Mercurial > repos > iuc > biobox_add_taxid

annotate biobox_add_taxid.xml @ 1:d368e312aebd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 3d970dee40d339c0af6eda9e5a9bb39140bbc9cd
author iuc
date Fri, 30 Aug 2024 14:39:04 +0000
parents 1e10251b9615
children 450a61fc097f
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1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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1 <tool id="biobox_add_taxid" name="Biobox add taxid" version="@SCRIPT_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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2 <description>Add taxid output from BAT or GTDB to biobox binning data</description>
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3 <macros>
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4 <import>macros.xml</import>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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5 <token name="@SCRIPT_VERSION@">0.4</token>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@SCRIPT_VERSION@">biobox_add_taxid</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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12
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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13 mkdir -p input &&
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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15 ln -s '${biobox_file}' '$biobox_file.element_identifier' &&
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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17 #for $i, $f in enumerate($tool_type.input):
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18 ln -s '$f' 'input/${i}.tsv' &&
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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19 #end for
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21 biobox_add_taxid.py
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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22 '$biobox_file.element_identifier'
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23 '$tool_type.is_select'
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24 'input'
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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25 #if $tool_type.is_select == 'GTDB':
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26 -g '$gtdb_to_taxdump'
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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27 -t '$taxonkit'
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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28 -c $column
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29 #end if
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30 &&
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31
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32 #if $tool_type.is_select == 'GTDB':
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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33 cp *_add_taxid_GTDB* $output
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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34 #else:
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35 cp *_add_taxid_BAT* $output
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36 #end if
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37
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38 ]]>
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39 </command>
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40 <inputs>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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41 <param name="biobox_file" type="data" format="tabular" label="CAMI amber biobox file input" help="Input the CAMI amber biobox file here which are corespond with the biner and the BAT/GTDB output which did used the biner as input! "/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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42 <conditional name="tool_type">
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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43 <param name="is_select" type="select" label="Select the tool which output should be used here" help="Select BAT when you use the bin2classifier file(s) or select GTDB when using the summary file(s)">
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44 <option value="BAT">BAT</option>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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45 <option value="GTDB">GTDB</option>
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46 </param>
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47 <when value="GTDB">
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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48 <param argument="--gtdb_to_taxdump" type="data" format="tabular" label="Input the output from gtdb_to_taxdump here" help="Use the output from gtdb_to_taxdump here since we need the mapped names from GTDB to NCBI to get the arcoding taxids from NCBI"/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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49 <param argument="--taxonkit" type="data" format="tabular" label="Input the output from Taxonkit here" help="Use the output from Taxonkit here since the need the mapped NCBI names to the arcording taxids"/>
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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50 <param argument="--column" type="data_column" data_ref="taxonkit" label="Input the colum with the NCBI names"/>
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51 <param name="input" type="data" multiple="true" format="tabular" label="Input the GTDB-Tk summary file(s) here"
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52 help="Use the GTDB-Tk file(s) which are coresponding with the binning file!"/>
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53 </when>
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54 <when value="BAT">
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55 <param name="input" type="data" multiple="true" format="tabular" label="Input bin2classifier file(s) from BAT here"
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56 help="Use the BAT file(s) which are coresponding with the binning file!"/>
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57 </when>
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58 </conditional>
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59 </inputs>
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60 <outputs>
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61 <data name="output" format="tabular" label="${tool.name}: BIOBOX ADD TAXID COLUMN"/>
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62 </outputs>
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63 <tests>
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64 <test expect_num_outputs="1">
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65 <param name="biobox_file" ftype="tabular" value="test_biobox_file.tsv"/>
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66 <conditional name="tool_type">
1e10251b9615 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 91090b1565baeddbd3c96e74bc08a37990fafd3a
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67 <param name="is_select" value="BAT"/>
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68 <param name="input" ftype="tabular" value="test_bat_file.tsv"/>
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69 </conditional>
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70 <output name="output" file="test_biobox_file_add_taxid_bat.tsv"/>
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71 </test>
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72 <test expect_num_outputs="1">
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73 <param name="biobox_file" ftype="tabular" value="test_biobox_file.tsv"/>
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74 <conditional name="tool_type">
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75 <param name="is_select" value="GTDB"/>
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76 <param name="gtdb_to_taxdump" ftype="tabular" value="test_gtdb_to_taxdump_file.tsv"/>
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77 <param name="taxonkit" ftype="tabular" value="test_taxonkit_file.tsv"/>
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78 <param name="column" value="1"/>
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79 <param name="input" ftype="tabular" value="test_gtdb_file.tsv"/>
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80 </conditional>
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81 <output name="output" file="test_biobox_file_add_taxid_gtdb.tsv"/>
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82 </test>
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83 </tests>
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84 <help>
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85 <![CDATA[
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86
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87 **USAGE OF THIS TOOL**
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88
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89 This tool was desgin for using the BAT/GTDB-Tk output to expand the CAMI amber biobox file with the taxid column to access taxa evaluation with amber!
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90
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91 **IMPORTAND NOTE WHEN USING GTDB OUTPUT**
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92
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93 Befor using GTDB-Tk output you have to use 2 other tools to map the GTDB names to the NCBI names and then map the NCBI names to there taxids.
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94 To map the GTDB names to the NCBI names you extract the GTDB names from the summary file and with them you can now use the gtdb_to_taxdum tool!
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95 After using the gtdb_to_taxdum tool you have the extract the NCBI names here and then use the tool Taxonkit[name2taxid] to finaly get the taxids.
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96
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97 **INPUTS**
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98 - The CAMI amber biobox file
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99 - BAT[bin2classifier] file(s) OR GTDB-Tk[Summary] file(s)
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100 - The gtdb_to_taxdum output[WHEN USING GTDB-Tk]
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101 - The Taxonkit[name2taxid] output[WHEN USING GTDB-Tk]
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102
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103 **OUTPUT**
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104
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105 A CAMI amber biobox file with a taxid colum
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106 ]]>
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107 </help>
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108 <citations>
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109 <citation type="bibtex">@misc{BibEntry2024Aug,
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110 title = {{biobox{$\_$}add{$\_$}taxid}},
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111 author = {Santino Faack (SantaMcCloud)},
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112 journal = {GitHub},
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113 year = {2024},
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114 month = aug,
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115 note = {[Online; accessed 22. Aug. 2024]},
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116 url = {https://github.com/SantaMcCloud/biobox_add_taxid/tree/release-0.3}
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117 }</citation>
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118 </citations>
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119 </tool>