Mercurial > repos > brinkmanlab > biopython_convert

annotate biopython-convert.xml @ 1:ff7e1478030d draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit c9aaa66e920a484ce941c85d4872861b2c03653a"
author brinkmanlab
date Thu, 13 Feb 2020 14:12:25 -0500
parents 869e206b3ca1
children d74dcad9132d
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869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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1 <tool id="biopython-convert" name="BioPython SeqIO Converter" version="1.0" profile="16.04">
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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2 <description>Interconvert between the various sequence file formats that BioPython supports</description>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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3 <edam_topics>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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4 <edam_topic>topic_0091</edam_topic>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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5 </edam_topics>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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6 <edam_operations>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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7 <edam_operation>operation_3434</edam_operation>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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8 <edam_operation>operation_0335</edam_operation>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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9 <edam_operation>operation_3359</edam_operation>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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10 <edam_operation>operation_0224</edam_operation>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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11 <edam_operation>operation_3695</edam_operation>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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12 </edam_operations>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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13 <requirements>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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14 <requirement type="package" version="3.7">python</requirement>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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15 <requirement type="package" version="1.0">biopython.convert</requirement>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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16 </requirements>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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17 <version_command><![CDATA[ biopython.convert -v ]]></version_command>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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18 <command detect_errors="aggressive"><![CDATA[
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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19 #if $bioperl
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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20 #set $script = 'python ' + $__tool_directory__ + '/bioperl_compat.py'
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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21 #else
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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22 #set $script = 'biopython.convert'
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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23 #end if
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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24 #if $split
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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25 mkdir -p output &&
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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26 $script $split $info
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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27 #if $query
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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28 -q '$query'
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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29 #end if
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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30 $input $input.ext output/record $output_type
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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31 #else
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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32 $script $split $info
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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33 #if $query
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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34 -q '$query'
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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35 #end if
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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36 $input $input.ext $output $output_type
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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37 #end if
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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38 #if $info
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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39 > $info_output
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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40 #end if
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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41 ]]></command>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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42 <inputs>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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43 <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" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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44 <param name="output_type" type="select" label="Output Format">
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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45 <option value="clustal">clustal</option>
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46 <option value="embl">embl</option>
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47 <option value="fasta">fasta</option>
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48 <option value="fasta-2line">fasta-2line</option>
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49 <option value="fastq-sanger">fastq-sanger</option>
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50 <option value="fastq">fastq</option>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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51 <option value="fastq-solexa">fastq-solexa</option>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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52 <option value="fastq-illumina">fastq-illumina</option>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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53 <option value="genbank">genbank</option>
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54 <option value="gb">gb</option>
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55 <option value="imgt">imgt</option>
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56 <option value="nexus">nexus</option>
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57 <option value="phd">phd</option>
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58 <option value="phylip">phylip</option>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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59 <option value="pir">pir</option>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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60 <option value="seqxml">seqxml</option>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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61 <option value="sff">sff</option>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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62 <option value="stockholm">stockholm</option>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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63 <option value="tab">tab</option>
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64 <option value="qual">qual</option>
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65 <option value="gff3">gff3</option>
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66 </param>
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67 <param name="split" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Split each record into a different file" />
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68 <param name="info" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Output record information while converting" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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69 <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.">
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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70 <sanitizer>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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71 <valid initial="string.printable">
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72 <remove value="&apos;" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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73 </valid>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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74 </sanitizer>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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75 </param>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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76 <param name="bioperl" type="boolean" checked="false" label="Modify biopython to generate files similar to bioperl" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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77 </inputs>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
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78 <outputs>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
79 <data name="info_output" format="gff3" label="Record Info from ${tool.name} on ${on_string}">
