Mercurial > repos > brinkmanlab > biopython_convert
changeset 0:869e206b3ca1 draft
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
| author | brinkmanlab |
|---|---|
| date | Fri, 24 Jan 2020 18:52:04 -0500 |
| parents | |
| children | ff7e1478030d |
| files | bioperl_compat.py biopython-convert.xml |
| diffstat | 2 files changed, 185 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bioperl_compat.py Fri Jan 24 18:52:04 2020 -0500 @@ -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:])) +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biopython-convert.xml Fri Jan 24 18:52:04 2020 -0500 @@ -0,0 +1,174 @@ +<tool id="biopython-convert" name="BioPython SeqIO Converter" version="1.0" profile="16.04"> + <description>Interconvert between the various sequence file formats that BioPython supports</description> + <edam_topics> + <edam_topic>topic_0091</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_3434</edam_operation> + <edam_operation>operation_0335</edam_operation> + <edam_operation>operation_3359</edam_operation> + <edam_operation>operation_0224</edam_operation> + <edam_operation>operation_3695</edam_operation> + </edam_operations> + <requirements> + <requirement type="package" version="3.7">python</requirement> + <requirement type="package" version="1.0">biopython.convert</requirement> + </requirements> + <version_command><![CDATA[ biopython.convert -v ]]></version_command> + <command detect_errors="aggressive"><![CDATA[ + #if $bioperl + #set $script = 'python ' + $__tool_directory__ + '/bioperl_compat.py' + #else + #set $script = 'biopython.convert' + #end if + #if $split + mkdir -p output && + $script $split $info + #if $query + -q '$query' + #end if + $input $input.ext output/record $output_type + #else + $script $split $info + #if $query + -q '$query' + #end if + $input $input.ext $output $output_type + #end if + #if $info + > $info_output + #end if + ]]></command> + <inputs> + <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" /> + <param name="output_type" type="select" label="Output Format"> + <option value="clustal">clustal</option> + <option value="embl">embl</option> + <option value="fasta">fasta</option> + <option value="fasta-2line">fasta-2line</option> + <option value="fastq-sanger">fastq-sanger</option> + <option value="fastq">fastq</option> + <option value="fastq-solexa">fastq-solexa</option> + <option value="fastq-illumina">fastq-illumina</option> + <option value="genbank">genbank</option> + <option value="gb">gb</option> + <option value="imgt">imgt</option> + <option value="nexus">nexus</option> + <option value="phd">phd</option> + <option value="phylip">phylip</option> + <option value="pir">pir</option> + <option value="seqxml">seqxml</option> + <option value="sff">sff</option> + <option value="stockholm">stockholm</option> + <option value="tab">tab</option> + <option value="qual">qual</option> + <option value="gff3">gff3</option> + </param> + <param name="split" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Split each record into a different file" /> + <param name="info" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Output record information while converting" /> + <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."> + <sanitizer> + <valid initial="string.printable"> + <remove value="'" /> + </valid> + </sanitizer> + </param> + <param name="bioperl" type="boolean" checked="false" label="Modify biopython to generate files similar to bioperl" /> + </inputs> + <outputs> + <data name="info_output" format="gff3" label="Record Info from ${tool.name} on ${on_string}"> + <filter>info</filter> + </data> + <data name="output" format="txt" label="Output from ${tool.name} on ${on_string}"> + <filter>not split</filter> + <change_format> + <when input="output_type" value="clustal" format="clustal" /> + <when input="output_type" value="embl" format="embl" /> + <when input="output_type" value="fasta" format="fasta" /> + <when input="output_type" value="fasta-2line" format="fasta-2line" /> + <when input="output_type" value="fastq-sanger" format="fastq-sanger" /> + <when input="output_type" value="fastq" format="fastq" /> + <when input="output_type" value="fastq-solexa" format="fastq-solexa" /> + <when input="output_type" value="fastq-illumina" format="fastq-illumina" /> + <when input="output_type" value="genbank" format="genbank" /> + <when input="output_type" value="gb" format="genbank" /> + <when input="output_type" value="imgt" format="imgt" /> + <when