Mercurial > repos > iuc > crosscontamination_barcode_filter
diff 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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--- a/crosscontamination_barcode_filter.xml Mon Jun 03 14:55:24 2019 -0400 +++ b/crosscontamination_barcode_filter.xml Wed Jun 12 04:58:19 2019 -0400 @@ -1,7 +1,7 @@ <tool id="crosscontamination_barcode_filter" name="Cross-contamination Barcode Filter" version="@VERSION@"> <description>for use in plate-based barcoded analyses</description> <macros> - <token name="@VERSION@">0.2</token> + <token name="@VERSION@">0.3</token> <macro name="sanitize_batch"> <sanitizer invalid_char=""> <valid initial="string.digits"> @@ -85,6 +85,7 @@ #end if regex.extract = '$advanced.regex_extract' regex.display = '$advanced.regex_display' +sort.cells = as.logical('$advanced.sort_sizes') out.pdf = '$out_plots' out.table = '$out_table' ]]> @@ -115,13 +116,14 @@ </repeat> </when> </conditional> - <section name="advanced" expanded="false" title="RegEx Parameters" > + <section name="advanced" expanded="false" title="Advanced Parameters" > <param name="regex_extract" type="text" value=".*P(\\d)_B(\\d)_([ACTG]+)" label="RegEx to extract Plate, Batch, and Barcodes from headers" > <expand macro="sanitize_regex" /> </param> <param name="regex_display" type="text" value="P\\1_B\\2_\\3" label="RegEx to replace Plate, Batch, and Barcodes from headers" > <expand macro="sanitize_regex" /> </param> + <param name="sort_sizes" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Sort Cells by Library Size" /> </section> </inputs> <outputs> @@ -165,12 +167,44 @@ <output name="out_plots" value="out.pdf" compare="sim_size" /> <output name="out_table" value="out.table" /> </test> + <test><!-- 12 Batch test --> + <param name="input_table" value="b12.matrix" /> + <param name="input_barcodes" value="celseq_barcodes.192.raw" /> + <conditional name="inbuilt_spec" > + <param name="select_use" value="custom" /> + <repeat name="barcode_format" > + <param name="range_start" value="1"/> + <param name="range_end" value="96" /> + <param name="batches" value="1,3,5,7,9,11" /> + </repeat> + <repeat name="barcode_format" > + <param name="range_start" value="97"/> + <param name="range_end" value="192" /> + <param name="batches" value="2,4,6,8,10,12" /> + </repeat> + <repeat name="plate_format" > + <param name="plate" value="1" /> + <param name="batches" value="1,2,3,4" /> + </repeat> + <repeat name="plate_format" > + <param name="plate" value="2" /> + <param name="batches" value="5,6,7,8" /> + </repeat> + <repeat name="plate_format" > + <param name="plate" value="3" /> + <param name="batches" value="9,10,11,12" /> + </repeat> + </conditional> + <output name="out_plots" value="b12.pdf" compare="sim_size" /> + <output name="out_table" value="b12.table" /> + </test> </tests> <help><![CDATA[ Cross-contamination Filter Plot ################################### 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. +*Note -- Do not reuse batch numbering across plates!* 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).