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comparison MT2MQ.xml @ 2:9c8e7137d331 draft

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"planemo upload commit 59afcdaf7afdf574c475f0faae73127f0e563328"
author galaxyp
date Wed, 12 Aug 2020 17:36:53 -0400
parents 6bee94458567
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1:e50ec3a9a3f9 2:9c8e7137d331
1 <tool id="mt2mq" name="MT2MQ" version="1.0"> 1 <tool id="mt2mq" name="MT2MQ" version="1.1.0">
2 <description>Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome</description> 2 <description>Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2.1">r-tidyverse</requirement> 4 <requirement type="package" version="1.2.1">r-tidyverse</requirement>
5 <requirement type="package" version="0.9.97">r-taxize</requirement>
5 </requirements> 6 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
7 8
8 #if $options.mode == "f" or $options.mode == "ft": 9 #if $options.mode == "f" or $options.mode == "ft":
9 Rscript '$__tool_directory__/MT2MQ.R' '$options.input_files' '$options.mode' $options.ontology '$mq_output' 10 Rscript --vanilla '$__tool_directory__/MT2MQ.R' '$options.input_files' '$options.mode' '$options.ontology' '$int_output' '$func_output' '$tax_output'
10 #elif $options.mode == "t": 11 #elif $options.mode == "t":
11 mkdir in_dir 12 mkdir in_dir
12 #for $input in $options.input_files: 13 #for $input in $options.input_files:
13 && cp '$input' 'in_dir/${input.name.rsplit('.',1)[0]}' 14 && cp '$input' 'in_dir/${input.name.rsplit('.',1)[0]}'
14 #end for 15 #end for
15 && Rscript '$__tool_directory__/MT2MQ.R' in_dir t NA '$mq_output' 16 && Rscript --vanilla '$__tool_directory__/MT2MQ.R' in_dir t NA '$int_output' '$func_output' '$tax_output'
16 #end if 17 #end if
17 18
18 ]]> 19 ]]>
19 </command> 20 </command>
20 21
47 </when> 48 </when>
48 </conditional> 49 </conditional>
49 </inputs> 50 </inputs>
50 51
51 <outputs> 52 <outputs>
52 <data name="mq_output" format="tabular" label="${options.mode}_output.tabular"/> 53 <data name="int_output" format="tabular" label="${options.mode}_int.tabular"/>
54 <data name="func_output" format="tabular" label="func.tabular">
55 <filter>options['mode'] == "f"</filter>
56 </data>
57 <data name="tax_output" format="tabular" label="tax.tabular">
58 <filter>options['mode'] == "t"</filter>
59 </data>
60
53 </outputs> 61 </outputs>
54 62
55 63
56 <tests> 64 <tests>
57 <test> 65 <test>
58 <conditional name="options"> 66 <conditional name="options">
59 <param name="mode" value="t"/> 67 <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"/> 68 <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"/> 69 <param name="ontology" value="NA"/>
62 </conditional> 70 </conditional>
63 <output name="mq_output"> 71 <output name="int_output">
64 <assert_contents> 72 <assert_contents>
65 <has_text text="rank"/> 73 <has_text text="rank"/>
66 <has_text text="genus"/> 74 <has_text text="genus"/>
67 <has_text text="Clostridium"/> 75 <has_text text="Clostridium"/>
68 </assert_contents> 76 </assert_contents>
72 <conditional name="options"> 80 <conditional name="options">
73 <param name="mode" value="f"/> 81 <param name="mode" value="f"/>
74 <param name="input_files" value="T4T7_func.tsv" ftype="tsv"/> 82 <param name="input_files" value="T4T7_func.tsv" ftype="tsv"/>
75 <param name="ontology" value="molecular_function"/> 83 <param name="ontology" value="molecular_function"/>
76 </conditional> 84 </conditional>
77 <output name="mq_output"> 85 <output name="int_output">
78 <assert_contents> 86 <assert_contents>
79 <has_text text="namespace"/> 87 <has_text text="namespace"/>
80 <has_text text="molecular_function"/> 88 <has_text text="molecular_function"/>
81 <has_text text="0000014"/> 89 <has_text text="0000014"/>
82 </assert_contents> 90 </assert_contents>
86 <conditional name="options"> 94 <conditional name="options">
87 <param name="mode" value="ft"/> 95 <param name="mode" value="ft"/>
88 <param name="input_files" value="T4T7_func.tsv" ftype="tsv"/> 96 <param name="input_files" value="T4T7_func.tsv" ftype="tsv"/>
89 <param name="ontology" value="biological_process"/> 97 <param name="ontology" value="biological_process"/>
90 </conditional> 98 </conditional>
91 <output name="mq_output"> 99 <output name="int_output">
92 <assert_contents> 100 <assert_contents>
93 <has_text text="namespace"/> 101 <has_text text="namespace"/>
94 <has_text text="genus"/> 102 <has_text text="genus"/>
95 <has_text text="biological_process"/> 103 <has_text text="biological_process"/>
96 <has_text text="Clostridium"/> 104 <has_text text="Clostridium"/>
109 117
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: 118 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:
111 119
112 - **Taxonomic**: takes in genus-level MetaPhlAn2 results for each sample. The input files should be named as the sample. 120 - **Taxonomic**: takes in genus-level MetaPhlAn2 results for each sample. The input files should be named as the sample.
113 121
114 - Output: a single tabular file formatted for use as input for Metaquantome's taxonomic mode. 122 - Output: a taxonomy file and an intensity file to use in Metaquantome's taxonomy mode. The "peptide" column name is "id" and the taxon column name is "tax".
115 123
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. 124 - **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.
117 125
118 - Output: a single tabular file formatted for use as input for Metaquantome's functional mode. 126 - Output: a function file and an intensity file to use in Metaquantome's functional mode. The "peptide" column name is "id" and the functional column name is "gos".
119 127
120 - **Functional/taxonomic**: takes the same input as the functional mode. User can choose which GO namespace(s) to include. 128 - **Functional/taxonomic**: takes the same input as the functional mode. User can choose which GO namespace(s) to include.
121 129
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. 130 - 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.
128 131
129 ]]></help> 132 ]]></help>
130 133
131 <citations> 134 <citations>
132 <citation type="bibtex"> 135 <citation type="bibtex">