| Next changeset 1:ff7e1478030d (2020-02-13) |
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Commit message:
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34" |
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added:
bioperl_compat.py biopython-convert.xml |
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| diff -r 000000000000 -r 869e206b3ca1 bioperl_compat.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bioperl_compat.py Fri Jan 24 18:52:04 2020 -0500 |
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| @@ -0,0 +1,11 @@ +#!/usr/bin/env python +import sys +from biopython_convert import get_args, convert +from Bio.SeqIO.InsdcIO import _InsdcWriter + +# Quote anticodon qualifiers +_InsdcWriter.FTQUAL_NO_QUOTE = tuple(v for v in _InsdcWriter.FTQUAL_NO_QUOTE if v not in ['anticodon', 'transl_except']) + +if __name__ == '__main__': + convert(*get_args(sys.argv[1:])) + |
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| diff -r 000000000000 -r 869e206b3ca1 biopython-convert.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biopython-convert.xml Fri Jan 24 18:52:04 2020 -0500 |
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| b'@@ -0,0 +1,174 @@\n+<tool id="biopython-convert" name="BioPython SeqIO Converter" version="1.0" profile="16.04">\n+ <description>Interconvert between the various sequence file formats that BioPython supports</description>\n+ <edam_topics>\n+ <edam_topic>topic_0091</edam_topic>\n+ </edam_topics>\n+ <edam_operations>\n+ <edam_operation>operation_3434</edam_operation>\n+ <edam_operation>operation_0335</edam_operation>\n+ <edam_operation>operation_3359</edam_operation>\n+ <edam_operation>operation_0224</edam_operation>\n+ <edam_operation>operation_3695</edam_operation>\n+ </edam_operations>\n+ <requirements>\n+ <requirement type="package" version="3.7">python</requirement>\n+ <requirement type="package" version="1.0">biopython.convert</requirement>\n+ </requirements>\n+ <version_command><![CDATA[ biopython.convert -v ]]></version_command>\n+ <command detect_errors="aggressive"><![CDATA[\n+ #if $bioperl\n+ #set $script = \'python \' + $__tool_directory__ + \'/bioperl_compat.py\'\n+ #else\n+ #set $script = \'biopython.convert\'\n+ #end if\n+ #if $split\n+ mkdir -p output &&\n+ $script $split $info\n+ #if $query\n+ -q \'$query\'\n+ #end if\n+ $input $input.ext output/record $output_type\n+ #else\n+ $script $split $info\n+ #if $query\n+ -q \'$query\'\n+ #end if\n+ $input $input.ext $output $output_type\n+ #end if\n+ #if $info\n+ > $info_output\n+ #end if\n+ ]]></command>\n+ <inputs>\n+ <param name="input" type="data" format="abi,abi-trim,ace,cif-atom,cif-seqres,clustal,embl,fasta,fasta-2line,fastq-sanger,fastq,fastq-solexa,fastq-illumina,genbank,gb,ig,imgt,nexus,pdb-seqres,pdb-atom,phd,phylip,pir,seqxml,sff,sff-trim,stockholm,swiss,tab,qual,uniprot-xml,gff3" label="Input" />\n+ <param name="output_type" type="select" label="Output Format">\n+ <option value="clustal">clustal</option>\n+ <option value="embl">embl</option>\n+ <option value="fasta">fasta</option>\n+ <option value="fasta-2line">fasta-2line</option>\n+ <option value="fastq-sanger">fastq-sanger</option>\n+ <option value="fastq">fastq</option>\n+ <option value="fastq-solexa">fastq-solexa</option>\n+ <option value="fastq-illumina">fastq-illumina</option>\n+ <option value="genbank">genbank</option>\n+ <option value="gb">gb</option>\n+ <option value="imgt">imgt</option>\n+ <option value="nexus">nexus</option>\n+ <option value="phd">phd</option>\n+ <option value="phylip">phylip</option>\n+ <option value="pir">pir</option>\n+ <option value="seqxml">seqxml</option>\n+ <option value="sff">sff</option>\n+ <option value="stockholm">stockholm</option>\n+ <option value="tab">tab</option>\n+ <option value="qual">qual</option>\n+ <option value="gff3">gff3</option>\n+ </param>\n+ <param name="split" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Split each record into a different file" />\n+ <param name="info" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Output