Mercurial > repos > bgruening > deeptools
annotate deepTools_macros.xml @ 65:9bee2c86eeb1 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
| author | iuc |
|---|---|
| date | Mon, 25 May 2015 05:16:10 -0400 |
| parents | 07513cab0338 |
| children | 1dbd76a58d8b |
| rev | line source |
|---|---|
| 61 | 1 <macros> |
| 2 <xml name="bamCorrelate_mode_actions"> | |
| 3 | |
| 4 <expand macro="region_limit_operation" /> | |
| 5 | |
| 6 <conditional name="advancedOpt"> | |
| 7 <param name="showAdvancedOpt" type="select" label="Show advanced options" > | |
| 8 <option value="no" selected="true">no</option> | |
| 9 <option value="yes">yes</option> | |
| 10 </param> | |
| 11 <when value="no" /> | |
| 12 <when value="yes"> | |
| 13 <expand macro="doNotExtendPairedEnds" /> | |
| 14 <expand macro="ignoreDuplicates" /> | |
| 15 <expand macro="minMappingQuality" /> | |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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16 <expand macro="includeZeros" /> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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17 <expand macro="zMin_zMax" /> |
| 61 | 18 <expand macro="colormap" /> |
| 19 </when> | |
| 20 </conditional> | |
| 21 </xml> | |
| 22 | |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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23 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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24 <xml name="bigwigCorrelate_mode_actions"> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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25 |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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26 <expand macro="region_limit_operation" /> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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27 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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28 <conditional name="advancedOpt"> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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29 <param name="showAdvancedOpt" type="select" label="Show advanced options" > |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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30 <option value="no" selected="true">no</option> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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31 <option value="yes">yes</option> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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32 </param> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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33 <when value="no" /> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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34 <when value="yes"> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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35 <expand macro="includeZeros" /> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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36 <expand macro="zMin_zMax" /> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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37 <expand macro="colormap" /> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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38 <expand macro="plotTitle" /> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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39 <expand macro="plotNumbers" /> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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40 </when> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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41 </conditional> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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42 </xml> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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43 |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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44 |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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45 <xml name="includeZeros"> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
parents:
