Mercurial > repos > iuc > humann_rename_table
diff humann_rename_table.xml @ 0:d24841f5c3d2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
| author | iuc |
|---|---|
| date | Wed, 12 May 2021 09:02:43 +0000 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/humann_rename_table.xml Wed May 12 09:02:43 2021 +0000 @@ -0,0 +1,117 @@ +<tool id="humann_rename_table" name="Rename features" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>of a HUMAnN generated table</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="edam_ontology"/> + <expand macro="requirements"/> + <expand macro="version"/> + <command detect_errors="exit_code"><![CDATA[ +humann_rename_table + --input '$input' + -o '$output' +#if $renaming.type == 'standard' + --names '$renaming.names' +#else if $renaming.type == 'advanced' + --custom '$renaming.names.fields.path' +#else + --custom '$renaming.custom' +#end if + $simplify + ]]></command> + <inputs> + <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/> + <conditional name="renaming"> + <param name="type" type="select" label="Type of feature renaming"> + <option value="standard">Basic feature renaming</option> + <option value="advanced">Advanced feature renaming</option> + <option value="custom">Custom feature renaming</option> + </param> + <when value="standard"> + <param argument="--names" type="select" label="Features to be renamed" help="More features can be renamed with advanced mode"> + <option value="metacyc-rxn" selected="true">MetaCyc reactions</option> + <option value="metacyc-pwy">MetaCyc pathways</option> + <option value="infogo1000">InfoGO1000</option> + <option value="kegg-module">KEGG Module</option> + <option value="ec">Enzyme commision (EC)</option> + <option value="go">Gene Ontology (GO)</option> + <option value="pfam">PFAM</option> + <option value="eggnog">eggNOG</option> + <option value="kegg-pathway">KEGG Pathway</option> + <option value="kegg-orthology">KEGG Orthology</option> + </param> + </when> + <when value="advanced"> + <param name="names" type="select" label="Features to be renamed"> + <options from_data_table="humann_utility_mapping"> + <validator message="No utility mapping is available" type="no_options" /> + <filter type="regexp" column="0" value=".*name" keep="true" /> + </options> + </param> + </when> + <when value="custom"> + <param argument="--custom" type="data" format="tsv,tabular" label="Mapping file" help="The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new value"/> + </when> + </conditional> + <param argument="--simplify" type="boolean" truevalue="--simplify" falsevalue="" checked="false" label="Remove non-alphanumeric characters from names?"/> + </inputs> + <outputs> + <data format="tabular" name="output"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input" value="regrouped_gene_families_to_infogo1000.tsv"/> + <conditional name="renaming"> + <param name="type" value="standard"/> + <param name="names" value="infogo1000" /> + </conditional> + <param name="simplify" value=""/> + <output name="output" ftype="tabular"> + <assert_contents> + <has_text text="GO:0000015: [CC] phosphopyruvate hydratase complex" /> + <has_text text="GO:0000287: [MF] magnesium ion binding" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input" value="demo_genefamilies.tsv"/> + <conditional name="renaming"> + <param name="type" value="advanced"/> + <param name="names" value="utility_mapping-full-map_uniref90_name-3.0.0-29042021"/> + </conditional> + <param name="simplify" value=""/> + <output name="output" ftype="tabular"> + <assert_contents> + <has_text text="UniRef90_A6L2T0: NO_NAME|g__Bacteroides.s__Bacteroides_vulgatus" /> + <has_text text="UniRef90_U5FT06: Hexosyltransferase|unclassified" /> + <has_text text="UniRef90_Q8GT21: Benzyl alcohol O-benzoyltransferase|unclassified" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input" value="demo_genefamilies.tsv"/> + <conditional name="renaming"> + <param name="type" value="custom"/> + <param name="custom" value="test-db/utility_mapping/map_uniref90_name.txt" /> + </conditional> + <param name="simplify" value=""/> + <output name="output" ftype="tabular"> + <assert_contents> + <has_text text="UniRef90_A6L2T0: NO_NAME|g__Bacteroides.s__Bacteroides_vulgatus" /> + <has_text text="UniRef90_U5FT06: Hexosyltransferase|unclassified" /> + <has_text text="UniRef90_Q8GT21: Benzyl alcohol O-benzoyltransferase|unclassified" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +@HELP_HEADER@ + +By default, HUMAnN outputs do not attach names (glosses) to individual feature IDs to keep file sizes down. +This tool is used to attach those names. + +The most common use for this tool is attaching gene names to UniRef90/UniRef50 features in the default gene family output files. +Features without names (common for many UniRef90/50 families) are assigned the default name: NO_NAME. + ]]></help> + <expand macro="citations"/> +</tool>