Mercurial > repos > bgruening > deeptools
annotate deepTools_macros.xml @ 31:7889d260cc37 draft default tip
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
| author | bgruening |
|---|---|
| date | Wed, 21 Oct 2015 02:50:24 -0400 |
| parents | 5231f398d784 |
| children |
| rev | line source |
|---|---|
| 26 | 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"> | |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
13 <expand macro="doNotExtendPairedEnds" /> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
14 <expand macro="ignoreDuplicates" /> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
15 <expand macro="minMappingQuality" /> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
16 <expand macro="includeZeros" /> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
17 <expand macro="zMin_zMax" /> |
| 26 | 18 <expand macro="colormap" /> |
| 19 </when> | |
| 20 </conditional> | |
| 21 </xml> | |
| 29 | 22 |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
23 |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
24 <xml name="bigwigCorrelate_mode_actions"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
25 |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
26 <expand macro="region_limit_operation" /> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
27 |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
28 <conditional name="advancedOpt"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
29 <param name="showAdvancedOpt" type="select" label="Show advanced options" > |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
30 <option value="no" selected="true">no</option> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
31 <option value="yes">yes</option> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
32 </param> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
33 <when value="no" /> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
34 <when value="yes"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
35 <expand macro="includeZeros" /> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
36 <expand macro="zMin_zMax" /> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
37 <expand macro="colormap" /> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
38 <expand macro="plotTitle" /> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
39 <expand macro="plotNumbers" /> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
40 </when> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
41 </conditional> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
42 </xml> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
43 |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
44 |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
45 <xml name="includeZeros"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
46 <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
47 label="Include zeros" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
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)" /> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
49 </xml> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
50 <xml name="zMin_zMax"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
51 <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
52 help="If not specified the value is set automatically. (--zMin)"/> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
53 <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
54 help="If not specified the value is set automatically. (--zMax)"/> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
55 </xml> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
56 |
| 26 | 57 <xml name="region_limit_operation"> |
| 58 <param name="region" type="text" value="" | |
| 59 label="Region of the genome to limit the operation to" | |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
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)" /> |
| 26 | 61 </xml> |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
62 |
| 26 | 63 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
64 <token name="@WRAPPER_VERSION@">1.5.11</token> |
| 26 | 65 <xml name="requirements"> |
| 66 <requirements> | |
|
31
7889d260cc37
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
30
diff
changeset
|
67 <requirement type="package" version="2.7.10">python</requirement> |
| 26 | 68 <requirement type="binary">@BINARY@</requirement> |
| 69 <requirement type="package" >deepTools</requirement> | |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
70 <requirement type="package" version="1.5.11">deepTools</requirement> |
| 26 | 71 <yield /> |
| 72 </requirements> | |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
73 <expand macro="stdio" /> |
| 26 | 74 <version_command>@BINARY@ --version</version_command> |
| 75 </xml> | |
| 76 | |
| 77 <xml name="kmeans_clustering"> | |
| 78 <conditional name="used_multiple_regions"> | |
| 79 <param name="used_multiple_regions_options" type="select" | |
| 28 | 80 label="Did you compute the matrix with more than one groups of regions?" |
| 26 | 81 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."> |
| 28 | 82 <option value="yes">Yes, I used multiple groups of regions</option> |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
83 <option value="no">No, I used only one group</option> |
| 26 | 84 </param> |
| 85 <when value="no"> | |
| 86 <conditional name="clustering"> | |
| 87 <param name="clustering_options" type="select" label="Clustering algorithm"> | |
