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comparison deepTools_macros.xml @ 9:6531acf8209f draft

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"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
author bgruening
date Sat, 25 Jan 2020 05:03:38 -0500
parents 0741d8c3bf35
children e5a296ce8fbb
comparison
equal deleted inserted replaced
8:0741d8c3bf35 9:6531acf8209f
1 <macros> 1 <macros>
2 2
3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> 3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
4 <token name="@WRAPPER_VERSION@">3.3.0.0</token> 4 <token name="@WRAPPER_VERSION@">3.3.2.0</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="3.3.0">deeptools</requirement> 7 <requirement type="package" version="3.3.2">deeptools</requirement>
8 <requirement type="package" version="1.9">samtools</requirement> 8 <requirement type="package" version="1.9">samtools</requirement>
9 </requirements> 9 </requirements>
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <version_command>@BINARY@ --version</version_command> 11 <version_command>@BINARY@ --version</version_command>
12 </xml> 12 </xml>
162 If more specific clustering methods are required it is advisable to save the underlying matrix and 162 If more specific clustering methods are required it is advisable to save the underlying matrix and
163 run the clustering using other software."/> 163 run the clustering using other software."/>
164 </when> 164 </when>
165 <when value="none" /> 165 <when value="none" />
166 </conditional> 166 </conditional>
167 <param argument="--silhouette" type="boolean" truevalue="--silhouette" falsevalue=""
168 label="Compute the silhouette score for each region"
169 help="Compute the silhouette score for regions. This is only applicable if clustering has been performed.
170 The silhouette score is a measure of how similar a region is to other regions in the same cluster as
171 opposed to those in other clusters. It will be reported in the final column of the BED file with regions.
172 The silhouette evaluation can be very slow when you have more than 100 000 regions." />
167 </when> 173 </when>
168 <when value="yes" /> 174 <when value="yes" />
169 </conditional> 175 </conditional>
170 </xml> 176 </xml>
171 177
179 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust': 185 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
180 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0: 186 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
181 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust 187 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
182 #end if 188 #end if
183 #end if 189 #end if
190 $advancedOpt.used_multiple_regions.silhouette
184 #end if 191 #end if
185 </token> 192 </token>
186 193
187 <xml name="samFlags"> 194 <xml name="samFlags">
188 <param argument="--samFlagInclude" type="integer" optional="True" value="" 195 <param argument="--samFlagInclude" type="integer" optional="True" value=""
215 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue="" 222 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
216 label="Use a metagene model" 223 label="Use a metagene model"
217 help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." /> 224 help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
218 <param argument="--transcriptID" optional="True" value="transcript" type="text" 225 <param argument="--transcriptID" optional="True" value="transcript" type="text"
219 label="transcript designator" 226 label="transcript designator"
220 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" /> 227 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as transcripts. Default: transcript" />
221 <param argument="--exonID" optional="True" value="exon" type="text" 228 <param argument="--exonID" optional="True" value="exon" type="text"
222 label="exon designator" 229 label="exon designator"
223 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" /> 230 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as exons. CDS would be another common value for this. Default: exon" />
224 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text" 231 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
225 label="transcriptID key designator" 232 label="transcriptID key designator"
226 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists) 233 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
227 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g., 234 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
228 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be 235 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
366 373
367 .. class:: infomark 374 .. class:: infomark
368 375
369 For more information on the tools, please visit our `help site`_. 376 For more information on the tools, please visit our `help site`_.
370 377
371 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com 378 For support or questions please post to `Biostars`_. For bug reports and feature requests please open an issue `on github`_.
372 379
373 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. 380 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
374 381
382 .. _Biostars: http://biostars.org
383 .. _on github: http://github.com
375 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac 384 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
376 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de 385 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
377 .. _help site: https://deeptools.readthedocs.org/ 386 .. _help site: https://deeptools.readthedocs.org/
378 387
379 </token> 388 </token>
822 <option value="bwr">bwr</option> 831 <option value="bwr">bwr</option>
823 <option value="hsv">hsv</option> 832 <option value="hsv">hsv</option>
824 <option value="brg">brg</option> 833 <option value="brg">brg</option>
825 <option value="jet">jet</option> 834 <option value="jet">jet</option>
826 <option value="afmhot">afmhot</option> 835 <option value="afmhot">afmhot</option>
836 <option value="Wistia">Wistia</option>
837 <option value="cividis">cividis</option>
838 <option value="icefire">icefire</option>
839 <option value="inferno">inferno</option>
840 <option value="magma">magma</option>
841 <option value="mako">mako</option>
842 <option value="nipy_spectral">nipy_spectral</option>
843 <option value="plasma">plasma</option>
844 <option value="rocket">rocket</option>
845 <option value="tab10">tab10</option>
846 <option value="tab20">tab20</option>
847 <option value="tab20b">tab20b</option>
848 <option value="tab20c">tab20c</option>
849 <option value="twilight">twilight</option>
850 <option value="twilight_shifted">twilight_shifted</option>
851 <option value="viridis">viridis</option>
852 <option value="vlag">vlag</option>
827 <option value="Accent_r">Accent reversed</option> 853 <option value="Accent_r">Accent reversed</option>
828 <option value="Spectral_r">Spectral reversed</option> 854 <option value="Spectral_r">Spectral reversed</option>
829 <option value="Set1_r">Set1 reversed</option> 855 <option value="Set1_r">Set1 reversed</option>
830 <option value="Set2_r">Set2 reversed</option> 856 <option value="Set2_r">Set2 reversed</option>
831 <option value="Set3_r">Set3 reversed</option> 857 <option value="Set3_r">Set3 reversed</option>
891 <option value="bwr_r">bwr reversed</option> 917 <option value="bwr_r">bwr reversed</option>
892 <option value="hsv_r">hsv reversed</option> 918 <option value="hsv_r">hsv reversed</option>
893 <option value="brg_r">brg reversed</option> 919 <option value="brg_r">brg reversed</option>
894 <option value="jet_r">jet reversed</option> 920 <option value="jet_r">jet reversed</option>
895 <option value="afmhot_r">afmhot reversed</option> 921 <option value="afmhot_r">afmhot reversed</option>
922 <option value="Wistia_r">Wistia reversed</option>
923 <option value="cividis_r">cividis reversed</option>
924 <option value="icefire_r">icefire reversed</option>
925 <option value="inferno_r">inferno reversed</option>
926 <option value="magma_r">magma reversed</option>
927 <option value="mako_r">mako reversed</option>
928 <option value="nipy_spectral_r">nipy_spectral reversed</option>
929 <option value="plasma_r">plasma reversed</option>
930 <option value="rocket_r">rocket reversed</option>
931 <option value="tab10_r">tab10 reversed</option>
932 <option value="tab20_r">tab20 reversed</option>
933 <option value="tab20b_r">tab20b reversed</option>
934 <option value="tab20c_r">tab20c reversed</option>
935 <option value="twilight_r">twilight reversed</option>
936 <option value="twilight_shifted_r">twilight_shifted reversed</option>
937 <option value="viridis_r">viridis reversed</option>
938 <option value="vlag_r">vlag reversed</option>
896 </param> 939 </param>
897 940
898 </xml> 941 </xml>
899 942
900 </macros> 943 </macros>