34 34
35 <expand macro="colormap" /> 35 <expand macro="colormap" />
36 </when> 36 </when>
37 </conditional> 37 </conditional>
38 </xml> 38 </xml>
39 39
40 <xml name="region_limit_operation"> 40 <xml name="region_limit_operation">
41 <param name="region" type="text" value="" 41 <param name="region" type="text" value=""
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 &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" /> 43 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
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 <token name="@WRAPPER_VERSION@">1.5.9.1</token>
48 <xml name="requirements"> 48 <xml name="requirements">
49 <requirements> 49 <requirements>
50 <requirement type="binary">@BINARY@</requirement> 50 <requirement type="binary">@BINARY@</requirement>
51 <requirement type="package" >samtools</requirement> 51 <requirement type="package" >samtools</requirement>
52 <requirement type="package" >deepTools</requirement> 52 <requirement type="package" >deepTools</requirement>
53 <requirement type="package" >ucsc_tools</requirement> 53 <requirement type="package" >ucsc_tools</requirement>
54 <requirement type="package" version="1.5.8_09023018b96c23f922aa2ea553090e9df8ecf41e">deepTools</requirement> 54 <requirement type="package" version="1.5.9.1">deepTools</requirement>
55 <requirement type="package" version="0.1">ucsc_tools</requirement> 55 <requirement type="package" version="0.1">ucsc_tools</requirement>
56 <requirement type="package" version="1.7.1">numpy</requirement> 56 <requirement type="package" version="1.7.1">numpy</requirement>
57 <requirement type="package" version="0.7.7">pysam</requirement> 57 <requirement type="package" version="0.7.7">pysam</requirement>
58 <requirement type="package" version="0.12.0">scipy</requirement> 58 <requirement type="package" version="0.12.0">scipy</requirement>
59 <requirement type="package" version="1.2.1">matplotlib</requirement> 59 <requirement type="package" version="1.2.1">matplotlib</requirement>
107 <regex match="Exception:" /> 107 <regex match="Exception:" />
108 <regex match="EXception:" /> 108 <regex match="EXception:" />
109 <regex match="Traceback" /> 109 <regex match="Traceback" />
110 </stdio> 110 </stdio>
111 </xml> 111 </xml>
112 <xml name="pseudocount">
113 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
114 </xml>
112 <token name="@REFERENCES@"> 115 <token name="@REFERENCES@">
113 116
114 .. class:: infomark 117 .. class:: infomark
115 118
116 For more information on the tools, please visit our `help site`_. 119 For more information on the tools, please visit our `help site`_.
117 120
118 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com 121 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
119 122
120 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. 123 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
121
122 124
123 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ 125 .. _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 126 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
125 .. _help site: https://github.com/fidelram/deepTools/wiki/ 127 .. _help site: https://github.com/fidelram/deepTools/wiki/
126 128
129 **References**
130
131 If you use this Galaxy tool in work leading to a scientific publication please
132 cite the following paper:
133
127 </token> 134 </token>
135 <xml name="citations">
136 <citations>
137 <citation type="doi">10.1093/nar/gku365</citation>
138 <yield />
139 </citations>
140 </xml>
128 141
129 <xml name="multiple_input_bams"> 142 <xml name="multiple_input_bams">
130 <repeat name="input_files" title="BAM files" min="2"> 143 <repeat name="input_files" title="BAM files" min="2">
131 <param name="bamfile" type="data" format="bam" 144 <param name="bamfile" type="data" format="bam"
132 label="Bam file" 145 label="Bam file"
215 <option value="pdf">pdf</option> 228 <option value="pdf">pdf</option>
216 <option value="svg">svg</option> 229 <option value="svg">svg</option>
217 <option value="eps">eps</option> 230 <option value="eps">eps</option>
218 <option value="emf">emf</option> 231 <option value="emf">emf</option>
219 </param> 232 </param>
233 </xml>
234
235 <xml name="missingDataAsZero">
236 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
237 label ="Treat missing data as zero"
238 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
220 </xml> 239 </xml>
221 240
222 <xml name="input_save_matrix_values"> 241 <xml name="input_save_matrix_values">
223 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> 242 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
224 </xml> 243 </xml>