| 88 <option value="none">No clustering</option> | |
| 89 <option value="kmeans">Kmeans clustering</option> | |
| 90 </param> | |
| 91 <when value="kmeans"> | |
| 92 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" | |
| 93 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)."/> | |
| 94 </when> | |
| 95 <when value="none" /> | |
| 96 </conditional> | |
| 97 </when> | |
| 98 <when value="yes" /> | |
| 99 </conditional> | |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
100 </xml> |
| 26 | 101 |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
102 <token name="@KMEANS_CLUSTERING@"> |
| 26 | 103 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': |
| 104 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': | |
| 105 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: | |
| 106 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans | |
| 107 #end if | |
| 108 #end if | |
| 109 #end if | |
| 110 </token> | |
| 111 | |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
112 <xml name="samFlag"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
113 <param name="samFlag" type="integer" optional="true" value="" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
114 label="Filter reads based on the SAM flag" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
115 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)"/> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
116 </xml> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
117 <xml name="plotNumbers"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
118 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
119 label="Plot the correlation value" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
120 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
121 </xml> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
122 <xml name="doNotExtendPairedEnds"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
123 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
124 label="Do not extend paired ends" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
125 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)"/> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
126 </xml> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
127 |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
128 <xml name="ignoreDuplicates"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
129 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
130 label="Ignore duplicates" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
131 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)" /> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
132 </xml> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
133 |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
134 <xml name="minMappingQuality"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
135 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
136 label="Minimum mapping quality" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
137 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)"/> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
138 </xml> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
139 |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
140 <xml name="skipZeros"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
141 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
142 label ="Skip zeros" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
143 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)" /> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
144 </xml> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
145 |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
146 <xml name="fragmentLength"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
147 <param name="fragmentLength" type="integer" value="300" min="1" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
148 label="Fragment length used for the sequencing" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
149 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
150 </xml> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
151 |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
152 <xml name="scaleFactor"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
153 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
154 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
155 </xml> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
156 |
| 26 | 157 <xml name="stdio"> |
| 158 <stdio> | |
| 159 <exit_code range="1:" /> | |
| 160 <exit_code range=":-1" /> | |
| 161 <regex match="Error:" /> | |
| 162 <regex match="Exception:" /> | |
| 163 <regex match="EXception:" /> | |
| 164 <regex match="Traceback" /> | |
| 165 </stdio> | |
| 166 </xml> | |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
167 |
| 29 | 168 <xml name="pseudocount"> |
| 169 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> | |
| 170 </xml> | |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
171 |
| 26 | 172 <token name="@REFERENCES@"> |
| 173 | |
| 174 .. class:: infomark | |
| 175 | |
| 176 For more information on the tools, please visit our `help site`_. | |
| 177 | |
| 178 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com | |
| 179 | |
| 180 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. | |
| 181 | |
| 182 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ | |
| 183 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de | |
