Mercurial > repos > peterjc > mira4_assembler
comparison tools/mira4/mira4_bait.xml @ 18:381aa262c8cb draft
Uploaded v0.0.2 preview 10, override /tmp via environment variable
| author | peterjc |
|---|---|
| date | Tue, 25 Mar 2014 07:37:50 -0400 |
| parents | b0ffe0e7282b |
| children | 8487d70e82aa |
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| 17:5bbaa930d7fa | 18:381aa262c8cb |
|---|---|
| 1 <tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.1"> | 1 <tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.2"> |
| 2 <description>Filter reads using kmer matches</description> | 2 <description>Filter reads using kmer matches</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="binary">mirabait</requirement> | 4 <requirement type="binary">mirabait</requirement> |
| 5 <requirement type="package" version="4.0">MIRA</requirement> | 5 <requirement type="package" version="4.0">MIRA</requirement> |
| 6 </requirements> | 6 </requirements> |
| 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' # $bait_file.name"> | 34 <data name="output_reads" format="input" metadata_source="input_reads" |
| 35 <!-- TODO - Replace this with format="input:input_reads" if/when that works --> | 35 label="$input_reads.name #if str($output_choice)=='pos' then 'matching' else 'excluding matches to' # $bait_file.name"/> |
| 36 <change_format> | |
| 37 <when input_dataset="input_reads" attribute="extension" value="fastq" format="fastq" /> | |
| 38 <when input_dataset="input_reads" attribute="extension" value="fastqsanger" format="fastqsanger" /> | |
| 39 <when input_dataset="input_reads" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> | |
| 40 <when input_dataset="input_reads" attribute="extension" value="fastqillumina" format="fastqillumina" /> | |
| 41 <when input_dataset="input_reads" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> | |
| 42 </change_format> | |
| 43 </data> | |
| 44 </outputs> | 36 </outputs> |
| 45 <tests> | 37 <tests> |
| 46 <test> | 38 <test> |
| 47 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> | 39 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> |
| 48 <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" /> | 40 <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" /> |