comparison taxonkit_profile2cami.xml @ 0:0fd79958fac6 draft

planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
author iuc
date Fri, 26 Jul 2024 09:26:02 +0000 (5 months ago)
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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>