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comparison deepTools_macros.xml @ 13:b4c5dd45778a draft

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author bgruening
date Mon, 16 Dec 2013 04:36:19 -0500
parents aea72b24dea0
children a7ae8ce85f45
comparison
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12:aea72b24dea0 13:b4c5dd45778a
1 <macros> 1 <macros>
2 <macro name="bamCorrelate_mode_actions"> 2 <xml name="bamCorrelate_mode_actions">
3 <conditional name="advancedOpt"> 3 <conditional name="advancedOpt">
4 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 4 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
5 <option value="no" selected="true">no</option> 5 <option value="no" selected="true">no</option>
6 <option value="yes">yes</option> 6 <option value="yes">yes</option>
7 </param> 7 </param>
34 help="If not specified the value is set automatically."/> 34 help="If not specified the value is set automatically."/>
35 35
36 <expand macro="colormap" /> 36 <expand macro="colormap" />
37 </when> 37 </when>
38 </conditional> 38 </conditional>
39 </macro> 39 </xml>
40 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> 40 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
41 <macro name="requirements"> 41 <xml name="requirements">
42 <requirements> 42 <requirements>
43 <requirement type="package" >samtools</requirement> 43 <requirement type="package" >samtools</requirement>
44 <requirement type="package" >deepTools</requirement> 44 <requirement type="package" >deepTools</requirement>
45 <requirement type="package" >ucsc_tools</requirement> 45 <requirement type="package" >ucsc_tools</requirement>
46 <requirement type="package" version="1.5.4_6765c227d9628f8e6ba690e6fde7f1d86c497b49">deepTools</requirement> 46 <requirement type="package" version="1.5.4_74aac0843a956ca352e3e85087f20c8f158e2f7d">deepTools</requirement>
47 <requirement type="package" version="0.1">ucsc_tools</requirement> 47 <requirement type="package" version="0.1">ucsc_tools</requirement>
48 <requirement type="package" version="1.7.1">numpy</requirement> 48 <requirement type="package" version="1.7.1">numpy</requirement>
49 <requirement type="package" version="0.7.7">pysam</requirement> 49 <requirement type="package" version="0.7.7">pysam</requirement>
50 <requirement type="package" version="0.12.0">scipy</requirement> 50 <requirement type="package" version="0.12.0">scipy</requirement>
51 <requirement type="package" version="1.2.1">matplotlib</requirement> 51 <requirement type="package" version="1.2.1">matplotlib</requirement>
52 <requirement type="package" version="0.1.19">samtools</requirement> 52 <requirement type="package" version="0.1.19">samtools</requirement>
53 <requirement type="package" version="12-2013">bx-python</requirement> 53 <requirement type="package" version="12-2013">bx-python</requirement>
