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comparison MT2MQ.xml @ 0:6bee94458567 draft

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"planemo upload commit 53bcf55b73cb251446150026242b4d47d49d3469"
author galaxyp
date Tue, 23 Jun 2020 07:46:07 -0400
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children 9c8e7137d331
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1 <tool id="mt2mq" name="MT2MQ" version="1.0">
2 <description>Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome</description>
3 <requirements>
4 <requirement type="package" version="1.2.1">r-tidyverse</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7
8 #if $options.mode == "f" or $options.mode == "ft":
9 Rscript '$__tool_directory__/MT2MQ.R' '$options.input_files' '$options.mode' $options.ontology '$mq_output'
10 #elif $options.mode == "t":
11 mkdir in_dir
12 #for $input in $options.input_files:
13 && cp '$input' 'in_dir/${input.name.rsplit('.',1)[0]}'
14 #end for
15 && Rscript '$__tool_directory__/MT2MQ.R' in_dir t NA '$mq_output'
16 #end if
17
18 ]]>
19 </command>
20
21 <inputs>
22 <conditional name="options">
23 <param type="select" display="radio" name="mode" label="Mode">
24 <option value="f">Functional</option>
25 <option value="t" selected="true">Taxonomic</option>
26 <option value="ft">Functional-Taxonomic</option>
27 </param>
28 <when value="t">
29 <param name="ontology" type="hidden" value="NA" />
30 <param type="data" name="input_files" format="tsv,tabular,txt" label="Files from ASaiM for all samples (named after sample)" multiple="true" />
31 </when>
32 <when value="f">
33 <param type="select" name="ontology" label="GO namespace" multiple="true" optional="false">
34 <option value="molecular_function">molecular function</option>
35 <option value="biological_process">biological proces</option>
36 <option value="cellular_component">cellular component</option>
37 </param>
38 <param type="data" name="input_files" format="tsv,tabular,txt" label="File from HUMAnN2 after regrouping, renaming, joining, and renormalizing" />
39 </when>
40 <when value="ft">
41 <param type="select" name="ontology" label="GO namespace" multiple="true" optional="false">
42 <option value="molecular_function">molecular function</option>
43 <option value="biological_process">biological proces</option>
44 <option value="cellular_component">cellular component</option>
45 </param>
46 <param type="data" name="input_files" format="tsv,tabular,txt" label="File from HUMAnN2 after regrouping, renaming, joining, and renormalizing" />
47 </when>
48 </conditional>
49 </inputs>
50
51 <outputs>
52 <data name="mq_output" format="tabular" label="${options.mode}_output.tabular"/>
53 </outputs>
54
55
56 <tests>
57 <test>
58 <conditional name="options">
59 <param name="mode" value="t"/>
60 <param name="input_files" value="T4A.tsv,T4B.tsv,T4C.tsv,T7A.tsv,T7B.tsv,T7C.tsv" ftype="tsv"/>
61 <param name="ontology" value="NA"/>
62 </conditional>
63 <output name="mq_output">
64 <assert_contents>
65 <has_text text="rank"/>
66 <has_text text="genus"/>
67 <has_text text="Clostridium"/>
68 </assert_contents>
69 </output>
70 </test>
71 <test>
72 <conditional name="options">
73 <param name="mode" value="f"/>
74 <param name="input_files" value="T4T7_func.tsv" ftype="tsv"/>
75 <param name="ontology" value="molecular_function"/>
76 </conditional>
77 <output name="mq_output">
78 <assert_contents>
79 <has_text text="namespace"/>
80 <has_text text="molecular_function"/>
81 <has_text text="0000014"/>
82 </assert_contents>
83 </output>
84 </test>
85 <test>
86 <conditional name="options">
87 <param name="mode" value="ft"/>
88 <param name="input_files" value="T4T7_func.tsv" ftype="tsv"/>
89 <param name="ontology" value="biological_process"/>
90 </conditional>
91 <output name="mq_output">
92 <assert_contents>
93 <has_text text="namespace"/>
94 <has_text text="genus"/>
95 <has_text text="biological_process"/>
96 <has_text text="Clostridium"/>
97 </assert_contents>
98 </output>
99 </test>
100 </tests>
101
102
103
104
105 <help><![CDATA[
106
107 **MT2MQ**: Metatranscriptomics to Metaquantome
108 ----------------------------------------------------
109
110 MT2MQ is a tool to prepare metatrascriptomic results from ASaiM for further analysis with MetaQuantome, which currently only supports metaproteomic data. This tool has three modes:
111
112 - **Taxonomic**: takes in genus-level MetaPhlAn2 results for each sample. The input files should be named as the sample.
113
114 - Output: a single tabular file formatted for use as input for Metaquantome's taxonomic mode.
115
116 - **Functional**: takes in a single file of HUMAnN2 results, regrouped and renamed to GO terms, with all samples joined together into one table, and renormalized to CPM. See the MT2MQ functional workflow for these processing steps. User can choose which GO namespace(s) to include.
117
118 - Output: a single tabular file formatted for use as input for Metaquantome's functional mode.
119
120 - **Functional/taxonomic**: takes the same input as the functional mode. User can choose which GO namespace(s) to include.
121
122 - Output: a single tabular file including all GO terms and the taxa which express them and their abundances for each sample. This file *cannot* be used as input for Metaquantome.
123
124 **Outputs**:
125 ------------
126
127 MT2MQ produces a single tabular output, formatted to be used as input for Metaquantome or for other analysis.
128
129 ]]></help>
130
131 <citations>
132 <citation type="bibtex">
133 @misc{MT2MQ,
134 author={Crane, Marie},
135 year={2020},
136 title={Metatranscriptomics to MetaQuantome}
137 }
138 </citation>
139 </citations>
140 </tool>