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comparison deepTools_macros.xml @ 30:5231f398d784 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
author bgruening
date Tue, 20 Oct 2015 14:43:12 -0400
parents 3a2aab18a217
children 7889d260cc37
comparison
equal deleted inserted replaced
29:3a2aab18a217 30:5231f398d784
8 <option value="no" selected="true">no</option> 8 <option value="no" selected="true">no</option>
9 <option value="yes">yes</option> 9 <option value="yes">yes</option>
10 </param> 10 </param>
11 <when value="no" /> 11 <when value="no" />
12 <when value="yes"> 12 <when value="yes">
13 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" 13 <expand macro="doNotExtendPairedEnds" />
14 label="Do not extend paired ends" 14 <expand macro="ignoreDuplicates" />
15 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/> 15 <expand macro="minMappingQuality" />
16 16 <expand macro="includeZeros" />
17 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" 17 <expand macro="zMin_zMax" />
18 label="Ignore duplicates"
19 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." />
20
21 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
22 label="Minimum mapping quality"
23 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."/>
24
25 <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
26 label ="Include zeros"
27 help ="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." />
28
29 <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
30 help="If not specified the value is set automatically."/>
31
32 <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
33 help="If not specified the value is set automatically."/>
34
35 <expand macro="colormap" /> 18 <expand macro="colormap" />
36 </when> 19 </when>
37 </conditional> 20 </conditional>
21 </xml>
22
23
24 <xml name="bigwigCorrelate_mode_actions">
25
26 <expand macro="region_limit_operation" />
27
28 <conditional name="advancedOpt">
29 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
30 <option value="no" selected="true">no</option>
31 <option value="yes">yes</option>
32 </param>
33 <when value="no" />
34 <when value="yes">
35 <expand macro="includeZeros" />
36 <expand macro="zMin_zMax" />
37 <expand macro="colormap" />
38 <expand macro="plotTitle" />
39 <expand macro="plotNumbers" />
40 </when>
41 </conditional>
42 </xml>
43
44
45 <xml name="includeZeros">
46 <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
47 label="Include zeros"
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)" />
49 </xml>
50 <xml name="zMin_zMax">
51 <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
52 help="If not specified the value is set automatically. (--zMin)"/>
53 <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
54 help="If not specified the value is set automatically. (--zMax)"/>
38 </xml> 55 </xml>
39 56
40 <xml name="region_limit_operation"> 57 <xml name="region_limit_operation">
41 <param name="region" type="text" value="" 58 <param name="region" type="text" value=""
42 label="Region of the genome to limit the operation to" 59 label="Region of the genome to limit the operation to"
43 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" /> 60 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;. (--region)" />
44 </xml> 61 </xml>
45 62
46 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> 63 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
47 <token name="@WRAPPER_VERSION@">1.5.9.1</token> 64 <token name="@WRAPPER_VERSION@">1.5.11</token>
48 <xml name="requirements"> 65 <xml name="requirements">
49 <requirements> 66 <requirements>
67 <requirement type="package" version="2.7">python</requirement>
50 <requirement type="binary">@BINARY@</requirement> 68 <requirement type="binary">@BINARY@</requirement>
51 <requirement type="package" >samtools</requirement>
52 <requirement type="package" >deepTools</requirement> 69 <requirement type="package" >deepTools</requirement>
53 <requirement type="package" >ucsc_tools</requirement> 70 <requirement type="package" version="1.5.11">deepTools</requirement>
54 <requirement type="package" version="1.5.9.1">deepTools</requirement>
55 <requirement type="package" version="0.1">ucsc_tools</requirement>
56 <requirement type="package" version="1.7.1">numpy</requirement>
57 <requirement type="package" version="0.7.7">pysam</requirement>
58 <requirement type="package" version="0.12.0">scipy</requirement>
59 <requirement type="package" version="1.2.1">matplotlib</requirement>
60 <requirement type="package" version="0.1.19">samtools</requirement>
61 <requirement type="package" version="12-2013">bx-python</requirement>
62 <yield /> 71 <yield />
63 </requirements> 72 </requirements>
73 <expand macro="stdio" />
64 <version_command>@BINARY@ --version</version_command> 74 <version_command>@BINARY@ --version</version_command>
65 </xml> 75 </xml>
66 76
67 <xml name="kmeans_clustering"> 77 <xml name="kmeans_clustering">
68 <conditional name="used_multiple_regions"> 78 <conditional name="used_multiple_regions">
69 <param name="used_multiple_regions_options" type="select" 79 <param name="used_multiple_regions_options" type="select"
70 label="Did you compute the matrix with more than one groups of regions?" 80 label="Did you compute the matrix with more than one groups of regions?"