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46 <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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47 label="Include zeros" |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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48 help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases. (--includeZeros)" /> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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49 </xml> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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50 <xml name="zMin_zMax"> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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51 <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities" |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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52 help="If not specified the value is set automatically. (--zMin)"/> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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53 <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities" |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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54 help="If not specified the value is set automatically. (--zMax)"/> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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55 </xml> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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56 |
| 61 | 57 <xml name="region_limit_operation"> |
| 58 <param name="region" type="text" value="" | |
| 59 label="Region of the genome to limit the operation to" | |
| 60 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". (--region)" /> | |
| 61 </xml> | |
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62 |
| 61 | 63 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> |
| 63 | 64 <token name="@WRAPPER_VERSION@">1.5.9.2</token> |
| 61 | 65 <xml name="requirements"> |
| 66 <requirements> | |
| 67 <requirement type="binary">@BINARY@</requirement> | |
| 68 <requirement type="package" >deepTools</requirement> | |
| 63 | 69 <requirement type="package" version="1.5.9">deepTools</requirement> |
| 61 | 70 <yield /> |
| 71 </requirements> | |
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72 <expand macro="stdio" /> |
| 61 | 73 <version_command>@BINARY@ --version</version_command> |
| 74 </xml> | |
| 75 | |
| 76 <xml name="kmeans_clustering"> | |
| 77 <conditional name="used_multiple_regions"> | |
| 78 <param name="used_multiple_regions_options" type="select" | |
| 79 label="Did you compute the matrix with more than one groups of regions?" | |
| 80 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."> | |
| 81 <option value="yes">Yes, I used multiple groups of regions</option> | |
| 82 <option value="no">No, I used only one region.</option> | |
| 83 </param> | |
| 84 <when value="no"> | |
| 85 <conditional name="clustering"> | |
| 86 <param name="clustering_options" type="select" label="Clustering algorithm"> | |
| 87 <option value="none">No clustering</option> | |
| 88 <option value="kmeans">Kmeans clustering</option> | |
| 89 </param> | |
| 90 <when value="kmeans"> | |
| 91 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" | |
| 92 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)."/> | |
| 93 </when> | |
| 94 <when value="none" /> | |
| 95 </conditional> | |
| 96 </when> | |
| 97 <when value="yes" /> | |
| 98 </conditional> | |
| 99 </xml> | |
| 100 | |
| 101 <token name="@KMEANS_CLUSTERING@"> | |
| 102 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': | |
| 103 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': | |
| 104 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: | |
| 105 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans | |
| 106 #end if | |
| 107 #end if | |
| 108 #end if | |
| 109 </token> | |
| 110 | |
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111 <xml name="samFlag"> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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112 <param name="samFlag" type="integer" optional="true" value="" |
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113 label="Filter reads based on the SAM flag" |
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114 help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/> |
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115 </xml> |
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116 <xml name="plotNumbers"> |
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117 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" |
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118 label="Plot the correlation value" |
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119 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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120 </xml> |
| 61 | 121 <xml name="doNotExtendPairedEnds"> |
| 122 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" | |
| 123 label="Do not extend paired ends" | |
| 124 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. (--doNotExtendPairedEnds)"/> | |
| 125 </xml> | |
| 126 | |
| 127 <xml name="ignoreDuplicates"> | |
| 128 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" | |
| 129 label="Ignore duplicates" | |
| 130 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" /> | |
| 131 </xml> | |
| 132 | |
| 133 <xml name="minMappingQuality"> | |
| 134 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1" | |
