Mercurial > repos > artbio > small_rna_maps

comparison small_rna_maps.xml @ 18:2c95c899d0a4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
author artbio
date Thu, 22 Nov 2018 03:07:41 -0500
parents b28dcd4051e8
children f33afecac67a
comparison
equal deleted inserted replaced
17:b28dcd4051e8 18:2c95c899d0a4
1 <tool id="small_rna_maps" name="small_rna_maps" version="2.8.0"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="2.9.0">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement> 4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> 5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
6 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> 6 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
36 --outputs '$output_tab' && 36 --outputs '$output_tab' &&
37 #elif str($plots_options.plots_options_selector ) == "cluster": 37 #elif str($plots_options.plots_options_selector ) == "cluster":
38 --plot_methods 'Counts' 38 --plot_methods 'Counts'
39 --outputs '$output_tab' 39 --outputs '$output_tab'
40 --cluster ${plots_options.cluster} 40 --cluster ${plots_options.cluster}
41 --bed '$output_bed'
42 --bed_skipcluster ${plots_options.skip_cluster}
41 ${plots_options.strandness} && 43 ${plots_options.strandness} &&
42 #else: 44 #else:
43 --plot_methods '${plots_options.first_plot}' 45 --plot_methods '${plots_options.first_plot}'
44 --outputs '$output_tab' && 46 --outputs '$output_tab' &&
45 #end if 47 #end if
48
46 49
47 Rscript '$__tool_directory__'/small_rna_maps.r 50 Rscript '$__tool_directory__'/small_rna_maps.r
48 --first_dataframe '$output_tab' 51 --first_dataframe '$output_tab'
49 --extra_dataframe '$extra_output_tab' 52 --extra_dataframe '$extra_output_tab'
50 --normalization 53 --normalization
126 <param name="first_plot" type="hidden" value="Counts"/> 129 <param name="first_plot" type="hidden" value="Counts"/>
127 <param name="cluster" type="integer" label="Aggregation distance in nucleotides" value="1" 130 <param name="cluster" type="integer" label="Aggregation distance in nucleotides" value="1"
128 help="Sets the distance (in nt) below which reads are clustered to a single median position" /> 131 help="Sets the distance (in nt) below which reads are clustered to a single median position" />
129 <param name="strandness" argument="--nostrand" type="boolean" truevalue="--nostrand" falsevalue="" checked="false" 132 <param name="strandness" argument="--nostrand" type="boolean" truevalue="--nostrand" falsevalue="" checked="false"
130 label="Ignore polarity of reads ?" help="Set if you wish to cluster reads regardless of whether they are forward or reverse"/> 133 label="Ignore polarity of reads ?" help="Set if you wish to cluster reads regardless of whether they are forward or reverse"/>
134 <param name="skip_cluster" type="integer" label="do not report cluster equal or less than the specified number of nucleotides" value="0"
135 help="Set the number of nucleotides in the cluster for which and below which a cluster is not reported in the bed output. Set to 0 (default) reports all including singlets" />
131 </when> 136 </when>
132 </conditional> 137 </conditional>
133 <conditional name="ylimits_cond"> 138 <conditional name="ylimits_cond">
134 <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?" 139 <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?"
135 help="This limit won't be applied to size distribution plots"/> 140 help="This limit won't be applied to size distribution plots"/>
142 </conditional> 147 </conditional>
143 </inputs> 148 </inputs>
144 149
145 <outputs> 150 <outputs>
146 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" /> 151 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" />
152 <data format="bed" name="output_bed" label="bed file for clusters" >
153 <filter>plots_options['plots_options_selector'] == 'cluster'</filter>
154 </data>
147 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe"> 155 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe">
148 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter> 156 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter>
149 </data> 157 </data>
150 <data format="pdf" name="output_pdf" label="small RNA maps" /> 158 <data format="pdf" name="output_pdf" label="small RNA maps" />
151 </outputs> 159 </outputs>
190 <param name="minsize" value="0" /> 198 <param name="minsize" value="0" />
191 <param name="maxsize" value="10000" /> 199 <param name="maxsize" value="10000" />
192 <param name="plots_options_selector" value="cluster" /> 200 <param name="plots_options_selector" value="cluster" />
193 <param name="first_plot" value="Counts" /> 201 <param name="first_plot" value="Counts" />
194 <param name="cluster" value="5" /> 202 <param name="cluster" value="5" />
203 <param name="skip_cluster" value="0" />
195 <param name="strandness" value="false" /> 204 <param name="strandness" value="false" />
196 <output file="clustering.tab" name="output_tab" /> 205 <output file="clustering.tab" name="output_tab" />
197 <output file="clustering.pdf" name="output_pdf" /> 206 <output file="clustering.pdf" name="output_pdf" />
207 <output file="bed1.bed" name="output_bed" />
198 </test> 208 </test>
199 <test> <!-- 3 --> 209 <test> <!-- 3 -->
200 <repeat name="series"> 210 <repeat name="series">
201 <param name="inputs" value="input1.bam" ftype="bam" /> 211 <param name="inputs" value="input1.bam" ftype="bam" />
202 <param name="normalization" value="1.0" /> 212 <param name="normalization" value="1.0" />
204 <param name="minsize" value="0" /> 214 <param name="minsize" value="0" />
205 <param name="maxsize" value="10000" /> 215 <param name="maxsize" value="10000" />
206 <param name="plots_options_selector" value="cluster" /> 216 <param name="plots_options_selector" value="cluster" />
207 <param name="first_plot" value="Counts" /> 217 <param name="first_plot" value="Counts" />
208 <param name="cluster" value="5" /> 218 <param name="cluster" value="5" />
219 <param name="skip_cluster" value="0" />
209 <param name="strandness" value="true" /> 220 <param name="strandness" value="true" />
210 <output file="clustering_unstranded.tab" name="output_tab" /> 221 <output file="clustering_unstranded.tab" name="output_tab" />
211 <output file="clustering_unstranded.pdf" name="output_pdf" /> 222 <output file="clustering_unstranded.pdf" name="output_pdf" />
223 <output file="bed2.bed" name="output_bed" />
224 </test>
225 <test> <!-- 3.1 -->
226 <repeat name="series">
227 <param name="inputs" value="input1.bam" ftype="bam" />
228 <param name="normalization" value="1.0" />
229 </repeat>
230 <param name="minsize" value="0" />
231 <param name="maxsize" value="10000" />
232 <param name="plots_options_selector" value="cluster" />
233 <param name="first_plot" value="Counts" />
234 <param name="cluster" value="5" />
235 <param name="skip_cluster" value="1" />
236 <param name="strandness" value="false" />
237 <output file="clustering.tab" name="output_tab" />
238 <output file="clustering.pdf" name="output_pdf" />
239 <output file="bed3.bed" name="output_bed" />
212 </test> 240 </test>
213 <test> <!-- 4 --> 241 <test> <!-- 4 -->
214 <repeat name="series"> 242 <repeat name="series">
215 <param name="inputs" value="input1.bam" ftype="bam" /> 243 <param name="inputs" value="input1.bam" ftype="bam" />
216 <param name="normalization" value="1.0" /> 244 <param name="normalization" value="1.0" />