Mercurial > repos > peterjc > mira4_assembler
comparison tools/mira4_0/mira4_bait.xml @ 4:1713289d9908 draft default tip
v0.0.11 tweak for use with bioconda dependencies
| author | peterjc |
|---|---|
| date | Thu, 10 Aug 2017 11:09:10 -0400 |
| parents | a4f602cc3aa9 |
| children |
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| 3:a4f602cc3aa9 | 4:1713289d9908 |
|---|---|
| 1 <tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.9"> | 1 <tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.11"> |
| 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> | |
| 5 <requirement type="package" version="4.0.2">MIRA</requirement> | 4 <requirement type="package" version="4.0.2">MIRA</requirement> |
| 6 </requirements> | 5 </requirements> |
| 7 <stdio> | 6 <version_command> |
| 8 <!-- Assume anything other than zero is an error --> | 7 python $__tool_directory__/mira4_bait.py --version |
| 9 <exit_code range="1:" /> | 8 </version_command> |
| 10 <exit_code range=":-1" /> | 9 <command detect_errors="aggressive"> |
| 11 </stdio> | 10 python $__tool_directory__/mira4_bait.py $input_reads.ext $output_choice $strand_choice $kmer_length $min_occurence '$bait_file' '$input_reads' '$output_reads' |
| 12 <version_command interpreter="python">mira4_bait.py --version</version_command> | |
| 13 <command interpreter="python"> | |
| 14 mira4_bait.py $input_reads.ext $output_choice $strand_choice $kmer_length $min_occurence "$bait_file" "$input_reads" "$output_reads" | |
| 15 </command> | 11 </command> |
| 16 <inputs> | 12 <inputs> |
| 17 <param name="bait_file" type="data" format="fasta,fastq,mira" required="true" label="Bait file (what to look for)" /> | 13 <param name="bait_file" type="data" format="fasta,fastq,mira" label="Bait file (what to look for)" /> |
| 18 <param name="input_reads" type="data" format="fasta,fastq,mira" required="true" label="Reads to search" /> | 14 <param name="input_reads" type="data" format="fasta,fastq,mira" label="Reads to search" /> |
| 19 <param name="output_choice" type="select" label="Output positive matches, or negative matches?"> | 15 <param name="output_choice" type="select" label="Output positive matches, or negative matches?"> |
| 20 <option value="pos">Just positive matches</option> | 16 <option value="pos">Just positive matches</option> |
| 21 <option value="neg">Just negative matches</option> | 17 <option value="neg">Just negative matches</option> |
| 22 </param> | 18 </param> |
| 23 <param name="strand_choice" type="select" label="Check for matches on both strands?"> | 19 <param name="strand_choice" type="select" label="Check for matches on both strands?"> |
| 30 label="Minimum k-mer occurence" | 26 label="Minimum k-mer occurence" |
| 31 help="How many k-mer matches do you want per read? Minimum one" /> | 27 help="How many k-mer matches do you want per read? Minimum one" /> |
| 32 </inputs> | 28 </inputs> |
| 33 <outputs> | 29 <outputs> |
| 34 <data name="output_reads" format_source="input_reads" metadata_source="input_reads" | 30 <data name="output_reads" format_source="input_reads" metadata_source="input_reads" |
| 35 label="$input_reads.name #if str($output_choice)=='pos' then 'matching' else 'excluding matches to' # $bait_file.name"/> | 31 label="$input_reads.name #if str($output_choice)=='pos' then 'matching' else 'excluding matches to' # $bait_file.name"/> |
| 36 </outputs> | 32 </outputs> |
| 37 <tests> | 33 <tests> |
| 38 <test> | 34 <test> |
| 39 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> | 35 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> |
| 40 <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" /> | 36 <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" /> |