Mercurial > repos > iuc > obi_convert

annotate obiconvert.xml @ 4:e328ced6cf0a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
author iuc
date Wed, 20 Mar 2024 13:15:46 +0000
parents 374fd9feb032
children
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4
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
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1 <tool id="obi_convert" name="obiconvert" version="@TOOL_VERSION@" profile="@PROFILE@">
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
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2 <description>converts sequence files to different output formats</description>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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3 <macros>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
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4 <import>macros.xml</import>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
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5 </macros>
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iuc
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6 <expand macro="bio_tools"/>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
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9 <command><![CDATA[
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10 @GUNZIP_INPUT@
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11
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12 obiconvert
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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13 #if $db
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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14 -d '$db'
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15 #end if
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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16 #if $tax
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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17 -t '$tax'
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18 #end if
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19 @INPUT_FORMAT@
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20 @OUT_FORMAT@
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21 ${uppercase}
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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22 ${ecopcrdb}
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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23 #if str( $ecopcrdb) == "--ecopcrdb"
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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24 --ecopcrdb-output=${ecopcrdb_output}
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25 #end if
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26 input
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27 @GZIP_OUTPUT@
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28 > '${output}'
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29 @GENERATE_GALAXY_JSON@
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30 ]]></command>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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31 <inputs>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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32 <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" help="database used for the in silico PCR. The database must be in the ecoPCR format (for example output of obiconvert)"/>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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33 <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database"/>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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34 <param name="tax" type="data" optional="true" format="txt,tabular" label="NCBI taxonomy dump repository"/>
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35 <expand macro="input_format_options_macro"/>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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36 <expand macro="out_format_macro"/>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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37 <param name="ecopcrdb" type="boolean" truevalue="--ecopcrdb" falsevalue="" label="Do you want to create an ecoPCR database from sequence records results?" help="Use this option if you want to generate an ecoPCR database output file"/>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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38 <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue="" label="Do you want to print sequences in upper case?"/>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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39 </inputs>
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40 <outputs>
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41 <data format="txt" name="ecopcrdb_output" label="${tool.name} on ${on_string}: ecopcrdb">
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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42 <filter>ecopcrdb == True</filter>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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43 </data>
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44 <data format="auto" name="output"/>
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45 </outputs>
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46 <tests>
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47 <test expect_num_outputs="1">
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48 <param name="input" value="output_obisort.fasta" />
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49 <param name="options_inputtype" value="--fasta"/>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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50 <param name="options_seqtype" value="--nuc"/>
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51 <param name="out_format" value="fasta"/>
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52 <param name="ecopcrdb" value="false"/>
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53 <param name="uppercase" value="true"/>
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54 <output name="output" file="output_obiconvert.fasta" ftype="fasta"/>
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58
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59 .. class:: infomark
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60
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61 **What it does**
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62
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63 obiconvert converts sequence files to different output formats. See the documentation for more details on the different formats.
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64
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65 Input files can be in :
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66
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67 fasta format
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68
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69 extended OBITools fasta format
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70
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71 Sanger fastq format
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72
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73 Solexa fastq format
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74
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75 ecoPCR format
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76
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77 ecoPCR database format
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78
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79 GenBank format
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80
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81 EMBL format
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82
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83 obiconvert converts those files to the :
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84
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85 extended OBITools fasta format
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86
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87 Sanger fastq format
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88
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89 ecoPCR database format
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90
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91 If no file name is specified, data is read from standard input.
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92
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93 @OBITOOLS_LINK@
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94
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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95 ]]>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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97 </help>
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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98 <expand macro="citation" />
e328ced6cf0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
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99 </tool>