Mercurial > repos > peterjc > mira4_assembler
comparison tools/mira4/mira4_bait.xml @ 15:b0ffe0e7282b draft
Uploaded v0.0.2 preview 7, fixed bash syntax error
| author | peterjc |
|---|---|
| date | Thu, 20 Feb 2014 05:07:19 -0500 |
| parents | 79759fdec6cb |
| children | 381aa262c8cb |
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| 14:133b863a8a40 | 15:b0ffe0e7282b |
|---|---|
| 12 <!-- Assume anything other than zero is an error --> | 12 <!-- Assume anything other than zero is an error --> |
| 13 <exit_code range="1:" /> | 13 <exit_code range="1:" /> |
| 14 <exit_code range=":-1" /> | 14 <exit_code range=":-1" /> |
| 15 </stdio> | 15 </stdio> |
| 16 <inputs> | 16 <inputs> |
| 17 <param name="bait_file" type="data" format="fasta,fastq,mira" required="true" label="Bait file (what to look for)" /> | 17 <param name="bait_file" type="data" format="fasta,fastq,mira" required="true" label="Bait file (what to look for)" /> |
| 18 <param name="input_reads" type="data" format="fasta,fastq,mira" required="true" label="Reads to search" /> | 18 <param name="input_reads" type="data" format="fasta,fastq,mira" required="true" label="Reads to search" /> |
| 19 <param name="output_choice" type="select" label="Output positive matches, or negative matches?"> | 19 <param name="output_choice" type="select" label="Output positive matches, or negative matches?"> |
| 20 <option value="pos">Just positive matches</option> | 20 <option value="pos">Just positive matches</option> |
| 21 <option value="neg">Just negative matches</option> | 21 <option value="neg">Just negative matches</option> |
| 22 </param> | 22 </param> |
| 23 <param name="strand_choice" type="select" label="Check for matches on both strands?"> | 23 <param name="strand_choice" type="select" label="Check for matches on both strands?"> |
| 24 <option value="both">Check both strands</option> | 24 <option value="both">Check both strands</option> |
| 25 <option value="fwd">Just forward strand</option> | 25 <option value="fwd">Just forward strand</option> |
| 26 </param> | 26 </param> |
| 27 <param name="kmer_length" type="integer" value="31" min="1" max="32" | 27 <param name="kmer_length" type="integer" value="31" min="1" max="32" |
| 28 label="k-mer length" help="Maximum 32" /> | 28 label="k-mer length" help="Maximum 32" /> |
| 29 <param name="min_occurence" type="integer" value="1" min="1" | 29 <param name="min_occurence" type="integer" value="1" min="1" |
| 30 label="Minimum k-mer occurence" | 30 label="Minimum k-mer occurence" |
| 31 help="How many k-mer matches do you want per read? Minimum one" /> | 31 help="How many k-mer matches do you want per read? Minimum one" /> |
| 32 </inputs> | 32 </inputs> |
| 33 <outputs> | 33 <outputs> |
| 34 <data name="output_reads" format="fasta" label="$input_reads.name #if str($output_choice)=='pos' then 'matching' else 'excluding matches to' # $bait_file.name"> | 34 <data name="output_reads" format="fasta" label="$input_reads.name #if str($output_choice)=='pos' then 'matching' else 'excluding matches to' # $bait_file.name"> |
| 35 <!-- TODO - Replace this with format="input:input_reads" if/when that works --> | 35 <!-- TODO - Replace this with format="input:input_reads" if/when that works --> |
| 36 <change_format> | 36 <change_format> |
| 38 <when input_dataset="input_reads" attribute="extension" value="fastqsanger" format="fastqsanger" /> | 38 <when input_dataset="input_reads" attribute="extension" value="fastqsanger" format="fastqsanger" /> |
| 39 <when input_dataset="input_reads" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> | 39 <when input_dataset="input_reads" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> |
| 40 <when input_dataset="input_reads" attribute="extension" value="fastqillumina" format="fastqillumina" /> | 40 <when input_dataset="input_reads" attribute="extension" value="fastqillumina" format="fastqillumina" /> |
| 41 <when input_dataset="input_reads" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> | 41 <when input_dataset="input_reads" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> |
| 42 </change_format> | 42 </change_format> |
| 43 </data> | 43 </data> |
| 44 </outputs> | 44 </outputs> |
| 45 <tests> | 45 <tests> |
| 46 <test> | 46 <test> |
| 47 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> | 47 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> |
| 48 <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" /> | 48 <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" /> |