Mercurial > repos > iuc > biobox_add_taxid

annotate biobox_add_taxid.xml @ 4:2e0af1e2d487 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041
author iuc
date Sat, 08 Feb 2025 11:33:03 +0000
parents 450a61fc097f
children
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4
2e0af1e2d487 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041
iuc
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1 <tool id="biobox_add_taxid" name="Biobox add taxid" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description>Add taxid output from BAT or GTDB to biobox binning data</description>
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3 <macros>
4
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4 <token name="@TOOL_VERSION@">1.2</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
2e0af1e2d487 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041
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6 <token name="@PROFILE@">24.1</token>
0
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">biobox_add_taxid</requirement>
0
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10 </requirements>
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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13
4
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14 ln -s '$biobox_file' 'biobox.tsv' &&
0
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15
4
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16 #if $input.is_select == 'contig':
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17 ln -s '$contig2taxid' 'contig.tsv' &&
2e0af1e2d487 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041
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18 #else:
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19 ln -s '$binid2taxid' 'bin.tsv' &&
2e0af1e2d487 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041
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20 #end if
2
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21
4
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22 biobox_add_taxid.py
2e0af1e2d487 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041
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23 'biobox.tsv'
2e0af1e2d487 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041
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24 #if $input.is_select == 'contig':
2e0af1e2d487 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041
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25 -c 'contig.tsv'
2e0af1e2d487 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041
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26 #else:
2e0af1e2d487 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041
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27 -b 'bin.tsv'
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28 #end if
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29 -k_c ${key_col}
2e0af1e2d487 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041
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30 -t_c ${taxid_col}
0
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31
4
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32 &&
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33
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34 cp 'modified_biobox_file.tsv' '$output'
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35
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36 ]]>
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37 </command>
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38 <inputs>
4
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39 <param name="biobox_file" type="data" format="tabular" label="Input biobox file"
2e0af1e2d487 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041
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40 help="This file can be generated with the utility tool from CAMI AMBER named convert to biobox"/>
2e0af1e2d487 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041
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41 <conditional name="input">
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42 <param name="is_select" type="select" label="Select typ of input">
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43 <option value="contig">ContigID2TaxID</option>
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44 <option value="bin">BinID2TaxID</option>
0
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45 </param>
4
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46 <when value="contig">
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47 <param argument="--contig2taxid" type="data" format="tabular" label="Input ConitgID2TaxID file"
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48 help="This input comes from Kraken2"/>
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49 <param argument="--key_col" type="data_column" data_ref="contig2taxid" label="Select the column where the ContigID are stated"/>
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50 <param argument="--taxid_col" type="data_column" data_ref="contig2taxid" label="Select the column where the TaxID are stated"/>
0
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51 </when>
4
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52 <when value="bin">
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53 <param argument="--binid2taxid" type="data" format="tabular" label="Input BinID2TaxID file"
2e0af1e2d487 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041
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54 help="This input comes from Kraken2"/>
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55 <param argument="--key_col" type="data_column" data_ref="binid2taxid" label="Select the column where the BinID are stated"/>
2e0af1e2d487 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit 09a7f1234811e6104671c0fbb51a515e13815041
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56 <param argument="--taxid_col" type="data_column" data_ref="binid2taxid" label="Select the column where the TaxID are stated"/>
0
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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>
4
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64 <test>
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65 <param name="biobox_file" value="biobox_file.tsv" ftype="tabular"/>
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66 <conditional name="input">
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67 <param name="is_select" value="bin"/>
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68 <param name="binid2taxid" value="binid2taxid.tsv" ftype="tabular"/>
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69 <param name="key_col" value="1"/>
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70 <param name="taxid_col" value="2"/>
0
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71 </conditional>
4
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72 <output name="output" file="modified_biobox_file_bin.tsv"/>
0
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73 </test>
4
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74 <test>
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75 <param name="biobox_file" value="biobox_file.tsv" ftype="tabular"/>
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76 <conditional name="input">
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77 <param name="is_select" value="contig"/>
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78 <param name="contig2taxid" value="kraken2.tsv" ftype="tabular"/>
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79 <param name="key_col" value="2"/>
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80 <param name="taxid_col" value="3"/>
0
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81 </conditional>
4
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82 <output name="output" file="modified_biobox_file_contig.tsv"/>
0
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83 </test>
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84 </tests>
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85 <help>
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86 <![CDATA[
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87
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88 **USAGE OF THIS TOOL**
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89
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90 This tool can be used to add the TaxID column to a biobox file.
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91
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92 **INPUTS**
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93
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94 - A biobox file. This file can be generated with the CAMI AMBER utility Tool named 'convert to biobox'
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95 - Either a Contig2TaxID file which is generated from Kraken2 (the classification file from Kraken2) or a BinID2TaxID which has to be done manualy
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96
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97 Example for a BinID2TaxID file
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98
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99 ::
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100
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101 #BinID TaxID
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102 test1 11056
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103 test2 444944
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104 ABC 888
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105
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106 **OUTPUT**
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107
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108 - A CAMI AMBER biobox file with a taxid column
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109
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110 ]]>
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111 </help>
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112 <citations>
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113 <citation type="bibtex">@misc{BibEntry2024Aug,
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114 title = {{biobox{$\_$}add{$\_$}taxid}},
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115 author = {Santino Faack (SantaMcCloud)},
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116 journal = {GitHub},
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117 year = {2024},
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118 month = aug,
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119 url = {https://github.com/SantaMcCloud/biobox_add_taxid/tree/release-1.0}
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120 }</citation>
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121 </citations>
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122 </tool>