input="output_type" value="nexus" format="nexus" /> + <when input="output_type" value="phd" format="phd" /> + <when input="output_type" value="phylip" format="phylip" /> + <when input="output_type" value="pir" format="pir" /> + <when input="output_type" value="seqxml" format="seqxml" /> + <when input="output_type" value="sff" format="sff" /> + <when input="output_type" value="stockholm" format="stockholm" /> + <when input="output_type" value="tab" format="tabular" /> + <when input="output_type" value="qual" format="qual" /> + <when input="output_type" value="gff3" format="gff3" /> + </change_format> + </data> + <collection name="split_output" type="list" label="Output split per record from ${tool.name} on ${on_string}"> + <filter>split</filter> + <discover_datasets pattern=".*" directory="output" format="$output_type" /> + </collection> + </outputs> + <tests> + <test expect_num_outputs="1"> + <!-- Test basic conversion to same format --> + <param name="input" value="BioPython-Convert/test-data/has_plasmids.gbff" ftype="genbank" /> + <param name="output_type" value="genbank" /> + <output name="output" checksum="sha256:2808187bb8e2231545e4d2d7a27dc802df4d1f7c0e953a8399300b2df6b0c737" ftype="genbank" /> + </test> + <test expect_num_outputs="1"> + <!-- Test basic conversion to same format with info --> + <param name="input" value="BioPython-Convert/test-data/has_plasmids.gbff" ftype="genbank" /> + <param name="info" value="-i" /> + <param name="output_type" value="genbank" /> + <output name="output" checksum="sha256:2808187bb8e2231545e4d2d7a27dc802df4d1f7c0e953a8399300b2df6b0c737" ftype="genbank" /> + <output name="info_output" checksum="sha256:a611656c5a7e7f719c3d64f6b348b67c1abcb8ed56fa82f51fc90cbe2125e5f0" ftype="gff3" /> + </test> + <test expect_num_outputs="1"> + <!-- Test basic conversion to different format --> + <param name="input" value="BioPython-Convert/test-data/has_plasmids.gbff" ftype="genbank" /> + <param name="output_type" value="embl" /> + <output name="output" checksum="sha256:5598cb679f5f6c31349968ddde3646fe97296da42ee528ed3f46dec3f5490cbd" ftype="embl" /> + </test> + <test expect_num_outputs="1"> + <!-- Test basic conversion to same format with filter --> + <param name="input" value="BioPython-Convert/test-data/has_plasmids.gbff" ftype="genbank" /> + <param name="query" value="[?!(features[?type==`source`].qualifiers.plasmid)]" /> + <param name="output_type" value="genbank" /> + <output name="output" checksum="sha256:e142d7e1fbd103c96e3b728e3b75f7af6955c97cdbddb87c3202f2c1e2f133d4" ftype="genbank" /> + </test> + <test expect_num_outputs="1"> + <!-- Test split --> + <param name="input" value="BioPython-Convert/test-data/has_plasmids.gbff" ftype="genbank" /> + <param name="output_type" value="genbank" /> + <output_collection name="split_output" type="list" count="3"> + <element name="record.0" ftype="genbank" checksum="sha256:8d02b2087c4cea42da7c5f0a69b7a40d544d953c1a9d611b97bd116cc1f8cd7f" /> + <element name="record.1" ftype="genbank" checksum="sha256:e37ecc4288ae8b2c3bea25484326a69ced9679fa791162ed593064fdf535944d" /> + <element name="record.2" ftype="genbank" checksum="sha256:e142d7e1fbd103c96e3b728e3b75f7af6955c97cdbddb87c3202f2c1e2f133d4" /> + </output_collection> + </test> + </tests> + <help><![CDATA[ + Interconvert between different file formats that BioPython SeqIO supports. Support for GFF3 has also been included. + + Included features are: + + - Split: Output a collection of datasets, one for each record in the input. + This is useful when a tool only accepts single records. + The resulting output collection can then be mapped over the receiving tool. + - Info: Output an additional GFF3 dataset that contains a summary record for each record in the output dataset. + This is useful for extracting sequence IDs, counting how many records are in the output dataset, and various + diagnostic processes. + - Query: Datasets can be queried or filtered using JMESPath query language. + For example ``[?!(features[?type==`source`].qualifiers.plasmid)]`` will remove any plasmid records sometimes + found in prokaryotic Genbank or EMBL reference genomes. + See http://jmespath.org/ for documentation, and https://biopython.org/DIST/docs/api/Bio.SeqFeature.SeqFeature-class.html + for the data structure. Single quotes `'` are not permitted in the query. + + ]]></help> + <citations> + <citation type="doi">10.5281/zenodo.3364782</citation> + <citation type="doi">10.5281/zenodo.3364789</citation> + </citations> +</tool>