Mercurial > repos > galaxyp > mt2mq
comparison MT2MQ.xml @ 2:9c8e7137d331 draft
"planemo upload commit 59afcdaf7afdf574c475f0faae73127f0e563328"
| author | galaxyp |
|---|---|
| date | Wed, 12 Aug 2020 17:36:53 -0400 |
| parents | 6bee94458567 |
| children |
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| 1:e50ec3a9a3f9 | 2:9c8e7137d331 |
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| 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"> |