| 135 label="Minimum mapping quality" | |
| 136 help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere. (--minMappingQuality)"/> | |
| 137 </xml> | |
| 138 | |
| 139 <xml name="skipZeros"> | |
| 140 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" | |
| 141 label ="Skip zeros" | |
| 142 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" /> | |
| 143 </xml> | |
| 144 | |
| 145 <xml name="fragmentLength"> | |
| 146 <param name="fragmentLength" type="integer" value="300" min="1" | |
| 147 label="Fragment length used for the sequencing" | |
| 148 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/> | |
| 149 </xml> | |
| 150 | |
| 151 <xml name="scaleFactor"> | |
| 152 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> | |
| 153 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> | |
| 154 </xml> | |
| 155 | |
| 156 <xml name="stdio"> | |
| 157 <stdio> | |
| 158 <exit_code range="1:" /> | |
| 159 <exit_code range=":-1" /> | |
| 160 <regex match="Error:" /> | |
| 161 <regex match="Exception:" /> | |
| 162 <regex match="EXception:" /> | |
| 163 <regex match="Traceback" /> | |
| 164 </stdio> | |
| 165 </xml> | |
| 166 | |
| 167 <xml name="pseudocount"> | |
| 168 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> | |
| 169 </xml> | |
| 170 | |
| 171 <token name="@REFERENCES@"> | |
| 172 | |
| 173 .. class:: infomark | |
| 174 | |
| 175 For more information on the tools, please visit our `help site`_. | |
| 176 | |
| 177 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com | |
| 178 | |
| 179 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. | |
| 180 | |
| 181 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ | |
| 182 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de | |
| 183 .. _help site: https://github.com/fidelram/deepTools/wiki/ | |
| 184 | |
| 185 </token> | |
| 186 <xml name="citations"> | |
| 187 <citations> | |
| 188 <citation type="doi">10.1093/nar/gku365</citation> | |
| 189 <yield /> | |
| 190 </citations> | |
| 191 </xml> | |
| 192 | |
| 193 <xml name="multiple_input_bams"> | |
| 194 <repeat name="input_files" title="BAM files" min="2"> | |
| 195 <param name="bamfile" type="data" format="bam" | |
| 196 label="Bam file" | |
| 197 help="The BAM file must be sorted."/> | |
| 198 <param name="label" type="text" size="30" optional="true" value="" | |
| 199 label="Label" | |
| 200 help="Label to use in the output. If not given the dataset name will be used instead."/> | |
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201 </repeat> |
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202 </xml> |
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203 |
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204 <xml name="multiple_input_bigwigs"> |
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205 <repeat name="input_files" title="BigWig files" min="2"> |
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206 <param name="bigwigfile" type="data" format="bigwig" |
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207 label="Bigwig file" |
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208 help="The Bigwig file must be sorted."/> |
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209 <param name="label" type="text" size="30" optional="true" value="" |
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210 label="Label" |
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211 help="Label to use in the output. If not given the dataset name will be used instead."/> |
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212 </repeat> |
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213 </xml> |
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214 |
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215 <xml name="plotTitle"> |
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216 <param name="plotTitle" type="text" value="" size="30" optional="True" |
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217 label="Title of the plot" |
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218 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" /> |
| 61 | 219 </xml> |
| 220 | |
| 221 <token name="@multiple_input_bams@"> | |
| 222 #import tempfile | |
| 223 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) | |
| 224 #set files=[] | |
| 225 #set labels=[] | |
| 226 #for $i in $input_files: | |
| 227 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) | |
| 228 #set $temp_input_path = $temp_input_handle.name | |
| 229 #silent $temp_input_handle.close() | |
| 230 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path)) | |
| 231 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path)) | |
| 232 #silent $files.append('%s.bam' % $temp_input_path) | |
| 233 | |
| 234 ##set $files += [str($i.bamfile)] | |
| 235 #if str($i.label.value) != "": | |
| 236 #set $labels += ["\"%s\"" % ($i.label.value)] | |
| 237 #else | |
