Mercurial > repos > artbio > yac_clipper
diff yac.xml @ 0:1dde0b3d5f6a draft default tip
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 9c5f0b8e89dfe4347c610f42923f0acad2ecc81b"
| author | artbio |
|---|---|
| date | Wed, 17 Mar 2021 22:08:17 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/yac.xml Wed Mar 17 22:08:17 2021 +0000 @@ -0,0 +1,169 @@ +<tool id="yac" name="Clip adapter" version="2.4.0"> + <description /> + <requirements> + <requirement type="package" version="3.7.6">python</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python $__tool_directory__/yac.py + --input $input + --output 'clip.tmp' + --output_format + #if $out_format == 'fasta' or $out_format == 'fastagz': + 'fasta' + #else + 'fastq' + #end if + --adapter_to_clip $clip_source.clip_sequence + --min $min + --max $max + --Nmode $Nmode && + #if ($out_format == 'fastagz') or ($out_format == 'fastqgz'): + gzip -c 'clip.tmp' > $output + #else + mv clip.tmp $output + #end if + ]]></command> + <inputs> + <param format="fasta,fastq" label="Source file" name="input" type="data" /> + <param label="min size" name="min" size="4" type="integer" value="15" /> + <param label="max size" name="max" size="4" type="integer" value="36" /> + <param label="Select output format" name="out_format" type="select" + help="be careful not to select a fastq format for your output if your input has a fasta format"> + <option value="fasta">Fasta</option> + <option value="fastq" selected="true" >Fastq (Sanger)</option> + <option value="fastagz">gzipped Fasta</option> + <option value="fastqgz">gzipped Fastq (Sanger)</option> + </param> + <param label="Accept reads containing N?" name="Nmode" type="select"> + <option selected="True" value="accept">accept</option> + <option value="reject">reject</option> + </param> + <conditional name="clip_source"> + <param help="Built-in adapters or User-provided" label="Source" name="clip_source_list" type="select"> + <option selected="True" value="prebuilt">Use a built-in adapter (select from the list below)</option> + <option value="user">Use custom sequence</option> + </param> + <when value="prebuilt"> + <param help="if your adapter is not listed, input your own sequence" label="Select Adapter to clip" name="clip_sequence" type="select"> + <option value="TCGTATGCCGTCTTCTGCTTG">Solexa TCGTATGCCGTCTTCTGCTTG</option> + <option value="ATCTCGTATGCCGTCTTCTGCTT">Illumina ATCTCGTATGCCGTCTTCTGCTT</option> + <option selected="True" value="TGGAATTCTCGGGTGCCAAG">Illumina TruSeq TGGAATTCTCGGGTGCCAAG</option> + <option value="CTGTAGGCACCATCAATCGT">IdT CTGTAGGCACCATCAATCGT</option> + </param> + </when> + <when value="user"> + <param label="Enter your Sequence" name="clip_sequence" size="35" type="text" value="GAATCC" /> + </when> + </conditional> + </inputs> + <outputs> + <data format_source="input" metadata_source="input" name="output" label="Clipped ${input.name}-then-${out_format}"> + <change_format> + <when input="out_format" value="fasta" format="fasta" /> + <when input="out_format" value="fastq" format="fastqsanger" /> + <when input="out_format" value="fastagz" format="fasta.gz" /> + <when input="out_format" value="fastqgz" format="fastqsanger.gz" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param ftype="fastqsanger" name="input" value="yac.fastq" /> + <param name="min" value="18" /> + <param name="max" value="29" /> + <param name="clip_source_list" value="prebuilt" /> + <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" /> + <param name="Nmode" value="accept" /> + <param name="out_format" value="fastq" /> + <output file="out.fastqsanger" name="output" /> + </test> + <test> + <param ftype="fastqsanger" name="input" value="yac.fastq" /> + <param name="min" value="18" /> + <param name="max" value="29" /> + <param name="clip_source_list" value="prebuilt" /> + <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" /> + <param name="Nmode" value="accept" /> + <param name="out_format" value="fasta" /> + <output file="out.fasta" name="output" /> + </test> + <test> + <param ftype="fastqsanger.gz" name="input" value="yac.fastqsanger.gz" /> + <param name="min" value="18" /> + <param name="max" value="29" /> + <param name="clip_source_list" value="prebuilt" /> + <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" /> + <param name="Nmode" value="accept" /> + <param name="out_format" value="fastqgz" /> + <output file="out.fastqsanger.gz" name="output" decompress="True" /> + </test> + <test> + <param ftype="fastqsanger.gz" name="input" value="yac.fastqsanger.gz" /> + <param name="min" value="18" /> + <param name="max" value="29" /> + <param name="clip_source_list" value="prebuilt" /> + <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" /> + <param name="Nmode" value="accept" /> + <param name="out_format" value="fastagz" /> + <output file="out.fasta.gz" name="output" decompress="True" /> + </test> + <test> + <param ftype="fasta.gz" name="input" value="yac.fasta.gz" /> + <param name="min" value="18" /> + <param name="max" value="29" /> + <param name="clip_source_list" value="prebuilt" /> + <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" /> + <param name="out_format" value="fasta" /> + <param name="Nmode" value="accept" /> + <output file="out.fasta" name="output" /> + </test> + <test> + <param ftype="fasta.gz" name="input" value="yac.fasta.gz" /> + <param name="min" value="18" /> + <param name="max" value="29" /> + <param name="clip_source_list" value="prebuilt" /> + <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" /> + <param name="Nmode" value="accept" /> + <param name="out_format" value="fastagz" /> + <output file="out.fasta.gz" name="output" decompress="True" /> + </test> + <test> + <param ftype="fastqsanger.gz" name="input" value="yac_with_empty_reads.fastqsanger.gz" /> + <param name="min" value="18" /> + <param name="max" value="30" /> + <param name="clip_source_list" value="prebuilt" /> + <param name="clip_sequence" value="TGGAATTCTCGGGTGCCAAG" /> + <param name="Nmode" value="accept" /> + <param name="out_format" value="fastagz" /> + <output file="out_with_empty_reads.fasta.gz" name="output" decompress="True" /> + </test> + </tests> + <help> + +**What it does** + ++ Clips adapter sequences ++ Renumbers sequence headers ++ Filters sequences on their size ++ Filters sequences containing unknown nucleotides (optional) + +------- + +**Inputs** + +1. A fastq or fasta file of reads to be clipped +2. Select the size of the reads to be kept +3. Select an output format. When input is a fastq file, this may be fastq or fasta, whereas +when input is a fasta file, this only may be a fasta. +4. Select whether you wish or do not wish to keep clipped sequences with unknown nucleotides (N) +5. Select a pre-built adapter sequence or enter your own sequence (at least 7 nucleotides long) + +------- + +**Output** + +A fastq or fasta file containing clipped sequences satisfying the selected criteria. + + </help> + <citations /> +</tool>