Mercurial > repos > iuc > crosscontamination_barcode_filter
comparison crosscontamination_barcode_filter.xml @ 2:5ade5cf200da draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 82a0fd493f5866b3ef65019709ae5c865998f802
author | iuc |
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date | Wed, 12 Jun 2019 04:58:19 -0400 |
parents | 253c9448f524 |
children |
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1:253c9448f524 | 2:5ade5cf200da |
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1 <tool id="crosscontamination_barcode_filter" name="Cross-contamination Barcode Filter" version="@VERSION@"> | 1 <tool id="crosscontamination_barcode_filter" name="Cross-contamination Barcode Filter" version="@VERSION@"> |
2 <description>for use in plate-based barcoded analyses</description> | 2 <description>for use in plate-based barcoded analyses</description> |
3 <macros> | 3 <macros> |
4 <token name="@VERSION@">0.2</token> | 4 <token name="@VERSION@">0.3</token> |
5 <macro name="sanitize_batch"> | 5 <macro name="sanitize_batch"> |
6 <sanitizer invalid_char=""> | 6 <sanitizer invalid_char=""> |
7 <valid initial="string.digits"> | 7 <valid initial="string.digits"> |
8 <add value=","/> | 8 <add value=","/> |
9 </valid> | 9 </valid> |
83 ) | 83 ) |
84 ) | 84 ) |
85 #end if | 85 #end if |
86 regex.extract = '$advanced.regex_extract' | 86 regex.extract = '$advanced.regex_extract' |
87 regex.display = '$advanced.regex_display' | 87 regex.display = '$advanced.regex_display' |
88 sort.cells = as.logical('$advanced.sort_sizes') | |
88 out.pdf = '$out_plots' | 89 out.pdf = '$out_plots' |
89 out.table = '$out_table' | 90 out.table = '$out_table' |
90 ]]> | 91 ]]> |
91 </configfile> | 92 </configfile> |
92 </configfiles> | 93 </configfiles> |
113 <expand macro="sanitize_batch" /> | 114 <expand macro="sanitize_batch" /> |
114 </param> | 115 </param> |
115 </repeat> | 116 </repeat> |
116 </when> | 117 </when> |
117 </conditional> | 118 </conditional> |
118 <section name="advanced" expanded="false" title="RegEx Parameters" > | 119 <section name="advanced" expanded="false" title="Advanced Parameters" > |
119 <param name="regex_extract" type="text" value=".*P(\\d)_B(\\d)_([ACTG]+)" label="RegEx to extract Plate, Batch, and Barcodes from headers" > | 120 <param name="regex_extract" type="text" value=".*P(\\d)_B(\\d)_([ACTG]+)" label="RegEx to extract Plate, Batch, and Barcodes from headers" > |
120 <expand macro="sanitize_regex" /> | 121 <expand macro="sanitize_regex" /> |
121 </param> | 122 </param> |
122 <param name="regex_display" type="text" value="P\\1_B\\2_\\3" label="RegEx to replace Plate, Batch, and Barcodes from headers" > | 123 <param name="regex_display" type="text" value="P\\1_B\\2_\\3" label="RegEx to replace Plate, Batch, and Barcodes from headers" > |
123 <expand macro="sanitize_regex" /> | 124 <expand macro="sanitize_regex" /> |
124 </param> | 125 </param> |
126 <param name="sort_sizes" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Sort Cells by Library Size" /> | |
125 </section> | 127 </section> |
126 </inputs> | 128 </inputs> |
127 <outputs> | 129 <outputs> |
128 <data name="out_plots" format="pdf" label="${tool.name} on ${on_string}: Plots" /> | 130 <data name="out_plots" format="pdf" label="${tool.name} on ${on_string}: Plots" /> |
129 <data name="out_table" format="tabular" label="${tool.name} on ${on_string}: Filtered Table" /> | 131 <data name="out_table" format="tabular" label="${tool.name} on ${on_string}: Filtered Table" /> |
163 </repeat> | 165 </repeat> |
164 </conditional> | 166 </conditional> |
165 <output name="out_plots" value="out.pdf" compare="sim_size" /> | 167 <output name="out_plots" value="out.pdf" compare="sim_size" /> |
166 <output name="out_table" value="out.table" /> | 168 <output name="out_table" value="out.table" /> |
167 </test> | 169 </test> |
170 <test><!-- 12 Batch test --> | |
171 <param name="input_table" value="b12.matrix" /> | |
172 <param name="input_barcodes" value="celseq_barcodes.192.raw" /> | |
173 <conditional name="inbuilt_spec" > | |
174 <param name="select_use" value="custom" /> | |
175 <repeat name="barcode_format" > | |
176 <param name="range_start" value="1"/> | |
177 <param name="range_end" value="96" /> | |
178 <param name="batches" value="1,3,5,7,9,11" /> | |
179 </repeat> | |
180 <repeat name="barcode_format" > | |
181 <param name="range_start" value="97"/> | |
182 <param name="range_end" value="192" /> | |
183 <param name="batches" value="2,4,6,8,10,12" /> | |
184 </repeat> | |
185 <repeat name="plate_format" > | |
186 <param name="plate" value="1" /> | |
187 <param name="batches" value="1,2,3,4" /> | |
188 </repeat> | |
189 <repeat name="plate_format" > | |
190 <param name="plate" value="2" /> | |
191 <param name="batches" value="5,6,7,8" /> | |
192 </repeat> | |
193 <repeat name="plate_format" > | |
194 <param name="plate" value="3" /> | |
195 <param name="batches" value="9,10,11,12" /> | |
196 </repeat> | |
197 </conditional> | |
198 <output name="out_plots" value="b12.pdf" compare="sim_size" /> | |
199 <output name="out_table" value="b12.table" /> | |
200 </test> | |
168 </tests> | 201 </tests> |
169 <help><![CDATA[ | 202 <help><![CDATA[ |
170 Cross-contamination Filter Plot | 203 Cross-contamination Filter Plot |
171 ################################### | 204 ################################### |
172 | 205 |
173 For a set of barcodes and an experimental setup that uses a subset of these barcodes for each batch, this tool compares each batch against the full range of barcodes in order to determine whether any cross-contamination between batches has occured. | 206 For a set of barcodes and an experimental setup that uses a subset of these barcodes for each batch, this tool compares each batch against the full range of barcodes in order to determine whether any cross-contamination between batches has occured. |
207 *Note -- Do not reuse batch numbering across plates!* | |
174 | 208 |
175 If a significant number of transcripts are shown in a batch for cell barcodes that were not designed for that batch, then this tool will show that. In the below plot, we can see that there is no significant cross-contamination taking place (pre-filter), and so we can filter out the false barcodes (post-filter). | 209 If a significant number of transcripts are shown in a batch for cell barcodes that were not designed for that batch, then this tool will show that. In the below plot, we can see that there is no significant cross-contamination taking place (pre-filter), and so we can filter out the false barcodes (post-filter). |
176 | 210 |
177 .. image:: $PATH_TO_IMAGES/crosscontam_pretopost.png | 211 .. image:: $PATH_TO_IMAGES/crosscontam_pretopost.png |
178 :scale: 50 % | 212 :scale: 50 % |