| 184 .. _help site: https://github.com/fidelram/deepTools/wiki/ | |
| 185 | |
| 186 </token> | |
| 29 | 187 <xml name="citations"> |
| 188 <citations> | |
| 189 <citation type="doi">10.1093/nar/gku365</citation> | |
| 190 <yield /> | |
| 191 </citations> | |
| 192 </xml> | |
| 26 | 193 |
| 194 <xml name="multiple_input_bams"> | |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
195 <param name="bamfiles" type="data" format="bam" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
196 label="Bam file" multiple="true" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
197 help="The BAM file must be sorted."/> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
198 </xml> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
199 |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
200 <xml name="multiple_input_bigwigs"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
201 <param name="bigwigfiles" type="data" format="bigwig" multiple="True" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
202 label="Bigwig file" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
203 help="The Bigwig file must be sorted."/> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
204 </xml> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
205 |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
206 <xml name="plotTitle"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
207 <param name="plotTitle" type="text" value="" size="30" optional="True" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
208 label="Title of the plot" |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
209 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" /> |
| 26 | 210 </xml> |
| 211 | |
| 212 <token name="@multiple_input_bams@"> | |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
213 <![CDATA[ |
| 26 | 214 #set files=[] |
| 215 #set labels=[] | |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
216 #for $counter, $bamfile in enumerate($bamfiles): |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
217 ln -s "${bamfile}" "./${counter}.bam" && |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
218 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" && |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
219 #silent $files.append('%s.bam' % $counter) |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
220 #silent $labels.append("'%s'" % ($bamfile.display_name)) |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
221 #end for |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
222 ]]> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
223 </token> |
| 26 | 224 |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
225 <token name="@multiple_input_bigwigs@"> |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
226 <![CDATA[ |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
227 #set files=[] |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
228 #set labels=[] |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
229 #for $counter, $bigwig in enumerate($bigwigfiles): |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
230 ln -s "${bigwig}" "${counter}.bw" && |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
231 #silent $files.append('%s.bw' % $counter) |
|
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
232 #silent $labels.append("'%s'" % ($bigwig.display_name)) |
| 26 | 233 #end for |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
234 ]]> |
| 26 | 235 </token> |
| 236 | |
| 237 <xml name="reference_genome_source"> | |
| 238 <conditional name="source"> | |
| 239 <param name="ref_source" type="select" label="Reference genome"> | |
| 240 <option value="cached">locally cached</option> | |
| 241 <option value="history">in your history</option> | |
| 242 </param> | |
| 243 <when value="cached"> | |
| 244 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> | |
|
30
5231f398d784
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
bgruening
parents:
29
diff
changeset
|
245 <options from_data_table="lastz_seqs"> |
| 26 | 246 <filter type="sort_by" column="1" /> |
| 247 <validator type="no_options" message="No indexes are available." /> | |
| 248 </options> | |
| 249 </param> | |
| 250 </when> | |
| 251 <when value="history"> | |
| 252 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> | |
| 253 </when> | |
| 254 </conditional> | |
| 255 </xml> | |
| 256 | |
| 257 <token name="@reference_genome_source@"> | |
| 258 #if $source.ref_source=="history": | |
| 259 --genome $source.input1 | |
| 260 #else: | |
| 261 --genome "${source.input1_2bit.fields.path}" | |
| 262 #end if | |
| 263 </token> | |
| 264 | |
| 265 <xml name="effectiveGenomeSize"> | |
| 266 <conditional name="effectiveGenomeSize"> | |
| 267 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" | |
| 268 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. | |
| 269 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. | |
| 270 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."> | |
| 271 <option value="93260000">ce10 (93260000)</option> | |
| 272 <option value="121400000">dm3 (121400000)</option> | |
| 273 <option value="2451960000" selected="true">hg19 (2451960000)</option> | |
| 274 <option value="2150570000">mm9 (2150570000)</option> | |
| 275 <option value="specific">user specified</option> | |
| 276 </param> | |
| 277 <when value="specific"> | |
| 278 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/> | |
| 279 </when> | |
| 280 <when value="2150570000" /> | |