71 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions."> 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.">
72 <option value="yes">Yes, I used multiple groups of regions</option> 82 <option value="yes">Yes, I used multiple groups of regions</option>
73 <option value="no">No, I used only one region.</option> 83 <option value="no">No, I used only one group</option>
74 </param> 84 </param>
75 <when value="no"> 85 <when value="no">
76 <conditional name="clustering"> 86 <conditional name="clustering">
77 <param name="clustering_options" type="select" label="Clustering algorithm"> 87 <param name="clustering_options" type="select" label="Clustering algorithm">
78 <option value="none">No clustering</option> 88 <option value="none">No clustering</option>
85 <when value="none" /> 95 <when value="none" />
86 </conditional> 96 </conditional>
87 </when> 97 </when>
88 <when value="yes" /> 98 <when value="yes" />
89 </conditional> 99 </conditional>
90 100 </xml>
91 </xml> 101
92 <token name="@kmeans_clusterin@"> 102 <token name="@KMEANS_CLUSTERING@">
93 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': 103 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
94 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': 104 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
95 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: 105 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
96 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans 106 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
97 #end if 107 #end if
98 #end if 108 #end if
99 #end if 109 #end if
100 </token> 110 </token>
111
112 <xml name="samFlag">
113 <param name="samFlag" type="integer" optional="true" value=""
114 label="Filter reads based on the SAM flag"
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)"/>
116 </xml>
117 <xml name="plotNumbers">
118 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
119 label="Plot the correlation value"
120 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
121 </xml>
122 <xml name="doNotExtendPairedEnds">
123 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
124 label="Do not extend paired ends"
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)"/>
126 </xml>
127
128 <xml name="ignoreDuplicates">
129 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
130 label="Ignore duplicates"
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)" />
132 </xml>
133
134 <xml name="minMappingQuality">
135 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
136 label="Minimum mapping quality"
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)"/>
138 </xml>
139
140 <xml name="skipZeros">
141 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
142 label ="Skip zeros"
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)" />
144 </xml>
145
146 <xml name="fragmentLength">
147 <param name="fragmentLength" type="integer" value="300" min="1"
148 label="Fragment length used for the sequencing"
149 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
150 </xml>
151
152 <xml name="scaleFactor">
153 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
154 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
155 </xml>
101 156
102 <xml name="stdio"> 157 <xml name="stdio">
103 <stdio> 158 <stdio>
104 <exit_code range="1:" /> 159 <exit_code range="1:" />
105 <exit_code range=":-1" /> 160 <exit_code range=":-1" />
107 <regex match="Exception:" /> 162 <regex match="Exception:" />
108 <regex match="EXception:" /> 163 <regex match="EXception:" />
109 <regex match="Traceback" /> 164 <regex match="Traceback" />
110 </stdio> 165 </stdio>
111 </xml> 166 </xml>
167
112 <xml name="pseudocount"> 168 <xml name="pseudocount">
113 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> 169 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
114 </xml> 170 </xml>
171
115 <token name="@REFERENCES@"> 172 <token name="@REFERENCES@">
116 173
117 .. class:: infomark 174 .. class:: infomark
118 175
119 For more information on the tools, please visit our `help site`_. 176 For more information on the tools, please visit our `help site`_.
