Mercurial > repos > artbio > yac_clipper
diff yac.xml @ 3:94d67b195acd draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 6884c90d521932ae0981532929db9f5f44c8b4a2
| author | artbio |
|---|---|
| date | Mon, 21 Jan 2019 18:46:04 -0500 |
| parents | da08e89abd18 |
| children | f7947c5a18b8 |
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--- a/yac.xml Sat Oct 13 17:09:16 2018 -0400 +++ b/yac.xml Mon Jan 21 18:46:04 2019 -0500 @@ -1,22 +1,36 @@ -<tool id="yac" name="Clip adapter" version="2.1.1"> +<tool id="yac" name="Clip adapter" version="2.2.0"> <description /> <command detect_errors="exit_code"><![CDATA[ python $__tool_directory__/yac.py --input $input - --output $output - --output_format "$out_format" + --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 + --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="fastq" label="Source file" name="input" type="data" /> + <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"> - <option selected="true" value="fasta">Fasta format</option> - <option value="fastq">Fastq (Sanger) format</option> + <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> @@ -41,9 +55,12 @@ </conditional> </inputs> <outputs> - <data format_source="input" metadata_source="input" name="output" label="Clipping of ${input.name}"> + <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> @@ -55,7 +72,8 @@ <param name="clip_source_list" value="prebuilt" /> <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" /> <param name="Nmode" value="accept" /> - <output file="yac.out" name="output" /> + <param name="out_format" value="fastq" /> + <output file="out.fastqsanger" name="output" /> </test> <test> <param ftype="fastqsanger" name="input" value="yac.fastq" /> @@ -64,8 +82,48 @@ <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="yac_fastq.out" name="output" /> + <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> </tests> <help> @@ -81,9 +139,10 @@ **Inputs** -1. A fastq file of reads to be clipped +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 fastq) +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)