Mercurial > repos > artbio > small_rna_maps
comparison small_rna_maps.xml @ 17:b28dcd4051e8 draft
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 |
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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" /> |