| 238 #set $labels += ["\"%s\"" % ($i.bamfile.name)] | |
| 239 #end if | |
| 240 #end for | |
| 241 </token> | |
| 242 | |
|
65
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243 <token name="@multiple_input_bigwigs@"> |
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244 #import tempfile |
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245 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) |
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246 #set files=[] |
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247 #set labels=[] |
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248 #for $i in $input_files: |
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249 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) |
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250 #set $temp_input_path = $temp_input_handle.name |
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251 #silent $temp_input_handle.close() |
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252 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path)) |
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253 #silent $files.append('%s.bw' % $temp_input_path) |
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254 |
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255 ##set $files += [str($i.bigwigfile)] |
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256 #if str($i.label.value) != "": |
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257 #set $labels += ["\"%s\"" % ($i.label.value)] |
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258 #else |
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259 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)] |
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260 #end if |
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261 #end for |
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262 </token> |
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263 |
| 61 | 264 <xml name="reference_genome_source"> |
| 265 <conditional name="source"> | |
| 266 <param name="ref_source" type="select" label="Reference genome"> | |
| 267 <option value="cached">locally cached</option> | |
| 268 <option value="history">in your history</option> | |
| 269 </param> | |
| 270 <when value="cached"> | |
| 271 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> | |
| 272 <options from_data_table="deepTools_seqs"> | |
| 273 <filter type="sort_by" column="1" /> | |
| 274 <validator type="no_options" message="No indexes are available." /> | |
| 275 </options> | |
| 276 </param> | |
| 277 </when> | |
| 278 <when value="history"> | |
| 279 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> | |
| 280 </when> | |
| 281 </conditional> | |
| 282 </xml> | |
| 283 | |
| 284 <token name="@reference_genome_source@"> | |
| 285 #if $source.ref_source=="history": | |
| 286 --genome $source.input1 | |
| 287 #else: | |
| 288 --genome "${source.input1_2bit.fields.path}" | |
| 289 #end if | |
| 290 </token> | |
| 291 | |
| 292 <xml name="effectiveGenomeSize"> | |
| 293 <conditional name="effectiveGenomeSize"> | |
| 294 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" | |
| 295 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. | |
| 296 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. | |
| 297 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."> | |
| 298 <option value="93260000">ce10 (93260000)</option> | |
| 299 <option value="121400000">dm3 (121400000)</option> | |
| 300 <option value="2451960000" selected="true">hg19 (2451960000)</option> | |
| 301 <option value="2150570000">mm9 (2150570000)</option> | |
| 302 <option value="specific">user specified</option> | |
| 303 </param> | |
| 304 <when value="specific"> | |
| 305 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/> | |
| 306 </when> | |
| 307 <when value="2150570000" /> | |
| 308 <when value="2451960000" /> | |
| 309 <when value="121400000" /> | |
| 310 <when value="93260000" /> | |
| 311 </conditional> | |
| 312 </xml> | |
| 313 | |
| 314 <xml name="image_file_format"> | |
| 315 <param name="outFileFormat" type="select" label="Image file format"> | |
| 316 <option value="png" selected="true">png</option> | |
| 317 <option value="pdf">pdf</option> | |
| 318 <option value="svg">svg</option> | |
| 319 <option value="eps">eps</option> | |
| 320 <option value="emf">emf</option> | |
| 321 </param> | |
| 322 </xml> | |
| 323 | |
| 324 <xml name="missingDataAsZero"> | |
| 325 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" | |
| 326 label ="Treat missing data as zero" | |
| 327 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." /> | |
| 328 </xml> | |
| 329 | |
| 330 <xml name="input_save_matrix_values"> | |
| 331 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> | |
| 332 </xml> | |
| 333 | |
| 334 <xml name="input_graphic_output_settings"> | |
| 335 <conditional name="output" > | |