54 <yield /> 54 <yield />
55 </requirements> 55 </requirements>
56 </macro> 56 </xml>
57 <macro name="stdio"> 57 <xml name="stdio">
58 <stdio> 58 <stdio>
59 <exit_code range="1:" /> 59 <exit_code range="1:" />
60 <exit_code range=":-1" /> 60 <exit_code range=":-1" />
61 <exit_code range="0" level="warning" description="Warning" />
62 <regex match="Error:" /> 61 <regex match="Error:" />
63 <regex match="Exception:" /> 62 <regex match="Exception:" />
64 <regex match="EXception:" /> 63 <regex match="EXception:" />
65 <regex match="Traceback" /> 64 <regex match="Traceback" />
66 </stdio> 65 </stdio>
67 </macro> 66 </xml>
68 <token name="@REFERENCES@"> 67 <token name="@REFERENCES@">
69 68
70 For more informations, please visit our `project site`_. 69 For more informations, please visit our `project site`_.
71 70
72 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com 71 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
78 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de 77 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
79 .. _project site: https://github.com/fidelram/deepTools 78 .. _project site: https://github.com/fidelram/deepTools
80 79
81 </token> 80 </token>
82 81
83 <macro name="multiple_input_bams"> 82 <xml name="multiple_input_bams">
84 <repeat name="input_files" title="BAM files" min="2"> 83 <repeat name="input_files" title="BAM files" min="2">
85 <param name="bamfile" type="data" format="bam" 84 <param name="bamfile" type="data" format="bam"
86 label="Bam file" 85 label="Bam file"
87 help="The BAM file must be sorted."/> 86 help="The BAM file must be sorted."/>
88 <param name="label" type="text" size="30" optional="true" value="" 87 <param name="label" type="text" size="30" optional="true" value=""
89 label="Label" 88 label="Label"
90 help="Label to use in the output. If not given the dataset name will be used instead."/> 89 help="Label to use in the output. If not given the dataset name will be used instead."/>
91 </repeat> 90 </repeat>
92 </macro> 91 </xml>
93 92
94 <token name="@multiple_input_bams@"> 93 <token name="@multiple_input_bams@">
95 #for $i in $input_files: 94 #for $i in $input_files:
96 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) 95 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
97 #set $temp_input_path = $temp_input_handle.name 96 #set $temp_input_path = $temp_input_handle.name
107 #set $labels += ["\"%s\"" % ($i.bamfile.name)] 106 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
108 #end if 107 #end if
109 #end for 108 #end for
110 </token> 109 </token>
111 110
112 <macro name="reference_genome_source"> 111 <xml name="reference_genome_source">
113 <conditional name="source"> 112 <conditional name="source">
114 <param name="ref_source" type="select" label="Reference genome"> 113 <param name="ref_source" type="select" label="Reference genome">
115 <option value="cached">locally cached</option> 114 <option value="cached">locally cached</option>
116 <option value="history">in your history</option> 115 <option value="history">in your history</option>
117 </param> 116 </param>
125 </when> 124 </when>
126 <when value="history"> 125 <when value="history">
127 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> 126 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
128 </when> 127 </when>
129 </conditional> 128 </conditional>
130 </macro> 129 </xml>
131 130
132 <token name="@reference_genome_source@"> 131 <token name="@reference_genome_source@">
133 #if $source.ref_source=="history": 132 #if $source.ref_source=="history":
134 --genome $source.input1 133 --genome $source.input1
135 #else: 134 #else:
136 --genome "${source.input1_2bit.fields.path}" 135 --genome "${source.input1_2bit.fields.path}"
137 #end if 136 #end if
138 </token> 137 </token>
139 138
140 <macro name="effectiveGenomeSize"> 139 <xml name="effectiveGenomeSize">
141 <conditional name="effectiveGenomeSize"> 140 <conditional name="effectiveGenomeSize">
142 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" 141 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
143 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. 142 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.
144 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. 143 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
145 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."> 144 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.">
151 </param> 150 </param>
152 <when value="specific"> 151 <when value="specific">
153 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" /> 152 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" />
154 </when> 153 </when>
155 </conditional> 154 </conditional>
156 </macro> 155 </xml>
157 156
158 <macro name="image_file_format"> 157 <xml name="image_file_format">
159 <param name="outFileFormat" type="select" label="Image file format"> 158 <param name="outFileFormat" type="select" label="Image file format">
160 <option value="png" selected="true">png</option> 159 <option value="png" selected="true">png</option>
161 <option value="pdf">pdf</option> 160 <option value="pdf">pdf</option>
162 <option value="svg">svg</option> 161 <option value="svg">svg</option>
163 <option value="eps">eps</option> 162 <option value="eps">eps</option>
