Mercurial > repos > recetox > recetox_xmsannotator_advanced
diff macros.xml @ 0:cfd2e19f00a9 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
| author | recetox |
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| date | Mon, 26 Jun 2023 13:55:56 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jun 26 13:55:56 2023 +0000 @@ -0,0 +1,144 @@ +<macros> +<token name="@TOOL_VERSION@">0.10.0</token> + +<xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">r-recetox-xmsannotator</requirement> + </requirements> +</xml> + +<xml name="creator"> + <creator> + <person + givenName="Jiří" + familyName="Novotný" + url="https://github.com/xtracko" + identifier="0000-0001-5449-3523" /> + <person + givenName="Martin" + familyName="Čech" + url="https://github.com/martenson" + identifier="0000-0002-9318-1781" /> + <person + givenName="Matej" + familyName="Troják" + url="https://github.com/xtrojak" + identifier="0000-0003-0841-2707" /> + <organization + url="https://www.recetox.muni.cz/" + email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" + name="RECETOX MUNI" /> + </creator> +</xml> + +<xml name="inputs"> + <param name="metadata_table" type="data" format="parquet,csv"> + <label>Metadata table</label> + <help><![CDATA[ + Peak metadata table*. + ]]></help> + </param> + <param name="intensity_table" type="data" format="parquet,csv"> + <label>Intensity table</label> + <help><![CDATA[ + Table with intensities** for features (rows) across samples (columns). + ]]></help> + </param> + <param name="compound_table" type="data" format="parquet,csv"> + <label>Compound database</label> + <help><![CDATA[ + Database of compounds according to which the annotation is performed. + The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>. + ]]></help> + </param> + <param name="adduct_table" type="data" format="parquet,csv" optional="true"> + <label>Adduct database</label> + <help><![CDATA[ + Database of adduct which is combined with the database of compound to form a molecule-adduct pairs. + The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>. + ]]></help> + </param> + <param name="adduct_weights" type="data" format="parquet,csv" optional="true"> + <label>Adduct weights</label> + <help> + A weight-by-adduct table. + </help> + </param> +</xml> + +<xml name="outputs"> + <data name="output_file" format="parquet"> + <change_format> + <when input="metadata_table.ext" value="csv" format="csv" /> + </change_format> + </data> +</xml> + +<xml name="tolerance"> + <param name="mass_tolerance_ppm" type="integer" min="0" value="5"> + <label>Mass tolerance [ppm]</label> + <help>Mass tolerance in ppm for database matching.</help> + </param> + <yield/> +</xml> + +<token name="@HELP@"> +Description +=========== + +Annotate the peak intensity table (e.g. from an apLCMS run) with compounds from the compounds database +using advanced methods. + +The annotation process generates all possible compound-adduct pairs and matches those pairs to the measured +peaks. A compound-adduct pair is pronounced as a match to a certain peak when the difference of their masses are +withing some tolerance. + +Then, a score and a confidence level is assigned to each match based on peak correlation +clustering, metabolite pathway associations, adducts expectations, and isotope conformations. + +Input tables description +------------------------ + +(*) Metadata table +~~~~~~~~~~~~~~~~~~ + +The output from recetox-aplcms tool. +The `npeaks` column denotes the number of peaks which have been grouped into this feature. +The columns with the sample names indicate whether this feature is present in the sample. +Only id, mz, and rt columns are required to be present. + ++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+ +| id | mz | mzmin | mzmax | rt | rtmin | rtmax | npeaks | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq | ++=======+==============+==============+===============+================+===============+===============+===========+========================+========================+========================+ +| 1 | 70.03707021 | 70.037066 | 70.0370750 | 294.1038014 | 294.0634942 | 294.149985 | 3 | 1 | 1 | 1 | ++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+ +| 2 | 70.06505677 | 70.065045 | 70.0650676 | 141.9560055 | 140.5762528 | 143.335758 | 2 | 1 | 0 | 1 | ++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+ +| 57 | 78.04643252 | 78.046429 | 78.0464325 | 294.0063397 | 293.9406777 | 294.072001 | 2 | 1 | 1 | 0 | ++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+ +| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ++-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+ + +(**) Intensity table +~~~~~~~~~~~~~~~~~~~~ + +The output from recetox-aplcms tool. +This table contains the peak area for aligned features in all samples. + ++-------+------------------------+------------------------+------------------------+ +| id | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq | ++=======+========================+========================+========================+ +| 1 | 13187487.20482895 | 7957395.699119729 | 11700594.397257797 | ++-------+------------------------+------------------------+------------------------+ +| 2 | 2075168.6398983458 | 0 | 2574362.159289044 | ++-------+------------------------+------------------------+------------------------+ +| 57 | 2934524.4406785755 | 1333044.5065971944 | 0 | ++-------+------------------------+------------------------+------------------------+ +| ... | ... | ... | ... | ++-------+------------------------+------------------------+------------------------+ +</token> + +<xml name="citations"> + <citation type="doi">10.1021/acs.analchem.6b01214</citation> +</xml> +</macros>