Mercurial > repos > bvalot > pymlst

annotate wgmlst_remove.xml @ 1:5b2c48fa0175 draft

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planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
author bvalot
date Wed, 07 Dec 2022 15:25:06 +0000
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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1 <tool id="wgmlst_remove_wrapper"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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2 name="Remove strain/gene to cg/wgMLST database"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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3 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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4 <description></description>
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5 <macros>
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6 <import>macro.xml</import>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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7 </macros>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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8 <expand macro="requirements" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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9 <stdio>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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10 <exit_code range="1:" level="fatal" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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11 </stdio>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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12 <version_command>wgMLST -v</version_command>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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13 <command><![CDATA[
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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14 cp '${database}' '${databaseout}' && wgMLST remove
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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15 #if $element == "strain"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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16 --strains
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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17 #else
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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18 --genes
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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19 #end if
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20 #if $data.input == "textinput"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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21 '${databaseout}'
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22 #for $strain in $data.textelement.split(" ")
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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23 '$strain'
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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24 #end for
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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25 #else
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26 -f '${data.fileelement}' '${databaseout}'
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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27 #end if
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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28 #if $log
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29 2> '${logfile}'
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30 #end if
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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31 ]]>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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32 </command>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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33 <inputs>
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34 <param name="database" type="data"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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35 format="sqlite"
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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36 label="cg/wgMLST database"
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37 help="Sqlite format from cg/wgMLST database" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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38 <param name="element" type="select" label="Select type of data to remove">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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39 <option value="strain" selected="true">Strain(s)</option>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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40 <option value="gene">Gene(s)</option>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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41 </param>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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42 <conditional name="data">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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43 <param name="input" type="select" label="Select source of data">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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44 <option value="textinput" selected="true">List elements manually</option>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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45 <option value="fileinput">List elements from file</option>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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46 </param>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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47 <when value="textinput">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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48 <param name="textelement" type="text" value="" optional="false" size="50"
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49 label="Name of strain/gene to removed from database"
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50 help="Separated each strain/gene by a space and quote it"/>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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51 </when>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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52 <when value="fileinput">
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53 <param name="fileelement" type="data" format="txt"
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54 label="File list of strain/gene to removed"
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55 help="txt format" />
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56 </when>
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57 </conditional>
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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58 <param name="log" type="boolean" checked="true"
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59 label="Write log file" />
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60 </inputs>
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61 <outputs>
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62 <data name="databaseout" format="sqlite" label="${database.name}">
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63 </data>
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64 <data name="logfile" format="txt" label="${tool.name} on ${database.name}: log">
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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65 <filter>log</filter>
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66 </data>
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67 </outputs>
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68 <tests>
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69 <test expect_num_outputs="2">
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70 <param name="database" value="wgmlst_ecoli.db" />
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71 <param name="element" value="strain" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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72 <conditional name="data">
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73 <param name="input" value="textinput" />
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74 <param name="textelement" value="EEES_003 EEES_004" />
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75 </conditional>
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76 <output name="logfile" ftype="txt">
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77 <assert_contents>
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78 <has_text text="EEES_004 : OK" />
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79 <has_text text="EEES_003 : OK" />
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80 </assert_contents>
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81 </output>
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82 </test>
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83 <test expect_num_outputs="2">
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84 <param name="database" value="wgmlst_ecoli.db" />
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85 <param name="element" value="gene" />
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86 <conditional name="data">
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87 <param name="input" value="fileinput" />
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88 <param name="fileelement" ftype="txt" value="wgmlst_ecoli.db.gene_to_removed" />
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89 </conditional>
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90 <output name="logfile" ftype="txt">
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91 <assert_contents>
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92 <has_text text="b0004 : OK" />
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93 <has_text text="C-RS24040 : OK" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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94 <has_text text="ECs4518 : OK" />
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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95 </assert_contents>
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96 </output>
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97 </test>
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98 </tests>
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99 <help>
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100 **What it does**
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101
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102 Remove STRAINS or GENES from a cg/wgMLST DATABASE.
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103
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104 You can indicated the STRAIN or GENE to remove:
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105 - Typing element separated by space
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106 - Using a file containing these elements
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107
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108 **Options:**
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109 --strains / --genes Choose the item you wish to remove
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110 -f, --file FILENAME File list of genes or strains to removed on the wgMLST database.
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111
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112 **License and citation**
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113
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114 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
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115 </help>
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116 <citations>
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117 </citations>
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118 </tool>