| 336 <param name="showOutputSettings" type="select" label="Show advanced output settings" > | |
| 337 <option value="no" selected="true">no</option> | |
| 338 <option value="yes">yes</option> | |
| 339 </param> | |
| 340 <when value="no" /> | |
| 341 <when value="yes"> | |
| 342 <yield /> | |
| 343 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/> | |
| 344 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> | |
| 345 </when> | |
| 346 </conditional> | |
| 347 </xml> | |
| 348 | |
| 349 <xml name="input_image_file_format"> | |
| 350 <param name="outFileFormat" type="select" label="Image file format"> | |
| 351 <option value="png" selected="true">png</option> | |
| 352 <option value="pdf">pdf</option> | |
| 353 <option value="svg">svg</option> | |
| 354 <option value="eps">eps</option> | |
| 355 <option value="emf">emf</option> | |
| 356 </param> | |
| 357 </xml> | |
| 358 | |
| 359 <xml name="output_image_file_format"> | |
| 360 <data format="png" name="outFileName" label="${tool.name} image"> | |
| 361 <change_format> | |
| 362 <when input="output.outFileFormat" value="pdf" format="pdf" /> | |
| 363 <when input="output.outFileFormat" value="svg" format="svg" /> | |
| 364 <when input="output.outFileFormat" value="eps" format="eps" /> | |
| 365 <when input="output.outFileFormat" value="emf" format="emf" /> | |
| 366 </change_format> | |
| 367 </data> | |
| 368 </xml> | |
| 369 | |
| 370 <xml name="output_save_matrix_values"> | |
| 371 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> | |
| 372 <filter> | |
| 373 (( | |
| 374 output['showOutputSettings'] == 'yes' and | |
| 375 output['saveMatrix'] is True | |
| 376 )) | |
| 377 </filter> | |
| 378 </data> | |
| 379 </xml> | |
| 380 | |
| 381 <xml name="output_graphic_outputs"> | |
| 382 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> | |
| 383 <filter> | |
| 384 (( | |
| 385 output['showOutputSettings'] == 'yes' and | |
| 386 output['saveData'] is True | |
| 387 )) | |
| 388 </filter> | |
| 389 </data> | |
| 390 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> | |
| 391 <filter> | |
| 392 (( | |
| 393 output['showOutputSettings'] == 'yes' and | |
| 394 output['saveSortedRegions'] is True | |
| 395 )) | |
| 396 </filter> | |
| 397 </data> | |
| 398 </xml> | |
| 399 | |
| 400 <xml name="colormap"> | |
| 401 <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/"> | |
| 402 <option value="RdYlBu" selected="true">RdYlBu</option> | |
| 403 <option value="Accent">Accent</option> | |
| 404 <option value="Spectral">Spectral</option> | |
| 405 <option value="Set1">Set1</option> | |
| 406 <option value="Set2">Set2</option> | |
| 407 <option value="Set3">Set3</option> | |
| 408 <option value="Dark2">Dark2</option> | |
| 409 <option value="Reds">Reds</option> | |
| 410 <option value="Oranges">Oranges</option> | |
| 411 <option value="Greens">Greens</option> | |
| 412 <option value="Blues">Blues</option> | |
| 413 <option value="Greys">Greys</option> | |
| 414 <option value="Purples">Purples</option> | |
| 415 <option value="Paired">Paired</option> | |
| 416 <option value="Pastel1">Pastel1</option> | |
| 417 <option value="Pastel2">Pastel2</option> | |
| 418 <option value="spring">spring</option> | |
| 419 <option value="summer">summer</option> | |
| 420 <option value="autumn">autumn</option> | |
| 421 <option value="winter">winter</option> | |
| 422 <option value="hot">hot</option> | |
| 423 <option value="coolwarm">coolwarm</option> | |
| 424 <option value="cool">cool</option> | |
| 425 <option value="seismic">seismic</option> | |
| 426 <option value="terrain">terrain</option> | |
| 427 <option value="ocean">ocean</option> | |
| 428 <option value="rainbow">rainbow</option> | |
| 429 <option value="bone">bone</option> | |
| 430 <option value="flag">flag</option> | |
| 431 <option value="prism">prism</option> | |
| 432 <option value="cubehelix">cubehelix</option> | |
| 433 <option value="binary">binary</option> | |
| 434 <option value="pink">pink</option> | |
| 435 <option value="gray">gray</option> | |
| 436 <option value="copper">copper</option> | |
| 437 <option value="BrBG">BrBG</option> | |
| 438 <option value="BuGn">BuGn</option> | |
| 439 <option value="BuPu">BuPu</option> | |
| 440 <option value="GnBu">GnBu</option> | |
| 441 <option value="OrRd">OrRd</option> | |
| 442 <option value="PiYG">PiYG</option> | |
| 443 <option value="PRGn">PRGn</option> | |
| 444 <option value="PuOr">PuOr</option> | |
| 445 <option value="PuRd">PuRd</option> | |
| 446 <option value="PuBu">PuBu</option> | |
| 447 <option value="RdBu">RdBu</option> | |
| 448 <option value="RdGy">RdGy</option> | |
| 449 <option value="RdPu">RdPu</option> | |
| 450 <option value="YlGn">YlGn</option> | |
| 451 <option value="PuBuGn">PuBuGn</option> | |
| 452 <option value="RdYlGn">RdYlGn</option> | |
| 453 <option value="YlGnBu">YlGnBu</option> | |
| 454 <option value="YlOrBr">YlOrBr</option> | |
| 455 <option value="YlOrRd">YlOrRd</option> | |
