Mercurial > repos > devteam > fastx_barcode_splitter
diff fastx_barcode_splitter.xml @ 4:015dc921d814 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author | iuc |
---|---|
date | Tue, 08 May 2018 13:27:14 -0400 |
parents | 8abdedf55101 |
children | 4bedca26c133 |
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--- a/fastx_barcode_splitter.xml Wed Nov 11 12:38:37 2015 -0500 +++ b/fastx_barcode_splitter.xml Tue May 08 13:27:14 2018 -0400 @@ -1,38 +1,94 @@ -<tool id="cshl_fastx_barcode_splitter" version="1.0.0" name="Barcode Splitter"> +<tool id="cshl_fastx_barcode_splitter" version="1.0.1" name="Barcode Splitter"> <description></description> - <requirements> - <requirement type="package" version="0.0.13">fastx_toolkit</requirement> - </requirements> - <command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' </command> - + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="aggressive"><![CDATA[ +mkdir split && +@CATS@ '$__tool_directory__/fastx_barcode_splitter.pl' --bcfile '$BARCODE' +--prefix 'split/' +--suffix '.$input.extension' +--mismatches $mismatches +--partial $partial +#if $refBarcodeLocation.barcodeLocation == "idxfile": + --idxfile '$refBarcodeLocation.idxfile' + --idxidstrip $refBarcodeLocation.idxidstrip +#else: + $refBarcodeLocation.EOL +#end if +> '$summary' + ]]></command> <inputs> - <param format="txt" name="BARCODE" type="data" label="Barcodes to use" /> - <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" /> + <param name="BARCODE" type="data" format="txt" label="Barcodes to use" /> + <param name="input" type="data" format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" label="Library to split" /> - <param name="EOL" type="select" label="Barcodes found at"> - <option value="--bol">Start of sequence (5' end)</option> - <option value="--eol">End of sequence (3' end)</option> - </param> + <conditional name="refBarcodeLocation"> + <param name="barcodeLocation" type="select" label="Barcodes found at"> + <option value="bol">Start of sequence (5' end)</option> + <option value="eol">End of sequence (3' end)</option> + <option value="idxfile">Separate index file</option> + </param> + <when value="bol"> + <param name="EOL" type="hidden" value="--bol" /> + </when> + <when value="eol"> + <param name="EOL" type="hidden" value="--eol" /> + </when> + <when value="idxfile"> + <param argument="--idxidstrip" type="integer" value="1" label="Characters to strip from the end of the sequence id before matching" /> + <param argument="--idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" /> + </when> + </conditional> + <param argument="--mismatches" type="integer" value="0" label="Number of allowed mismatches" /> + <param argument="--partial" type="integer" value="0" label="Number of allowed barcodes nucleotide deletions" /> + </inputs> - <param name="mismatches" type="integer" value="2" label="Number of allowed mismatches" /> + <outputs> + <data name="summary" format="tabular" label="${tool.name} on ${on_string}: Summary" /> + <collection name="split_output" type="list" format_source="input" label="${tool.name} on ${on_string}"> + <discover_datasets pattern="__designation_and_ext__" directory="split" visible="false" /> + </collection> + </outputs> - <param name="partial" type="integer" value="0" label="Number of allowed barcodes nucleotide deletions" /> - </inputs> - <outputs> - <data format="html" name="output" /> - </outputs> <tests> <test> <!-- Split a FASTQ file --> <param name="BARCODE" value="fastx_barcode_splitter1.txt" /> <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" /> - <param name="EOL" value="Start of sequence (5' end)" /> + <param name="barcodeLocation" value="bol" /> <param name="mismatches" value="2" /> <param name="partial" value="0" /> - <output name="output" file="fastx_barcode_splitter1.out" /> + <output name="summary" file="fastx_barcode_splitter1.out" /> + <output_collection name="split_output" type="list"> + <element name="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" /> + <element name="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" /> + <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" /> + <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" /> + <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" /> + </output_collection> + </test> + + <test> + <!-- Split a FASTQ file, using separate index read --> + <param name="BARCODE" value="fastx_barcode_splitter1.txt" /> + <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" /> + <param name="idxfile" value="fastx_barcode_splitter_index.fastq" ftype="fastqsolexa" /> + <param name="barcodeLocation" value="idxfile" /> + <param name="mismatches" value="2" /> + <param name="partial" value="0" /> + <output name="summary" file="fastx_barcode_splitter1.out" /> + <output_collection name="split_output" type="list"> + <element name="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" /> + <element name="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" /> + <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" /> + <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" /> + <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" /> + </output_collection> </test> </tests> - <help> + + <help><![CDATA[ **What it does** This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria. @@ -62,12 +118,12 @@ .. image:: barcode_splitter_output_example.png - ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - </help> + ]]></help> + <expand macro="citations" /> <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool>