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comparison deepTools_macros.xml @ 18:5ea8782d650c draft

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author bgruening
date Mon, 03 Feb 2014 13:44:35 -0500
parents ef65d6b68ccc
children e95b45f1ecbb
comparison
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17:ef65d6b68ccc 18:5ea8782d650c
1 <macros> 1 <macros>
2 <xml name="bamCorrelate_mode_actions"> 2 <xml name="bamCorrelate_mode_actions">
3
4 <expand macro="region_limit_operation" />
5
3 <conditional name="advancedOpt"> 6 <conditional name="advancedOpt">
4 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 7 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
5 <option value="no" selected="true">no</option> 8 <option value="no" selected="true">no</option>
6 <option value="yes">yes</option> 9 <option value="yes">yes</option>
7 </param> 10 </param>
8 <when value="no" /> 11 <when value="no" />
9 <when value="yes"> 12 <when value="yes">
10 <param name="region" type="text" value=""
11 label="Region of the genome to limit the operation to"
12 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;" />
13
14 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" 13 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
15 label="Do not extend paired ends" 14 label="Do not extend paired ends"
16 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/> 15 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
17 16
18 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" 17 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
35 34
36 <expand macro="colormap" /> 35 <expand macro="colormap" />
37 </when> 36 </when>
38 </conditional> 37 </conditional>
39 </xml> 38 </xml>
39
40 <xml name="region_limit_operation">
41 <param name="region" type="text" value=""
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;" />
44 </xml>
45
40 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> 46 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
41 <xml name="requirements"> 47 <xml name="requirements">
42 <requirements> 48 <requirements>
49 <requirement type="binary">@BINARY@</requirement>
43 <requirement type="package" >samtools</requirement> 50 <requirement type="package" >samtools</requirement>
44 <requirement type="package" >deepTools</requirement> 51 <requirement type="package" >deepTools</requirement>
45 <requirement type="package" >ucsc_tools</requirement> 52 <requirement type="package" >ucsc_tools</requirement>
46 <requirement type="package" version="1.5.4_e5c75f3e967be0fa1d6dbcbb63a0f992e1cdcd61">deepTools</requirement> 53 <requirement type="package" version="1.5.4_1093b2d281576f23ee04740bd5eae3f7b8422f7e">deepTools</requirement>
47 <requirement type="package" version="0.1">ucsc_tools</requirement> 54 <requirement type="package" version="0.1">ucsc_tools</requirement>
48 <requirement type="package" version="1.7.1">numpy</requirement> 55 <requirement type="package" version="1.7.1">numpy</requirement>
49 <requirement type="package" version="0.7.7">pysam</requirement> 56 <requirement type="package" version="0.7.7">pysam</requirement>
50 <requirement type="package" version="0.12.0">scipy</requirement> 57 <requirement type="package" version="0.12.0">scipy</requirement>
51 <requirement type="package" version="1.2.1">matplotlib</requirement> 58 <requirement type="package" version="1.2.1">matplotlib</requirement>
52 <requirement type="package" version="0.1.19">samtools</requirement> 59 <requirement type="package" version="0.1.19">samtools</requirement>
53 <requirement type="package" version="12-2013">bx-python</requirement> 60 <requirement type="package" version="12-2013">bx-python</requirement>
54 <yield /> 61 <yield />
55 </requirements> 62 </requirements>
56 </xml> 63 <version_command>@BINARY@ --version</version_command>
64 </xml>
65
66 <xml name="kmeans_clustering">
67
68 <conditional name="used_multiple_regions">
69 <param name="used_multiple_regions_options" type="select"
70 label="Did you used 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.">
72 <option value="yes">Yes, I used multiple regions.</option>
73 <option value="no">No, I used only one region.</option>
74 </param>
75 <when value="no">
76 <conditional name="clustering">
77 <param name="clustering_options" type="select" label="Clustering algorithm">
78 <option value="none">No clustering</option>
79 <option value="kmeans">Kmeans clustering</option>
80 </param>
81 <when value="kmeans">
82 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
83 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
84 </when>
85 <when value="none" />
86 </conditional>
87 </when>
88 <when value="yes" />
89 </conditional>
90
91 </xml>
92 <token name="@kmeans_clusterin@">
93 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
94 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
95 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
96 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
97 #end if
98 #end if
99 #end if
100 </token>
101
57 <xml name="stdio"> 102 <xml name="stdio">
58 <stdio> 103 <stdio>
59 <exit_code range="1:" /> 104 <exit_code range="1:" />
60 <exit_code range=":-1" /> 105 <exit_code range=":-1" />
61 <regex match="Error:" /> 106 <regex match="Error:" />
64 <regex match="Traceback" /> 109 <regex match="Traceback" />
65 </stdio> 110 </stdio>
66 </xml> 111 </xml>
67 <token name="@REFERENCES@"> 112 <token name="@REFERENCES@">
68 113
69 For more informations, please visit our `project site`_. 114 .. class:: infomark
115
116 For more informations, please visit the `project site`_.
70 117
71 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
72 119
73 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`_.
74 121
75 122
76 .. _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/
77 .. _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
78 .. _project site: https://github.com/fidelram/deepTools 125 .. _project site: https://github.com/fidelram/deepTools/wiki/
79 126
80 </token> 127 </token>
81 128
82 <xml name="multiple_input_bams"> 129 <xml name="multiple_input_bams">
83 <repeat name="input_files" title="BAM files" min="2"> 130 <repeat name="input_files" title="BAM files" min="2">
144 <conditional name="effectiveGenomeSize"> 191 <conditional name="effectiveGenomeSize">
145 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" 192 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
146 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. 193 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
147 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. 194 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
148 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes."> 195 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
149 <option value="2150570000">mm9</option> 196 <option value="93260000">ce10 (93260000)</option>
150 <option value="2451960000">hg19</option> 197 <option value="121400000">dm3 (121400000)</option>
151 <option value="121400000">dm3</option> 198 <option value="2451960000" selected="true">hg19 (2451960000)</option>
152 <option value="93260000">ce10</option> 199 <option value="2150570000">mm9 (2150570000)</option>
153 <option value="specific">user specified</option> 200 <option value="specific">user specified</option>
154 </param> 201 </param>
155 <when value="specific"> 202 <when value="specific">
156 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" /> 203 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" />
157 </when> 204 </when>
205 <when value="2150570000" />
206 <when value="2451960000" />
207 <when value="121400000" />
208 <when value="93260000" />
158 </conditional> 209 </conditional>
159 </xml> 210 </xml>
160 211
161 <xml name="image_file_format"> 212 <xml name="image_file_format">
162 <param name="outFileFormat" type="select" label="Image file format"> 213 <param name="outFileFormat" type="select" label="Image file format">