| 281 <when value="2451960000" /> | |
| 282 <when value="121400000" /> | |
| 283 <when value="93260000" /> | |
| 284 </conditional> | |
| 285 </xml> | |
| 286 | |
| 287 <xml name="image_file_format"> | |
| 288 <param name="outFileFormat" type="select" label="Image file format"> | |
| 289 <option value="png" selected="true">png</option> | |
| 290 <option value="pdf">pdf</option> | |
| 291 <option value="svg">svg</option> | |
| 292 <option value="eps">eps</option> | |
| 293 <option value="emf">emf</option> | |
| 294 </param> | |
| 295 </xml> | |
| 296 | |
| 29 | 297 <xml name="missingDataAsZero"> |
| 298 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" | |
| 299 label ="Treat missing data as zero" | |
| 300 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." /> | |
| 301 </xml> | |
| 302 | |
| 26 | 303 <xml name="input_save_matrix_values"> |
| 304 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> | |
| 305 </xml> | |
| 306 | |
| 307 <xml name="input_graphic_output_settings"> | |
| 308 <conditional name="output" > | |
| 309 <param name="showOutputSettings" type="select" label="Show advanced output settings" > | |
| 310 <option value="no" selected="true">no</option> | |
| 311 <option value="yes">yes</option> | |
| 312 </param> | |
| 313 <when value="no" /> | |
| 314 <when value="yes"> | |
| 315 <yield /> | |
| 316 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/> | |
| 317 <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."/> | |
| 318 </when> | |
| 319 </conditional> | |
| 320 </xml> | |
| 321 | |
| 322 <xml name="input_image_file_format"> | |
| 323 <param name="outFileFormat" type="select" label="Image file format"> | |
| 324 <option value="png" selected="true">png</option> | |
| 325 <option value="pdf">pdf</option> | |
| 326 <option value="svg">svg</option> | |
| 327 <option value="eps">eps</option> | |
| 328 <option value="emf">emf</option> | |
| 329 </param> | |
| 330 </xml> | |
| 331 | |
| 332 <xml name="output_image_file_format"> | |
| 333 <data format="png" name="outFileName" label="${tool.name} image"> | |
| 334 <change_format> | |
| 335 <when input="output.outFileFormat" value="pdf" format="pdf" /> | |
| 336 <when input="output.outFileFormat" value="svg" format="svg" /> | |
| 337 <when input="output.outFileFormat" value="eps" format="eps" /> | |
| 338 <when input="output.outFileFormat" value="emf" format="emf" /> | |
| 339 </change_format> | |
| 340 </data> | |
| 341 </xml> | |
| 342 | |
| 343 <xml name="output_save_matrix_values"> | |
| 344 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> | |
| 345 <filter> | |
| 346 (( | |
| 347 output['showOutputSettings'] == 'yes' and | |
| 348 output['saveMatrix'] is True | |
| 349 )) | |
| 350 </filter> | |
| 351 </data> | |
| 352 </xml> | |
| 353 | |
| 354 <xml name="output_graphic_outputs"> | |
| 355 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> | |
| 356 <filter> | |
| 357 (( | |
| 358 output['showOutputSettings'] == 'yes' and | |
| 359 output['saveData'] is True | |
| 360 )) | |
| 361 </filter> | |
| 362 </data> | |
| 363 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> | |
| 364 <filter> | |
| 365 (( | |
| 366 output['showOutputSettings'] == 'yes' and | |
| 367 output['saveSortedRegions'] is True | |
| 368 )) | |
| 369 </filter> | |
| 370 </data> | |
| 371 </xml> | |
| 372 | |
| 373 <xml name="colormap"> | |
| 374 <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/"> | |
| 375 <option value="RdYlBu" selected="true">RdYlBu</option> | |
| 376 <option value="Accent">Accent</option> | |
| 377 <option value="Spectral">Spectral</option> | |
| 378 <option value="Set1">Set1</option> | |
| 379 <option value="Set2">Set2</option> | |
| 380 <option value="Set3">Set3</option> | |
| 381 <option value="Dark2">Dark2</option> | |
| 382 <option value="Reds">Reds</option> | |
| 383 <option value="Oranges">Oranges</option> | |
| 384 <option value="Greens">Greens</option> | |
| 385 <option value="Blues">Blues</option> | |
| 386 <option value="Greys">Greys</option> | |
| 387 <option value="Purples">Purples</option> | |
| 388 <option value="Paired">Paired</option> | |
| 389 <option value="Pastel1">Pastel1</option> | |
| 390 <option value="Pastel2">Pastel2</option> | |
| 391 <option value="spring">spring</option> | |
| 392 <option value="summer">summer</option> | |
| 393 <option value="autumn">autumn</option> | |
| 394 <option value="winter">winter</option> | |
| 395 <option value="hot">hot</option> | |
| 396 <option value="coolwarm">coolwarm</option> | |
| 397 <option value="cool">cool</option> | |
| 398 <option value="seismic">seismic</option> | |
| 399 <option value="terrain">terrain</option> | |
| 400 <option value="ocean">ocean</option> | |
| 401 <option value="rainbow">rainbow</option> | |
| 402 <option value="bone">bone</option> | |
| 403 <option value="flag">flag</option> | |
| 404 <option value="prism">prism</option> | |
| 405 <option value="cubehelix">cubehelix</option> | |
| 406 <option value="binary">binary</option> | |
| 407 <option value="pink">pink</option> | |
| 408 <option value="gray">gray</option> | |
| 409 <option value="copper">copper</option> | |
| 410 <option value="BrBG">BrBG</option> | |
| 411 <option value="BuGn">BuGn</option> | |
| 412 <option value="BuPu">BuPu</option> | |
| 413 <option value="GnBu">GnBu</option> | |
| 414 <option value="OrRd">OrRd</option> | |
| 415 <option value="PiYG">PiYG</option> | |
| 416 <option value="PRGn">PRGn</option> | |
