Mercurial > repos > iuc > obi_convert

annotate obiconvert.xml @ 3:10fdaec7480e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
author iuc
date Mon, 10 May 2021 19:30:53 +0000
parents a464eff3d3c2
children c62e77c0a83c
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3
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
iuc
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1 <tool id="obi_convert" name="obiconvert" version="@TOOL_VERSION@" profile="@PROFILE@">
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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2 <description>converts sequence files to different output formats</description>
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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3 <macros>
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4 <import>macros.xml</import>
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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5 </macros>
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <command><![CDATA[
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9 @GUNZIP_INPUT@
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10
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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11 obiconvert
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12 #if $db
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13 -d '$db'
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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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 @INPUT_FORMAT@
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19 @OUT_FORMAT@
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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20 ${uppercase}
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21 ${ecopcrdb}
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22 #if str( $ecopcrdb) == "--ecopcrdb"
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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23 --ecopcrdb-output=${ecopcrdb_output}
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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24 #end if
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25 input
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26 @GZIP_OUTPUT@
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27 > '${output}'
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28 @GENERATE_GALAXY_JSON@
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29 ]]></command>
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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30 <inputs>
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31 <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)" />
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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32 <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database" />
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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33 <param name="tax" type="data" optional="true" format="txt,tabular" label="NCBI taxonomy dump repository"/>
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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34 <expand macro="input_format_options_macro"/>
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35 <expand macro="out_format_macro"/>
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36 <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" />
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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37 <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue="" label="Do you want to print sequences in upper case?" />
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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38 </inputs>
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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39 <outputs>
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40 <data format="txt" name="ecopcrdb_output" label="${tool.name} on ${on_string}: ecopcrdb">
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41 <filter>ecopcrdb == True</filter>
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42 </data>
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43 <data format="auto" name="output"/>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="input" value="output_obisort.fasta" />
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48 <param name="options_inputtype" value="--fasta"/>
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49 <param name="options_seqtype" value="--nuc"/>
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50 <param name="out_format" value="fasta"/>
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51 <param name="ecopcrdb" value="false"/>
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52 <param name="uppercase" value="true"/>
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53 <output name="output" file="output_obiconvert.fasta" ftype="fasta"/>
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54 </test>
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55 </tests>
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56 <help><![CDATA[
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57
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58 .. class:: infomark
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59
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60 **What it does**
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61
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62 obiconvert converts sequence files to different output formats. See the documentation for more details on the different formats.
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63
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64 Input files can be in :
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65
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66 fasta format
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67
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68 extended OBITools fasta format
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69
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70 Sanger fastq format
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71
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72 Solexa fastq format
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73
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74 ecoPCR format
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75
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76 ecoPCR database format
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77
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78 GenBank format
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79
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80 EMBL format
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81
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82 obiconvert converts those files to the :
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83
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84 extended OBITools fasta format
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85
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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86 Sanger fastq format
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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87
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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88 ecoPCR database format
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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89
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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90 If no file name is specified, data is read from standard input.
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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91
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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92 @OBITOOLS_LINK@
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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93
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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94 ]]>
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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95
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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96 </help>
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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97 <expand macro="citation" />
10fdaec7480e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
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98 </tool>