record information while converting" />\n+ <param name="query" type="text" label="Query records, keeping only what matches path" help="Provide a JMESPath selecting records to keep. The root is the list of records. The path must return a list of records.">\n+ <sanitizer>\n+ <valid initial="string.printable">\n+ <remove value="'" />\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ <param name="bioperl" type="boolean" checked="false" label="Modify biopython to generate files similar to bioperl" />\n+ </inputs>\n+ <outputs>'..b'ank" />\n+ <param name="output_type" value="genbank" />\n+ <output name="output" checksum="sha256:2808187bb8e2231545e4d2d7a27dc802df4d1f7c0e953a8399300b2df6b0c737" ftype="genbank" />\n+ </test>\n+ <test expect_num_outputs="1">\n+ <!-- Test basic conversion to same format with info -->\n+ <param name="input" value="BioPython-Convert/test-data/has_plasmids.gbff" ftype="genbank" />\n+ <param name="info" value="-i" />\n+ <param name="output_type" value="genbank" />\n+ <output name="output" checksum="sha256:2808187bb8e2231545e4d2d7a27dc802df4d1f7c0e953a8399300b2df6b0c737" ftype="genbank" />\n+ <output name="info_output" checksum="sha256:a611656c5a7e7f719c3d64f6b348b67c1abcb8ed56fa82f51fc90cbe2125e5f0" ftype="gff3" />\n+ </test>\n+ <test expect_num_outputs="1">\n+ <!-- Test basic conversion to different format -->\n+ <param name="input" value="BioPython-Convert/test-data/has_plasmids.gbff" ftype="genbank" />\n+ <param name="output_type" value="embl" />\n+ <output name="output" checksum="sha256:5598cb679f5f6c31349968ddde3646fe97296da42ee528ed3f46dec3f5490cbd" ftype="embl" />\n+ </test>\n+ <test expect_num_outputs="1">\n+ <!-- Test basic conversion to same format with filter -->\n+ <param name="input" value="BioPython-Convert/test-data/has_plasmids.gbff" ftype="genbank" />\n+ <param name="query" value="[?!(features[?type==`source`].qualifiers.plasmid)]" />\n+ <param name="output_type" value="genbank" />\n+ <output name="output" checksum="sha256:e142d7e1fbd103c96e3b728e3b75f7af6955c97cdbddb87c3202f2c1e2f133d4" ftype="genbank" />\n+ </test>\n+ <test expect_num_outputs="1">\n+ <!-- Test split -->\n+ <param name="input" value="BioPython-Convert/test-data/has_plasmids.gbff" ftype="genbank" />\n+ <param name="output_type" value="genbank" />\n+ <output_collection name="split_output" type="list" count="3">\n+ <element name="record.0" ftype="genbank" checksum="sha256:8d02b2087c4cea42da7c5f0a69b7a40d544d953c1a9d611b97bd116cc1f8cd7f" />\n+ <element name="record.1" ftype="genbank" checksum="sha256:e37ecc4288ae8b2c3bea25484326a69ced9679fa791162ed593064fdf535944d" />\n+ <element name="record.2" ftype="genbank" checksum="sha256:e142d7e1fbd103c96e3b728e3b75f7af6955c97cdbddb87c3202f2c1e2f133d4" />\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ Interconvert between different file formats that BioPython SeqIO supports. Support for GFF3 has also been included.\n+\n+ Included features are:\n+\n+ - Split: Output a collection of datasets, one for each record in the input.\n+ This is useful when a tool only accepts single records.\n+ The resulting output collection can then be mapped over the receiving tool.\n+ - Info: Output an additional GFF3 dataset that contains a summary record for each record in the output dataset.\n+ This is useful for extracting sequence IDs, counting how many records are in the output dataset, and various\n+ diagnostic processes.\n+ - Query: Datasets can be queried or filtered using JMESPath query language.\n+ For example ``[?!(features[?type==`source`].qualifiers.plasmid)]`` will remove any plasmid records sometimes\n+ found in prokaryotic Genbank or EMBL reference genomes.\n+ See http://jmespath.org/ for documentation, and https://biopython.org/DIST/docs/api/Bio.SeqFeature.SeqFeature-class.html\n+ for the data structure. Single quotes `\'` are not permitted in the query.\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.5281/zenodo.3364782</citation>\n+ <citation type="doi">10.5281/zenodo.3364789</citation>\n+ </citations>\n+</tool>\n' |