123 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. 180 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
124 181
125 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ 182 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
126 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de 183 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
127 .. _help site: https://github.com/fidelram/deepTools/wiki/ 184 .. _help site: https://github.com/fidelram/deepTools/wiki/
128
129 **References**
130
131 If you use this Galaxy tool in work leading to a scientific publication please
132 cite the following paper:
133 185
134 </token> 186 </token>
135 <xml name="citations"> 187 <xml name="citations">
136 <citations> 188 <citations>
137 <citation type="doi">10.1093/nar/gku365</citation> 189 <citation type="doi">10.1093/nar/gku365</citation>
138 <yield /> 190 <yield />
139 </citations> 191 </citations>
140 </xml> 192 </xml>
141 193
142 <xml name="multiple_input_bams"> 194 <xml name="multiple_input_bams">
143 <repeat name="input_files" title="BAM files" min="2"> 195 <param name="bamfiles" type="data" format="bam"
144 <param name="bamfile" type="data" format="bam" 196 label="Bam file" multiple="true"
145 label="Bam file" 197 help="The BAM file must be sorted."/>
146 help="The BAM file must be sorted."/> 198 </xml>
147 <param name="label" type="text" size="30" optional="true" value="" 199
148 label="Label" 200 <xml name="multiple_input_bigwigs">
149 help="Label to use in the output. If not given the dataset name will be used instead."/> 201 <param name="bigwigfiles" type="data" format="bigwig" multiple="True"
150 </repeat> 202 label="Bigwig file"
203 help="The Bigwig file must be sorted."/>
204 </xml>
205
206 <xml name="plotTitle">
207 <param name="plotTitle" type="text" value="" size="30" optional="True"
208 label="Title of the plot"
209 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
151 </xml> 210 </xml>
152 211
153 <token name="@multiple_input_bams@"> 212 <token name="@multiple_input_bams@">
154 #import tempfile 213 <![CDATA[
155 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
156 #set files=[] 214 #set files=[]
157 #set labels=[] 215 #set labels=[]
158 #for $i in $input_files: 216 #for $counter, $bamfile in enumerate($bamfiles):
159 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) 217 ln -s "${bamfile}" "./${counter}.bam" &&
160 #set $temp_input_path = $temp_input_handle.name 218 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
161 #silent $temp_input_handle.close() 219 #silent $files.append('%s.bam' % $counter)
162 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path)) 220 #silent $labels.append("'%s'" % ($bamfile.display_name))
163 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
164 #silent $files.append('%s.bam' % $temp_input_path)
165
166 ##set $files += [str($i.bamfile)]
167 #if str($i.label.value) != "":
168 #set $labels += ["\"%s\"" % ($i.label.value)]
169 #else
170 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
171 #end if
172 #end for 221 #end for
222 ]]>
223 </token>
224
225 <token name="@multiple_input_bigwigs@">
226 <![CDATA[
227 #set files=[]
228 #set labels=[]
229 #for $counter, $bigwig in enumerate($bigwigfiles):
230 ln -s "${bigwig}" "${counter}.bw" &&
231 #silent $files.append('%s.bw' % $counter)
232 #silent $labels.append("'%s'" % ($bigwig.display_name))
233 #end for
234 ]]>
173 </token> 235 </token>
174 236
175 <xml name="reference_genome_source"> 237 <xml name="reference_genome_source">
176 <conditional name="source"> 238 <conditional name="source">
177 <param name="ref_source" type="select" label="Reference genome"> 239 <param name="ref_source" type="select" label="Reference genome">
178 <option value="cached">locally cached</option> 240 <option value="cached">locally cached</option>
179 <option value="history">in your history</option> 241 <option value="history">in your history</option>
180 </param> 242 </param>
181 <when value="cached"> 243 <when value="cached">
182 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> 244 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
183 <options from_data_table="deepTools_seqs"> 245 <options from_data_table="lastz_seqs">
184 <filter type="sort_by" column="1" /> 246 <filter type="sort_by" column="1" />
185 <validator type="no_options" message="No indexes are available." /> 247 <validator type="no_options" message="No indexes are available." />
186 </options> 248 </options>
187 </param> 249 </param>
188 </when> 250 </when>