| 456 <option value="gist_gray">gist_gray</option> | |
| 457 <option value="gist_stern">gist_stern</option> | |
| 458 <option value="gist_earth">gist_earth</option> | |
| 459 <option value="gist_yarg">gist_yarg</option> | |
| 460 <option value="gist_ncar">gist_ncar</option> | |
| 461 <option value="gist_rainbow">gist_rainbow</option> | |
| 462 <option value="gist_heat">gist_heat</option> | |
| 463 <option value="gnuplot">gnuplot</option> | |
| 464 <option value="gnuplot2">gnuplot2</option> | |
| 465 <option value="CMRmap">CMRmap</option> | |
| 466 <option value="bwr">bwr</option> | |
| 467 <option value="hsv">hsv</option> | |
| 468 <option value="brg">brg</option> | |
| 469 <option value="jet">jet</option> | |
| 470 <option value="afmhot">afmhot</option> | |
| 471 <option value="Accent_r">Accent reversed</option> | |
| 472 <option value="Spectral_r">Spectral reversed</option> | |
| 473 <option value="Set1_r">Set1 reversed</option> | |
| 474 <option value="Set2_r">Set2 reversed</option> | |
| 475 <option value="Set3_r">Set3 reversed</option> | |
| 476 <option value="Dark2_r">Dark2 reversed</option> | |
| 477 <option value="Reds_r">Reds reversed</option> | |
| 478 <option value="Oranges_r">Oranges reversed</option> | |
| 479 <option value="Greens_r">Greens reversed</option> | |
| 480 <option value="Blues_r">Blues reversed</option> | |
| 481 <option value="Greys_r">Greys reversed</option> | |
| 482 <option value="Purples_r">Purples reversed</option> | |
| 483 <option value="Paired_r">Paired reversed</option> | |
| 484 <option value="Pastel1_r">Pastel1 reversed</option> | |
| 485 <option value="Pastel2_r">Pastel2 reversed</option> | |
| 486 <option value="spring_r">spring reversed</option> | |
| 487 <option value="summer_r">summer reversed</option> | |
| 488 <option value="autumn_r">autumn reversed</option> | |
| 489 <option value="winter_r">winter reversed</option> | |
| 490 <option value="hot_r">hot reversed</option> | |
| 491 <option value="coolwarm_r">coolwarm reversed</option> | |
| 492 <option value="cool_r">cool reversed</option> | |
| 493 <option value="seismic_r">seismic reversed</option> | |
| 494 <option value="terrain_r">terrain reversed</option> | |
| 495 <option value="ocean_r">ocean reversed</option> | |
| 496 <option value="rainbow_r">rainbow reversed</option> | |
| 497 <option value="bone_r">bone reversed</option> | |
| 498 <option value="flag_r">flag reversed</option> | |
| 499 <option value="prism_r">prism reversed</option> | |
| 500 <option value="cubehelix_r">cubehelix reversed</option> | |
| 501 <option value="binary_r">binary reversed</option> | |
| 502 <option value="pink_r">pink reversed</option> | |
| 503 <option value="gray_r">gray reversed</option> | |
| 504 <option value="copper_r">copper reversed</option> | |
| 505 <option value="BrBG_r">BrBG reversed</option> | |
| 506 <option value="BuGn_r">BuGn reversed</option> | |
| 507 <option value="BuPu_r">BuPu reversed</option> | |
| 508 <option value="GnBu_r">GnBu reversed</option> | |
| 509 <option value="OrRd_r">OrRd reversed</option> | |
| 510 <option value="PiYG_r">PiYG reversed</option> | |
| 511 <option value="PRGn_r">PRGn reversed</option> | |
| 512 <option value="PuOr_r">PuOr reversed</option> | |
| 513 <option value="PuRd_r">PuRd reversed</option> | |
| 514 <option value="PuBu_r">PuBu reversed</option> | |
| 515 <option value="RdBu_r">RdBu reversed</option> | |
| 516 <option value="RdGy_r">RdGy reversed</option> | |
| 517 <option value="RdPu_r">RdPu reversed</option> | |
| 518 <option value="YlGn_r">YlGn reversed</option> | |
| 519 <option value="PuBuGn_r">PuBuGn reversed</option> | |
| 520 <option value="RdYlBu_r">RdYlBu reversed</option> | |
| 521 <option value="RdYlGn_r">RdYlGn reversed</option> | |
| 522 <option value="YlGnBu_r">YlGnBu reversed</option> | |
| 523 <option value="YlOrBr_r">YlOrBr reversed</option> | |
| 524 <option value="YlOrRd_r">YlOrRd reversed</option> | |
| 525 <option value="gist_gray_r">gist_gray reversed</option> | |
| 526 <option value="gist_stern_r">gist_stern reversed</option> | |
| 527 <option value="gist_earth_r">gist_earth reversed</option> | |
| 528 <option value="gist_yarg_r">gist_yarg reversed</option> | |
| 529 <option value="gist_ncar_r">gist_ncar reversed</option> | |
| 530 <option value="gist_rainbow_r">gist_rainbow reversed</option> | |
| 531 <option value="gist_heat_r">gist_heat reversed</option> | |
| 532 <option value="gnuplot_r">gnuplot reversed</option> | |
| 533 <option value="gnuplot2_r">gnuplot2 reversed</option> | |
| 534 <option value="CMRmap_r">CMRmap reversed</option> | |
| 535 <option value="bwr_r">bwr reversed</option> | |
| 536 <option value="hsv_r">hsv reversed</option> | |
| 537 <option value="brg_r">brg reversed</option> | |
| 538 <option value="jet_r">jet reversed</option> | |
| 539 <option value="afmhot_r">afmhot reversed</option> | |
| 540 </param> | |
| 541 | |
| 542 </xml> | |
| 543 | |
| 544 </macros> |