Mercurial > repos > iuc > profile2cami
comparison taxonkit_profile2cami.xml @ 0:0fd79958fac6 draft
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
author | iuc |
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date | Fri, 26 Jul 2024 09:26:02 +0000 (5 months ago) |
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-1:000000000000 | 0:0fd79958fac6 |
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1 <tool id="profile2cami" name="Profile2CAMI" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
2 <description>Convert metagenomic profile table to CAMI format</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="biotools"/> | |
7 <expand macro="requirements" /> | |
8 <command detect_errors="exit_code"> | |
9 <![CDATA[ | |
10 taxonkit profile2cami | |
11 --data-dir '${taxonomy.fields.path}' | |
12 --abundance-field '${abundance_field}' | |
13 --taxid-field '${taxid_field}' | |
14 | |
15 $percentage | |
16 $recompute_abd | |
17 $keep_zero | |
18 $no_sum_up | |
19 | |
20 #if $sample_id: | |
21 -s '${sample_id}' | |
22 #end if | |
23 #if $taxonomy_id: | |
24 -t '${taxonomy_id}' | |
25 #end if | |
26 #if $ranks: | |
27 --show-rank '${ranks}' | |
28 #end if | |
29 ${input_file} | |
30 > '${cami_output}' | |
31 ]]> | |
32 </command> | |
33 <inputs> | |
34 <param name="input_file" type="data" format="txt" label="Input Profile File" help="A tab-delimited profile file with TaxId and abundance columns." /> | |
35 <param argument="--taxonomy" type="select" label="NCBI taxonomy" help="This NCBI database is used to map human-readable taxon names to TaxId's."> | |
36 <options from_data_table="ncbi_taxonomy"> | |
37 <validator message="No NCBI database is available" type="no_options"/> | |
38 </options> | |
39 </param> | |
40 <param name="abundance_field" type="integer" value="2" label="Abundance Field Index" help="Field index of abundance in the input data." /> | |
41 <param name="taxid_field" type="integer" value="1" label="TaxId Field Index" help="Field index of TaxId in the input data." /> | |
42 <param name="percentage" type="boolean" value="false" label="Abundance in Percentage" help="Check if the abundance values are in percentage." truevalue="-p" falsevalue=""/> | |
43 <param name="recompute_abd" type="boolean" value="false" label="Recompute Abundance" help="Check to recompute abundance if some TaxIds are deleted in the current taxonomy version." truevalue="-R" falsevalue=""/> | |
44 <param name="keep_zero" type="boolean" value="false" label="Keep Zero Abundances" help="Check to keep taxons with abundance of zero." truevalue="-0" falsevalue=""/> | |
45 <param name="no_sum_up" type="boolean" value="false" label="Do Not Sum Up Abundance" help="Do not sum up abundance from child to parent TaxIds." truevalue="-S" falsevalue="" /> | |
46 <param name="sample_id" type="text" value="" label="Sample ID" help="Optional sample ID to include in the result file." /> | |
47 <param name="taxonomy_id" type="text" value="" label="Taxonomy ID" help="Optional taxonomy ID to include in the result file." /> | |
48 <param name ="ranks" argument="--show-rank" type="select" multiple="true" label="Show Ranks" help="Specify the ranks to show in the result file (default [superkingdom,phylum,class,order,family,genus,species,strain])."> | |
49 <option value="superkingdom">Superkingdom</option> | |
50 <option value="phylum">Phylum</option> | |
51 <option value="class">Class</option> | |
52 <option value="order">Order</option> | |
53 <option value="family">Family</option> | |
54 <option value="genus">Genus</option> | |
55 <option value="species">Species</option> | |
56 <option value="strain">Strain</option> | |
57 </param> | |
58 </inputs> | |
59 <outputs> | |
60 <data name="cami_output" format="tsv" label="${tool.name} on ${on_string}" /> | |
61 </outputs> | |
62 <tests> | |
63 <!-- Test 1: Basic functionality with default parameters --> | |
64 <test expect_num_outputs="1"> | |
65 <param name="input_file" value="abundance.tsv" ftype="tsv" /> | |
66 <output name="cami_output" file="output1_basic_functionality.tsv" /> | |
67 </test> | |
68 | |
69 <!-- Test 2: Using percentage flag --> | |
70 <test expect_num_outputs="1"> | |
71 <param name="input_file" value="abundance.tsv" ftype="tsv" /> | |
72 <param name="percentage" value="true" /> | |
73 <output name="cami_output" file="output2_percentage_flag.tsv" /> | |
74 </test> | |
75 | |
76 <!-- Test 3: Recomputing abundance with deleted TaxIds --> | |
77 <test expect_num_outputs="1"> | |
78 <param name="input_file" value="abundance.tsv" ftype="tsv" /> | |
79 <param name="recompute_abd" value="true" /> | |
80 <output name="cami_output" file="output3_recompute_abd.tsv" /> | |
81 </test> | |
82 | |
83 <!-- Test 4: Profile2Cami with all parameters checked --> | |
84 <test expect_num_outputs="1"> | |
85 <param name="input_file" value="abundance.tsv" ftype="tsv" /> | |
86 <param name="percentage" value="true" /> | |
87 <param name="recompute_abd" value="true" /> | |
88 <param name="keep_zero" value="true" /> | |
89 <param name="no_sum_up" value="true" /> | |
90 <output name="cami_output" file="output4_all_param.tsv" /> | |
91 </test> | |
92 </tests> | |
93 <help> | |
94 <![CDATA[ | |
95 **What is Profile2CAMI** | |
96 | |
97 Profile2CAMI is a tool for converting metagenomic profile tables to CAMI format. | |
98 | |
99 **Inputs** | |
100 | |
101 - A tab-delimited profile file with TaxId and abundance columns. | |
102 | |
103 **Outputs** | |
104 | |
105 - A CAMI formatted file. | |
106 | |
107 For more information, please refer to the tool's documentation. | |
108 ]]> | |
109 </help> | |
110 <expand macro="citations" /> | |
111 </tool> |