Mercurial > repos > peterjc > blast_rbh
comparison tools/blast_rbh/blast_rbh.xml @ 33:692366540172 draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh commit 21f6d9932d322034e4cea5fee23b24bf0b1e1e85-dirty
| author | peterjc |
|---|---|
| date | Thu, 18 May 2017 12:43:55 -0400 |
| parents | b662383a4bdc |
| children | 5c78f5e6cdf2 |
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| 32:b662383a4bdc | 33:692366540172 |
|---|---|
| 1 <tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.11"> | 1 <tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.12"> |
| 2 <description>from two FASTA files</description> | 2 <description>from two FASTA files</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.67">biopython</requirement> | 4 <requirement type="package" version="1.67">biopython</requirement> |
| 5 <requirement type="package" version="2.5.0">blast</requirement> | 5 <requirement type="package" version="2.5.0">blast</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 <stdio> | 7 <version_command> |
| 8 <!-- Anything other than zero is an error --> | 8 python $__tool_directory__/blast_rbh.py --version |
| 9 <exit_code range="1:" /> | |
| 10 <exit_code range=":-1" /> | |
| 11 </stdio> | |
| 12 <version_command interpreter="python"> | |
| 13 blast_rbh.py --version | |
| 14 </version_command> | 9 </version_command> |
| 15 <command interpreter="python"> | 10 <command detect_errors="aggressive"> |
| 16 blast_rbh.py "$fasta_a" "$fasta_b" | 11 python $__tool_directory__/blast_rbh.py '$fasta_a' '$fasta_b' |
| 17 -a $seq.dbtype | 12 -a $seq.dbtype |
| 18 #if $seq.dbtype=="nucl" | 13 #if $seq.dbtype=="nucl" |
| 19 -t $seq.nucl_type | 14 -t $seq.nucl_type |
| 20 #else | 15 #else |
| 21 -t $seq.prot_type | 16 -t $seq.prot_type |
| 22 #end if | 17 #end if |
| 23 $make_nr | 18 $make_nr |
| 24 -i $identity | 19 -i $identity |
| 25 -c $q_cover | 20 -c $q_cover |
| 26 -o "$output" | 21 -o '$output' |
| 27 </command> | 22 </command> |
| 28 <inputs> | 23 <inputs> |
| 29 <!-- Galaxy does not have sub-types for protein vs nucletide FASTA --> | 24 <!-- Galaxy does not have sub-types for protein vs nucletide FASTA --> |
| 30 <param name="fasta_a" type="data" format="fasta" | 25 <param name="fasta_a" type="data" format="fasta" |
| 31 label="Genes/proteins from species A" | 26 label="Genes/proteins from species A" |