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
80 <filter>info</filter>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
81 </data>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
82 <data name="output" format="txt" label="Output from ${tool.name} on ${on_string}">
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
83 <filter>not split</filter>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
84 <change_format>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
85 <when input="output_type" value="clustal" format="clustal" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
86 <when input="output_type" value="embl" format="embl" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
87 <when input="output_type" value="fasta" format="fasta" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
88 <when input="output_type" value="fasta-2line" format="fasta-2line" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
89 <when input="output_type" value="fastq-sanger" format="fastq-sanger" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
90 <when input="output_type" value="fastq" format="fastq" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
91 <when input="output_type" value="fastq-solexa" format="fastq-solexa" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
92 <when input="output_type" value="fastq-illumina" format="fastq-illumina" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
93 <when input="output_type" value="genbank" format="genbank" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
94 <when input="output_type" value="gb" format="genbank" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
95 <when input="output_type" value="imgt" format="imgt" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
96 <when input="output_type" value="nexus" format="nexus" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
97 <when input="output_type" value="phd" format="phd" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
98 <when input="output_type" value="phylip" format="phylip" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
99 <when input="output_type" value="pir" format="pir" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
100 <when input="output_type" value="seqxml" format="seqxml" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
101 <when input="output_type" value="sff" format="sff" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
102 <when input="output_type" value="stockholm" format="stockholm" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
103 <when input="output_type" value="tab" format="tabular" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
104 <when input="output_type" value="qual" format="qual" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
105 <when input="output_type" value="gff3" format="gff3" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
106 </change_format>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
107 </data>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
108 <collection name="split_output" type="list" label="Output split per record from ${tool.name} on ${on_string}">
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
109 <filter>split</filter>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
110 <discover_datasets pattern=".*" directory="output" format="$output_type" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
111 </collection>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
112 </outputs>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
113 <tests>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
114 <test expect_num_outputs="1">
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
115 <!-- Test basic conversion to same format -->
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
116 <param name="input" value="BioPython-Convert/test-data/has_plasmids.gbff" ftype="genbank" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
117 <param name="output_type" value="genbank" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
118 <output name="output" checksum="sha256:2808187bb8e2231545e4d2d7a27dc802df4d1f7c0e953a8399300b2df6b0c737" ftype="genbank" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
119 </test>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
120 <test expect_num_outputs="1">
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
121 <!-- Test basic conversion to same format with info -->
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
122 <param name="input" value="BioPython-Convert/test-data/has_plasmids.gbff" ftype="genbank" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
123 <param name="info" value="-i" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
124 <param name="output_type" value="genbank" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
125 <output name="output" checksum="sha256:2808187bb8e2231545e4d2d7a27dc802df4d1f7c0e953a8399300b2df6b0c737" ftype="genbank" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
126 <output name="info_output" checksum="sha256:a611656c5a7e7f719c3d64f6b348b67c1abcb8ed56fa82f51fc90cbe2125e5f0" ftype="gff3" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
127 </test>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
128 <test expect_num_outputs="1">
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
129 <!-- Test basic conversion to different format -->
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
130 <param name="input" value="BioPython-Convert/test-data/has_plasmids.gbff" ftype="genbank" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
131 <param name="output_type" value="embl" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
132 <output name="output" checksum="sha256:5598cb679f5f6c31349968ddde3646fe97296da42ee528ed3f46dec3f5490cbd" ftype="embl" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
133 </test>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
134 <test expect_num_outputs="1">
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
135 <!-- Test basic conversion to same format with filter -->
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
136 <param name="input" value="BioPython-Convert/test-data/has_plasmids.gbff" ftype="genbank" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
137 <param name="query" value="[?!(features[?type==`source`].qualifiers.plasmid)]" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
138 <param name="output_type" value="genbank" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
139 <output name="output" checksum="sha256:e142d7e1fbd103c96e3b728e3b75f7af6955c97cdbddb87c3202f2c1e2f133d4" ftype="genbank" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
140 </test>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
141 <test expect_num_outputs="1">
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
142 <!-- Test split -->
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
143 <param name="input" value="BioPython-Convert/test-data/has_plasmids.gbff" ftype="genbank" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
144 <param name="output_type" value="genbank" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
145 <output_collection name="split_output" type="list" count="3">
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
146 <element name="record.0" ftype="genbank" checksum="sha256:8d02b2087c4cea42da7c5f0a69b7a40d544d953c1a9d611b97bd116cc1f8cd7f" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
147 <element name="record.1" ftype="genbank" checksum="sha256:e37ecc4288ae8b2c3bea25484326a69ced9679fa791162ed593064fdf535944d" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
148 <element name="record.2" ftype="genbank" checksum="sha256:e142d7e1fbd103c96e3b728e3b75f7af6955c97cdbddb87c3202f2c1e2f133d4" />
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
149 </output_collection>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
150 </test>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
151 </tests>
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
parents:
diff changeset
152 <help><![CDATA[
869e206b3ca1 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/biopython-convert commit 2f8c5be3bf3117a8d3296a6b82655ff08edd2f34"
brinkmanlab
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153 Interconvert between different file formats that BioPython SeqIO supports. Support for GFF3 has also been included.
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154
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155 Included features are:
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156
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157 - Split: Output a collection of datasets, one for each record in the input.
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158 This is useful when a tool only accepts single records.
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159 The resulting output collection can then be mapped over the receiving tool.
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160 - Info: Output an additional GFF3 dataset that contains a summary record for each record in the output dataset.
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161 This is useful for extracting sequence IDs, counting how many records are in the output dataset, and various
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162 diagnostic processes.
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163 - Query: Datasets can be queried or filtered using JMESPath query language.
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164 For example ``[?!(features[?type==`source`].qualifiers.plasmid)]`` will remove any plasmid records sometimes
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165 found in prokaryotic Genbank or EMBL reference genomes.
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166 See http://jmespath.org/ for documentation, and https://biopython.org/DIST/docs/api/Bio.SeqFeature.SeqFeature-class.html
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167 for the data structure. Single quotes `'` are not permitted in the query.
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168
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169 ]]></help>
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170 <citations>
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171 <citation type="doi">10.5281/zenodo.3364782</citation>
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172 <citation type="doi">10.5281/zenodo.3364789</citation>
1
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173 <citation type="doi">10.1093/bioinformatics/btp163</citation>
0
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174 </citations>
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175 </tool>