Mercurial > repos > workflow4metabolomics > kmd_hmdb_data_plot
diff macro.xml @ 0:59c8bad5f6bc draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
author | workflow4metabolomics |
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date | Tue, 29 Aug 2023 09:45:16 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macro.xml Tue Aug 29 09:45:16 2023 +0000 @@ -0,0 +1,170 @@ +<macros> + + <token name="@DEFAULT_MZ@">303.05</token> + <token name="@DEFAULT_TOLERENCE@">10.0</token> + <token name="@DEFAULT_ADDUCT@">M+H</token> + <token name="@DEFAULT_DATABASE@">HMDB</token> + + <xml name="get_data_inputs"> + <param argument="--mz-ratio" type="float" min="1" max="1000" value="@DEFAULT_MZ@" + help=" + The database will give us all compounds with m/z = + m/zRatio±MassTolerance and we will plot those + compounds. + Choose the mass tolerance according to this information. + " + label="M/z Ratio" + /> + + <param argument="--mass-tolerance" type="float" value="@DEFAULT_TOLERENCE@" + help=" + The database will give us all compounds with m/z = + m/zRatio±MassTolerance and we will plot those + compounds. + Choose the mass tolerance according to this information. + " + label="Mass Tolerance" + /> + + <param argument="--database" type="select" value="@DEFAULT_DATABASE@" + label="Which database to interrogate" + help=" + Those databases are sub-databases of KMD-HMDB Metabolites + and contains compounds with their KMD. + " + > + <option selected="true" value="hmdb">HMDB</option> + <option value="farid">KMD Metabolites</option> + </param> + + <param argument="--adducts" type="select" multiple="true" + label="Adducts" + help="Which adducts to retrieve" + > + <option selected="true" value="M+H">M+H</option> + <option value="M+2H">M+2H</option> + <option value="M+H+NH4">M+H+NH4</option> + <option value="M+H+Na">M+H+Na</option> + <option value="M+H+K">M+H+K</option> + <option value="M+ACN+2H">M+ACN+2H</option> + <option value="M+2Na">M+2Na</option> + <option value="M+H-2H2O">M+H-2H2O</option> + <option value="M+H-H2O">M+H-H2O</option> + <option value="M+NH4">M+NH4</option> + <option value="M+Na">M+Na</option> + <option value="M+CH3OH+H">M+CH3OH+H</option> + <option value="M+K">M+K</option> + <option value="M+ACN+H">M+ACN+H</option> + <option value="M+2Na-H">M+2Na-H</option> + <option value="M+IsoProp+H">M+IsoProp+H</option> + <option value="M+ACN+Na">M+ACN+Na</option> + <option value="M+2K+H">M+2K+H</option> + <option value="M+DMSO+H">M+DMSO+H</option> + <option value="M+2ACN+H">M+2ACN+H</option> + <option value="2M+H">2M+H</option> + <option value="2M+NH4">2M+NH4</option> + <option value="2M+Na">2M+Na</option> + <option value="2M+K">2M+K</option> + <option value="M-H">M-H</option> + <option value="M-2H">M-2H</option> + <option value="M-H2O-H">M-H2O-H</option> + <option value="M+Cl">M+Cl</option> + <option value="M+FA-H">M+FA-H</option> + <option value="M+Hac-H">M+Hac-H</option> + <option value="M-H+HCOONa">M-H+HCOONa</option> + <option value="M+Br">M+Br</option> + <option value="M+TFA-H">M+TFA-H</option> + <option value="2M-H">2M-H</option> + <option value="2M+FA-H">2M+FA-H</option> + <option value="2M+Hac-H">2M+Hac-H</option> + </param> + </xml> + + <xml name="produce_plot_inputs"> + <param name="tsv_input" type="data" format="tsv" + help="Tabular file to use to produce the plot." + label="A Tabular Input File" + /> + <param + name="annotation_columns" + type="data_column" + data_ref="tsv_input" + use_header_names="true" + multiple="true" + optional="true" + help="Select columns to show when a point of the graph is hovered" + label="Annotation columns" + /> + <param + name="x_columns" + type="data_column" + data_ref="tsv_input" + use_header_names="true" + optional="true" + multiple="true" + help=" + Select one or multiple column to use as X values + to generate the graph. See the help section to better + understand the usage of multiple values + " + label="X Axis" + /> + <param + name="y_columns" + type="data_column" + data_ref="tsv_input" + use_header_names="true" + optional="true" + multiple="true" + help=" + Select one or multiple column to use as Y values + to generate the graph. See the help section to better + understand the usage of multiple values + " + label="Y Axis" + /> + </xml> + + <xml name="not_get_data"> + <param name="mz_ratio" value="unknown" type="hidden" /> + <param name="mass_tolerance" value="unknown" type="hidden" /> + <param name="database" value="unknown" type="hidden" /> + <param name="adducts" value="unknown" type="hidden" /> + </xml> + + <xml name="not_produce_plot"> + <param name="tsv_input" value="unknown" type="hidden" /> + <param name="annotation_columns" type="hidden" /> + <param name="x_columns" type="hidden" /> + <param name="y_columns" type="hidden" /> + </xml> + + <xml name="get_data_outputs"> + <data name="output_path" format="tsv" + label="tsv - ${tool.name} on ${what.mz_ratio}±${what.mass_tolerance} - ${what.database}" + > + <filter>"get_data" in str(what['to_do'])</filter> + <actions> + <action name="column_names" type="metadata" + default="database,metabolite_name,chemical_formula,hmdb_id,inchikey,compound_id,adduct,kendricks_mass,kendricks_mass_defect,monisotopic_molecular_weight,nominal_mass,polarity,annotation_id" + /> + </actions> + </data> + </xml> + + <xml name="produce_plot_outputs"> + <data name="output" format="html" + label="html - ${tool.name} on ${ + ' - ' + + str($what['mz_ratio']) + + '±' + str($what['mass_tolerance']) + + ' - ' + str($what['database']) + if 'get_data' in str($what['to_do']) + else ''' ' ''' + $what.csv_input.name + ''' ' ''' + }" + > + <filter>"produce_plot" in str(what['to_do'])</filter> + </data> + </xml> + +</macros> \ No newline at end of file