Mercurial > repos > iuc > crosscontamination_barcode_filter
diff crosscontamination_barcode_filter.xml @ 1:253c9448f524 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
| author | iuc |
|---|---|
| date | Mon, 03 Jun 2019 14:55:24 -0400 |
| parents | 582b7bd4ae4c |
| children | 5ade5cf200da |
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--- a/crosscontamination_barcode_filter.xml Thu Jan 24 09:52:58 2019 -0500 +++ b/crosscontamination_barcode_filter.xml Mon Jun 03 14:55:24 2019 -0400 @@ -1,15 +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@">0.1</token> - <macro name="assert_conts" > - <assert_contents> - <has_text text="/CreationDate" /> - <has_text text="/Producer" /> - <has_line line="startxref" /> - <has_line line="%%EOF" /> - </assert_contents> - </macro> + <token name="@VERSION@">0.2</token> <macro name="sanitize_batch"> <sanitizer invalid_char=""> <valid initial="string.digits"> @@ -35,10 +27,11 @@ <add value=")"/> <!-- right parenthesis --> </valid> </sanitizer> - </macro> + </macro> </macros> <requirements> - <requirement type="package" version="2.2.1" >r-ggplot2</requirement> + <requirement type="package" version="3.1.1">r-ggplot2</requirement> + <requirement type="package" version="1.12.2">r-data.table </requirement> </requirements> <version_command><![CDATA[ Rscript '$__tool_directory__/scripts/crosscontamination_filter.R' | head -1 | cut -d' ' -f 2 @@ -61,12 +54,12 @@ spec = list( barcodes = '$input_barcodes', format = list( - "1-96" = c(1,3,5,7), - "97-192" = c(2,4,6,8) + "1-96" = c(1,3), + "97-192" = c(2,4) ), plates = list( - "1" = c(1,2,3,4), - "2" = c(5,6,7,8) + "1" = c(1,2), + "2" = c(3,4) ) ) #elif str($inbuilt_spec.select_use) == "custom": @@ -74,7 +67,7 @@ barcodes = '$input_barcodes', format = list( #for $i, $s in enumerate($inbuilt_spec.barcode_format) - "${s.range_start}-${s.range_end}" = c( ${s.batches} ) + "${s.range_start}-${s.range_end}" = c( ${s.batches} ) #if $i < len(list($inbuilt_spec.barcode_format)) - 1 , #end if @@ -123,7 +116,7 @@ </when> </conditional> <section name="advanced" expanded="false" title="RegEx Parameters" > - <param name="regex_extract" type="text" value=".*P(\\d)_(\\d)_([ACTG]+)" label="RegEx to extract Plate, Batch, and Barcodes from headers" > + <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" > @@ -137,44 +130,40 @@ </outputs> <tests> <test><!-- Inbuilt MPI --> - <param name="input_table" value="out3.subtable" /> + <param name="input_table" value="test.matrix" /> <param name="input_barcodes" value="celseq_barcodes.192.raw" /> <conditional name="inbuilt_spec" > <param name="select_use" value="mpi_sagar" /> </conditional> - <output name="out_plots" > - <expand macro="assert_conts" /> - </output> - <output name="out_table" value="test.table" /> + <output name="out_plots" value="out.pdf" compare="sim_size" /> + <output name="out_table" value="out.table" /> </test> <test><!-- Plate and Lane test --> - <param name="input_table" value="out3.subtable" /> + <param name="input_table" value="test.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" /> + <param name="batches" value="1,3" /> </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" /> + <param name="batches" value="2,4" /> </repeat> <repeat name="plate_format" > <param name="plate" value="1" /> - <param name="batches" value="1,2,3,4" /> + <param name="batches" value="1,2" /> </repeat> <repeat name="plate_format" > <param name="plate" value="2" /> - <param name="batches" value="5,6,7,8" /> + <param name="batches" value="3,4" /> </repeat> </conditional> - <output name="out_plots" > - <expand macro="assert_conts" /> - </output> - <output name="out_table" value="test.table" /> + <output name="out_plots" value="out.pdf" compare="sim_size" /> + <output name="out_table" value="out.table" /> </test> </tests> <help><![CDATA[ @@ -194,10 +183,10 @@ Consider the following experimental setup, with a list of 100 possible barcodes, used over 3 sequencing plates, with each plate containing 4 unique batches, and each plate using a specific subset of the 100 barcodes. -:: +:: Barcodes - + 1 - 10 | AAA AAC AAT AAG ACA AGA ATA CAC GAG TAT 11 - 20 | CCC CCA CCT CCG CTC CGC TCT GCG TCT CGT . @@ -209,7 +198,7 @@ Plate 1 +-------+-------+-------+-------+ | B1 | B2 | B3 | B4 | +-------+-------+-------+-------+ - 1-50 51-100 51-100 1-50 + 1-50 51-100 51-100 1-50 Plate 2 +-------+-------+-------+-------+ | B5 | B6 | B7 | B8 | @@ -219,7 +208,7 @@ Plate 3 +-------+-------+-------+-------+ | B9 | B10 | B11 | B12 | +-------+-------+-------+-------+ - 1-40 41-80 1-40 41-80 + 1-40 41-80 1-40 41-80 **** @@ -244,4 +233,3 @@ <citation type="doi">10.1007/978-1-4939-7768-0_15</citation> </citations> </tool> -