| 417 <option value="PuOr">PuOr</option> | |
| 418 <option value="PuRd">PuRd</option> | |
| 419 <option value="PuBu">PuBu</option> | |
| 420 <option value="RdBu">RdBu</option> | |
| 421 <option value="RdGy">RdGy</option> | |
| 422 <option value="RdPu">RdPu</option> | |
| 423 <option value="YlGn">YlGn</option> | |
| 424 <option value="PuBuGn">PuBuGn</option> | |
| 425 <option value="RdYlGn">RdYlGn</option> | |
| 426 <option value="YlGnBu">YlGnBu</option> | |
| 427 <option value="YlOrBr">YlOrBr</option> | |
| 428 <option value="YlOrRd">YlOrRd</option> | |
| 429 <option value="gist_gray">gist_gray</option> | |
| 430 <option value="gist_stern">gist_stern</option> | |
| 431 <option value="gist_earth">gist_earth</option> | |
| 432 <option value="gist_yarg">gist_yarg</option> | |
| 433 <option value="gist_ncar">gist_ncar</option> | |
| 434 <option value="gist_rainbow">gist_rainbow</option> | |
| 435 <option value="gist_heat">gist_heat</option> | |
| 436 <option value="gnuplot">gnuplot</option> | |
| 437 <option value="gnuplot2">gnuplot2</option> | |
| 438 <option value="CMRmap">CMRmap</option> | |
| 439 <option value="bwr">bwr</option> | |
| 440 <option value="hsv">hsv</option> | |
| 441 <option value="brg">brg</option> | |
| 442 <option value="jet">jet</option> | |
| 443 <option value="afmhot">afmhot</option> | |
| 444 <option value="Accent_r">Accent reversed</option> | |
| 445 <option value="Spectral_r">Spectral reversed</option> | |
| 446 <option value="Set1_r">Set1 reversed</option> | |
| 447 <option value="Set2_r">Set2 reversed</option> | |
| 448 <option value="Set3_r">Set3 reversed</option> | |
| 449 <option value="Dark2_r">Dark2 reversed</option> | |
| 450 <option value="Reds_r">Reds reversed</option> | |
| 451 <option value="Oranges_r">Oranges reversed</option> | |
| 452 <option value="Greens_r">Greens reversed</option> | |
| 453 <option value="Blues_r">Blues reversed</option> | |
| 454 <option value="Greys_r">Greys reversed</option> | |
| 455 <option value="Purples_r">Purples reversed</option> | |
| 456 <option value="Paired_r">Paired reversed</option> | |
| 457 <option value="Pastel1_r">Pastel1 reversed</option> | |
| 458 <option value="Pastel2_r">Pastel2 reversed</option> | |
| 459 <option value="spring_r">spring reversed</option> | |
| 460 <option value="summer_r">summer reversed</option> | |
| 461 <option value="autumn_r">autumn reversed</option> | |
| 462 <option value="winter_r">winter reversed</option> | |
| 463 <option value="hot_r">hot reversed</option> | |
| 464 <option value="coolwarm_r">coolwarm reversed</option> | |
| 465 <option value="cool_r">cool reversed</option> | |
| 466 <option value="seismic_r">seismic reversed</option> | |
| 467 <option value="terrain_r">terrain reversed</option> | |
| 468 <option value="ocean_r">ocean reversed</option> | |
| 469 <option value="rainbow_r">rainbow reversed</option> | |
| 470 <option value="bone_r">bone reversed</option> | |
| 471 <option value="flag_r">flag reversed</option> | |
| 472 <option value="prism_r">prism reversed</option> | |
| 473 <option value="cubehelix_r">cubehelix reversed</option> | |
| 474 <option value="binary_r">binary reversed</option> | |
| 475 <option value="pink_r">pink reversed</option> | |
| 476 <option value="gray_r">gray reversed</option> | |
| 477 <option value="copper_r">copper reversed</option> | |
| 478 <option value="BrBG_r">BrBG reversed</option> | |
| 479 <option value="BuGn_r">BuGn reversed</option> | |
| 480 <option value="BuPu_r">BuPu reversed</option> | |
| 481 <option value="GnBu_r">GnBu reversed</option> | |
| 482 <option value="OrRd_r">OrRd reversed</option> | |
| 483 <option value="PiYG_r">PiYG reversed</option> | |
| 484 <option value="PRGn_r">PRGn reversed</option> | |
| 485 <option value="PuOr_r">PuOr reversed</option> | |
| 486 <option value="PuRd_r">PuRd reversed</option> | |
| 487 <option value="PuBu_r">PuBu reversed</option> | |
| 488 <option value="RdBu_r">RdBu reversed</option> | |
| 489 <option value="RdGy_r">RdGy reversed</option> | |
| 490 <option value="RdPu_r">RdPu reversed</option> | |
| 491 <option value="YlGn_r">YlGn reversed</option> | |
| 492 <option value="PuBuGn_r">PuBuGn reversed</option> | |
| 493 <option value="RdYlBu_r">RdYlBu reversed</option> | |
| 494 <option value="RdYlGn_r">RdYlGn reversed</option> | |
| 495 <option value="YlGnBu_r">YlGnBu reversed</option> | |
| 496 <option value="YlOrBr_r">YlOrBr reversed</option> | |
| 497 <option value="YlOrRd_r">YlOrRd reversed</option> | |
| 498 <option value="gist_gray_r">gist_gray reversed</option> | |
| 499 <option value="gist_stern_r">gist_stern reversed</option> | |
| 500 <option value="gist_earth_r">gist_earth reversed</option> | |
| 501 <option value="gist_yarg_r">gist_yarg reversed</option> | |
| 502 <option value="gist_ncar_r">gist_ncar reversed</option> | |
| 503 <option value="gist_rainbow_r">gist_rainbow reversed</option> | |
| 504 <option value="gist_heat_r">gist_heat reversed</option> | |
| 505 <option value="gnuplot_r">gnuplot reversed</option> | |
| 506 <option value="gnuplot2_r">gnuplot2 reversed</option> | |
| 507 <option value="CMRmap_r">CMRmap reversed</option> | |
| 508 <option value="bwr_r">bwr reversed</option> | |
| 509 <option value="hsv_r">hsv reversed</option> | |
| 510 <option value="brg_r">brg reversed</option> | |
| 511 <option value="jet_r">jet reversed</option> | |
| 512 <option value="afmhot_r">afmhot reversed</option> | |
| 513 </param> | |
| 514 | |
| 515 </xml> | |
| 516 | |
| 517 </macros> |