blast_rbh: tools/blast_rbh/blast

comparison tools/blast_rbh/blast_rbh.xml @ 5:8f4500f6f2aa draft

Refactored to use more than one Python file (internal change only).

author	peterjc
date	Tue, 06 Dec 2022 15:53:36 +0000
parents	d8d9a9069586
children	b2f91cbed8d9

comparison

equal deleted inserted replaced

-:d8d9a9069586
+:8f4500f6f2aa
-<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.11">
+<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.2.0">
 <description>from two FASTA files</description>
 <requirements>
 <requirement type="package" version="1.67">biopython</requirement>
 <requirement type="package" version="2.5.0">blast</requirement>
 </requirements>
-<stdio>
+<version_command>
-<!-- Anything other than zero is an error -->
+python $__tool_directory__/blast_rbh.py --version
-<exit_code range="1:" />
-<exit_code range=":-1" />
-</stdio>
-<version_command interpreter="python">
-blast_rbh.py --version
 </version_command>
-<command interpreter="python">
+<command detect_errors="aggressive">
-blast_rbh.py "$fasta_a" "$fasta_b"
+python $__tool_directory__/blast_rbh.py '$fasta_a' '$fasta_b'
 -a $seq.dbtype
 #if $seq.dbtype=="nucl"
 -t $seq.nucl_type
 #else
 -t $seq.prot_type
 #end if
 $make_nr
 -i $identity
 -c $q_cover
--o "$output"
+-o '$output'
 </command>
 <inputs>
 <!-- Galaxy does not have sub-types for protein vs nucletide FASTA -->
 <param name="fasta_a" type="data" format="fasta"
-	       label="Genes/proteins from species A"
+label="Genes/proteins from species A"
-	       help="FASTA file, one sequence per gene/protein." />
+help="FASTA file, one sequence per gene/protein."/>
 <param name="fasta_b" type="data" format="fasta"
-	       label="Genes/proteins from species B"
+label="Genes/proteins from species B"
-	       help="FASTA file, one sequence per gene/protein." />
+help="FASTA file, one sequence per gene/protein."/>
 <conditional name="seq">
 <param name="dbtype" type="select" label="Molecule type of FASTA inputs">
 <option value="prot">protein</option>
 <option value="nucl">nucleotide</option>
 </param>
 <option value="dc-megablast">dc-megablast - Discontiguous megablast used to find more distant (e.g., interspecies) sequences</option>
 <option value="tblastx">tblastx - TBLASTX program using translated query against translated database (protein level matches)</option>
 </param>
 </when>
 </conditional>
-	<param name="identity" type="float" value="70" min="0" max="100"
+<param name="identity" type="float" value="70" min="0" max="100"
-	       label="Minimum percentage identity for BLAST matches"
+label="Minimum percentage identity for BLAST matches"
-	       help="Default is 70%, use 0 for no filtering." />
+help="Default is 70%, use 0 for no filtering." />
 <param name="q_cover" type="float" value="50" min="0" max="100"
-	       label="Minimum percentage query coverage for BLAST matches"
+label="Minimum percentage query coverage for BLAST matches"
-	       help="Default is 50%, use 0 for no filtering." />
+help="Default is 50%, use 0 for no filtering." />
 <param name="make_nr" type="boolean" checked="false" truevalue="--nr" falsevalue=""
-	       label="Process input FASTA files to collapse identical sequences"
+label="Process input FASTA files to collapse identical sequences"
 help="i.e. First make the input non-redundant" />
 </inputs>
 <outputs>
 <data name="output" format="tabular" label="BLAST RBH: $fasta_a.name vs $fasta_b.name" />
 </outputs>
 <param name="nucl_type" value="megablast"/>
 <param name="identity" value="92.5"/>
 <param name="q_cover" value="86"/>
 <output name="output" file="rbh_none.tabular" ftype="tabular"/>
 </test>
-	<!-- push the coverage over the 86% level -->
+<!-- push the coverage over the 86% level -->
 <test>
 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/>
 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/>
 <param name="dbtype" value="nucl"/>
 <param name="nucl_type" value="megablast"/>
 <param name="nucl_type" value="blastn"/>
 <param name="identity" value="0.0"/>
 <param name="q_cover" value="0.0"/>
 <output name="output" file="rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular" ftype="tabular"/>
 </test>
 <!-- this pair of examples test tied best hits -->
 <test>
 <param name="fasta_a" value="k12_ten_proteins.fasta" ftype="fasta"/>
 <param name="fasta_b" value="k12_edited_proteins.fasta" ftype="fasta"/>
 <param name="dbtype" value="prot"/>
 <param name="nucl_type" value="blastp"/>
 coverage threshold or similiar. See:
 Punta and Ofran (2008) The Rough Guide to In Silico Function Prediction,
 or How To Use Sequence and Structure Information To Predict Protein
 Function. PLoS Comput Biol 4(10): e1000160.
-http://dx.doi.org/10.1371/journal.pcbi.1000160
+https://doi.org/10.1371/journal.pcbi.1000160
 The defaults are to require 70% sequence identity over the aligned region
 (using ``pident`` in the BLAST+ tabular output), and that the HSP alignment
 covers at least 50% of the query sequence (using ``qcovhsp`` in the BLAST+
 tabular output).
 Please cite:
 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo (2015).
 NCBI BLAST+ integrated into Galaxy.
 *GigaScience* 4:39
-http://dx.doi.org/10.1186/s13742-015-0080-7
+https://doi.org/10.1186/s13742-015-0080-7
 Christiam Camacho et al. (2009).
 BLAST+: architecture and applications.
 *BMC Bioinformatics* 15;10:421.
-http://dx.doi.org/10.1186/1471-2105-10-421
+https://doi.org/10.1186/1471-2105-10-421
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
 </help>
 <citations>

Mercurial > repos > peterjc > blast_rbh

comparison tools/blast_rbh/blast_rbh.xml @ 5:8f4500f6f2aa draft