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comparison small_rna_maps.xml @ 17:b28dcd4051e8 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 16f15e5ab2b79590a8ae410f76434aa6690c1fc4
author artbio
date Thu, 15 Nov 2018 12:29:57 -0500
parents 600e2498bd21
children 2c95c899d0a4
comparison
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16:600e2498bd21 17:b28dcd4051e8
1 <tool id="small_rna_maps" name="small_rna_maps" version="2.7.0"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="2.8.0">
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>
35 --plot_methods 'Size' 35 --plot_methods 'Size'
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 ${plots_options.strandness} &&
41 #else: 42 #else:
42 --plot_methods '${plots_options.first_plot}' 43 --plot_methods '${plots_options.first_plot}'
43 --outputs '$output_tab' && 44 --outputs '$output_tab' &&
44 #end if 45 #end if
45 46
123 </when> 124 </when>
124 <when value="cluster"> 125 <when value="cluster">
125 <param name="first_plot" type="hidden" value="Counts"/> 126 <param name="first_plot" type="hidden" value="Counts"/>
126 <param name="cluster" type="integer" label="Aggregation distance in nucleotides" value="1" 127 <param name="cluster" type="integer" label="Aggregation distance in nucleotides" value="1"
127 help="Sets the distance (in nt) below which reads are clustered to a single median position" /> 128 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"
130 label="Ignore polarity of reads ?" help="Set if you wish to cluster reads regardless of whether they are forward or reverse"/>
128 </when> 131 </when>
129 </conditional> 132 </conditional>
130 <conditional name="ylimits_cond"> 133 <conditional name="ylimits_cond">
131 <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?" 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?"
132 help="This limit won't be applied to size distribution plots"/> 135 help="This limit won't be applied to size distribution plots"/>
146 </data> 149 </data>
147 <data format="pdf" name="output_pdf" label="small RNA maps" /> 150 <data format="pdf" name="output_pdf" label="small RNA maps" />
148 </outputs> 151 </outputs>
149 152
150 <tests> 153 <tests>
151 <test> <!-- 1 --> 154 <test> <!-- 0 -->
152 <repeat name="series"> 155 <repeat name="series">
153 <param name="inputs" value="input1.bam" ftype="bam" /> 156 <param name="inputs" value="input1.bam" ftype="bam" />
154 <param name="normalization" value="1.0" /> 157 <param name="normalization" value="1.0" />
155 </repeat> 158 </repeat>
156 <repeat name="series"> 159 <repeat name="series">
162 <param name="plots_options_selector" value="one_plot" /> 165 <param name="plots_options_selector" value="one_plot" />
163 <param name="first_plot" value="Counts" /> 166 <param name="first_plot" value="Counts" />
164 <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" /> 167 <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" />
165 <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" /> 168 <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
166 </test> 169 </test>
167 <test> <!-- 2 --> 170 <test> <!-- 1 -->
168 <repeat name="series"> 171 <repeat name="series">
169 <param name="inputs" value="input1.bam" ftype="bam" /> 172 <param name="inputs" value="input1.bam" ftype="bam" />
170 <param name="normalization" value="1.0" /> 173 <param name="normalization" value="1.0" />
171 </repeat> 174 </repeat>
172 <param name="minsize" value="0" /> 175 <param name="minsize" value="0" />
177 <param name="plots_options_selector" value="one_plot" /> 180 <param name="plots_options_selector" value="one_plot" />
178 <param name="first_plot" value="Counts" /> 181 <param name="first_plot" value="Counts" />
179 <output file="input1_counts_yminneg5_5.tab" name="output_tab" /> 182 <output file="input1_counts_yminneg5_5.tab" name="output_tab" />
180 <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" /> 183 <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" />
181 </test> 184 </test>
182 <test> <!-- 3 --> 185 <test> <!-- 2 -->
183 <repeat name="series"> 186 <repeat name="series">
184 <param name="inputs" value="input1.bam" ftype="bam" /> 187 <param name="inputs" value="input1.bam" ftype="bam" />
185 <param name="normalization" value="1.0" /> 188 <param name="normalization" value="1.0" />
186 </repeat> 189 </repeat>
187 <param name="minsize" value="0" /> 190 <param name="minsize" value="0" />
188 <param name="maxsize" value="10000" /> 191 <param name="maxsize" value="10000" />
189 <param name="plots_options_selector" value="cluster" /> 192 <param name="plots_options_selector" value="cluster" />
190 <param name="first_plot" value="Counts" /> 193 <param name="first_plot" value="Counts" />
191 <param name="cluster" value="5" /> 194 <param name="cluster" value="5" />
195 <param name="strandness" value="false" />
192 <output file="clustering.tab" name="output_tab" /> 196 <output file="clustering.tab" name="output_tab" />
193 <output file="clustering.pdf" name="output_pdf" /> 197 <output file="clustering.pdf" name="output_pdf" />
198 </test>
199 <test> <!-- 3 -->
200 <repeat name="series">
201 <param name="inputs" value="input1.bam" ftype="bam" />
202 <param name="normalization" value="1.0" />
203 </repeat>
204 <param name="minsize" value="0" />
205 <param name="maxsize" value="10000" />
206 <param name="plots_options_selector" value="cluster" />
207 <param name="first_plot" value="Counts" />
208 <param name="cluster" value="5" />
209 <param name="strandness" value="true" />
210 <output file="clustering_unstranded.tab" name="output_tab" />
211 <output file="clustering_unstranded.pdf" name="output_pdf" />
194 </test> 212 </test>
195 <test> <!-- 4 --> 213 <test> <!-- 4 -->
196 <repeat name="series"> 214 <repeat name="series">
197 <param name="inputs" value="input1.bam" ftype="bam" /> 215 <param name="inputs" value="input1.bam" ftype="bam" />
198 <param name="normalization" value="1.0" /> 216 <param name="normalization" value="1.0" />