164 <option value="emf">emf</option> 163 <option value="emf">emf</option>
165 </param> 164 </param>
166 </macro> 165 </xml>
167 166
168 <macro name="graphic_output_settings"> 167 <xml name="input_save_matrix_values">
168 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
169 </xml>
170
171 <xml name="input_graphic_output_settings">
169 <conditional name="output" > 172 <conditional name="output" >
170 <param name="showOutputSettings" type="select" label="Show advanced output settings" > 173 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
171 <option value="no" selected="true">no</option> 174 <option value="no" selected="true">no</option>
172 <option value="yes">yes</option> 175 <option value="yes">yes</option>
173 </param> 176 </param>
174 <when value="no" /> 177 <when value="no" />
175 <when value="yes"> 178 <when value="yes">
176 <yield /> 179 <yield />
177 <param name="saveData" type="boolean" label="Save the data underlying data for the average profile"/> 180 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
178 <param name="saveMatrix" type="boolean" label="Save the the matrix of values underlying the heatmap"/>
179 <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."/> 181 <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."/>
180 </when> 182 </when>
181 </conditional> 183 </conditional>
182 </macro> 184 </xml>
183 185
184 <macro name="input_image_file_format"> 186 <xml name="input_image_file_format">
185 <param name="outFileFormat" type="select" label="Image file format"> 187 <param name="outFileFormat" type="select" label="Image file format">
186 <option value="png" selected="true">png</option> 188 <option value="png" selected="true">png</option>
187 <option value="pdf">pdf</option> 189 <option value="pdf">pdf</option>
188 <option value="svg">svg</option> 190 <option value="svg">svg</option>
189 <option value="eps">eps</option> 191 <option value="eps">eps</option>
190 <option value="emf">emf</option> 192 <option value="emf">emf</option>
191 </param> 193 </param>
192 </macro> 194 </xml>
193 195
194 <macro name="output_image_file_format"> 196 <xml name="output_image_file_format">
195 <data format="png" name="outFileName" label="${tool.name} image"> 197 <data format="png" name="outFileName" label="${tool.name} image">
196 <change_format> 198 <change_format>
197 <when input="output.outFileFormat" value="pdf" format="pdf" /> 199 <when input="output.outFileFormat" value="pdf" format="pdf" />
198 <when input="output.outFileFormat" value="svg" format="svg" /> 200 <when input="output.outFileFormat" value="svg" format="svg" />
199 <when input="output.outFileFormat" value="eps" format="eps" /> 201 <when input="output.outFileFormat" value="eps" format="eps" />
200 <when input="output.outFileFormat" value="emf" format="emf" /> 202 <when input="output.outFileFormat" value="emf" format="emf" />
201 </change_format> 203 </change_format>
202 </data> 204 </data>
203 </macro> 205 </xml>
204 206
205 <macro name="output_graphic_outputs"> 207 <xml name="output_save_matrix_values">
206 <yield /> 208 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
209 <filter>
210 ((
211 output['showOutputSettings'] == 'yes' and
212 output['saveMatrix'] is True
213 ))
214 </filter>
215 </data>
216 </xml>
217
218 <xml name="output_graphic_outputs">
207 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> 219 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
208 <filter> 220 <filter>
209 (( 221 ((
210 output['showOutputSettings'] == 'yes' and 222 output['showOutputSettings'] == 'yes' and
211 output['saveData'] is True 223 output['saveData'] is True
212 ))
213 </filter>
214 </data>
215 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
216 <filter>
217 ((
218 output['showOutputSettings'] == 'yes' and
219 output['saveMatrix'] is True
220 )) 224 ))
221 </filter> 225 </filter>
222 </data> 226 </data>
223 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> 227 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
224 <filter> 228 <filter>
226 output['showOutputSettings'] == 'yes' and 230 output['showOutputSettings'] == 'yes' and
227 output['saveSortedRegions'] is True 231 output['saveSortedRegions'] is True
228 )) 232 ))
229 </filter> 233 </filter>
230 </data> 234 </data>
231 </macro> 235 </xml>
232 236
233 <macro name="colormap"> 237 <xml name="colormap">
234 <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/"> 238 <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/">
235 <option value="RdYlBu" selected="true">RdYlBu</option> 239 <option value="RdYlBu" selected="true">RdYlBu</option>
236 <option value="Accent">Accent</option> 240 <option value="Accent">Accent</option>
237 <option value="Spectral">Spectral</option> 241 <option value="Spectral">Spectral</option>
238 <option value="Set1">Set1</option> 242 <option value="Set1">Set1</option>
370 <option value="brg_r">brg reversed</option> 374 <option value="brg_r">brg reversed</option>
371 <option value="jet_r">jet reversed</option> 375 <option value="jet_r">jet reversed</option>
372 <option value="afmhot_r">afmhot reversed</option> 376 <option value="afmhot_r">afmhot reversed</option>
373 </param> 377 </param>
374 378
375 </macro> 379 </xml>
376 380
377 </macros> 381 </macros>