Mercurial > repos > iuc > obi_convert

annotate obiconvert.xml @ 2:4d705e3443a7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author iuc
date Thu, 28 Nov 2019 15:51:00 -0500
parents 6259965de501
children 374fd9feb032
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6259965de501 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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1 <tool id="obi_convert" name="obiconvert" version="@TOOL_VERSION@">
0
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2 <description>converts sequence files to different output formats</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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9 <command>
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10 <![CDATA[
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11 obiconvert
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12 #if $db
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13 -d '$db'
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14 #end if
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15 #if $tax
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16 -t '$tax'
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17 #end if
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18 ${options_inputtype}
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19 ${options_seqtype}
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20 --${out_format}-output
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21 ${uppercase}
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22 ${ecopcrdb}
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23 #if str( $ecopcrdb) == "--ecopcrdb"
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24 --ecopcrdb-output=${ecopcrdb_output}
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25 #end if
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26 '${input}' > '${output}'
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27 ]]>
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29 </command>
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31 <inputs>
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32 <param name="input" type="data" format="fastq,fasta,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)" />
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33 <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database" />
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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 <param name="options_inputtype" type="select" label="Specify the input datatype">
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36 <expand macro="inputtype"/>
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37 </param>
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38 <param name="options_seqtype" type="select" label="Specify the sequence datatype" >
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39 <option value="--nuc" selected="true">nucleic</option>
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40 <option value="--prot">protein</option>
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41 </param>
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42 <param name="out_format" type="select" label="Output data type">
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43 <option value="fasta" selected="true">fasta</option>
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44 <option value="fastq">fastq</option>
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45 </param>
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46 <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" />
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47 <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue="" label="Do you want to print sequences in upper case?" />
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48
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49 </inputs>
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50 <outputs>
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51 <data format="txt" name="ecopcrdb_output" label="result.ecopcrdb with ${tool.name} on ${on_string}">
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52 <filter>ecopcrdb == True</filter>
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53 </data>
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54 <data format="fasta" name="output" label="output with ${tool.name} on ${on_string}" >
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55 <change_format>
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56 <when input="out_format" value="fastq" format="fastq" />
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57 </change_format>
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58 </data>
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="input" value="output_obisort.fasta" />
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63 <param name="options_inputtype" value="fasta"/>
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64 <param name="options_seqtype" value="--nuc"/>
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65 <param name="out_format" value="fasta"/>
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66 <param name="ecopcrdb" value="False"/>
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67 <param name="uppercase" value="True"/>
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68 <output name="output" file="output_obiconvert.fasta" ftype="fasta"/>
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69 </test>
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70 </tests>
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71 <help><![CDATA[
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72
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73 .. class:: infomark
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74
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75 **What it does**
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77 obiconvert converts sequence files to different output formats. See the documentation for more details on the different formats.
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78
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79 Input files can be in :
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81 fasta format
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82
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83 extended OBITools fasta format
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84
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85 Sanger fastq format
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86
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87 Solexa fastq format
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88
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89 ecoPCR format
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90
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91 ecoPCR database format
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92
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93 GenBank format
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94
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95 EMBL format
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96
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97 obiconvert converts those files to the :
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98
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99 extended OBITools fasta format
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100
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101 Sanger fastq format
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102
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103 ecoPCR database format
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104
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105 If no file name is specified, data is read from standard input.
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106
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107 @OBITOOLS_LINK@
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108
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109 ]]>
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110
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111 </help>
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112 <expand macro="citation" />
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113 </tool>