Mercurial > repos > tomnl > mzml2isa
diff mzml2isa.xml @ 2:26b1c61f7b4c draft
planemo upload for repository https://github.com/ISA-tools/mzml2isa commit d9868158b4c63574b9d0d72461b9aa4443e612ba-dirty
| author | computational-metabolomics |
|---|---|
| date | Wed, 07 Dec 2022 14:54:23 +0000 |
| parents | |
| children | 7f958f54468e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mzml2isa.xml Wed Dec 07 14:54:23 2022 +0000 @@ -0,0 +1,159 @@ +<tool id="mzml2isa" name="mzml2isa" version="1.1.1+galaxy0"> + <description>Parser to get meta information from mzML files and create an ISA-Tab structure</description> + + <requirements> + <requirement type="package" version="1.1.1">mzml2isa</requirement> + </requirements> + + <stdio> + <exit_code range="1:" /> + </stdio> + + <command detect_errors="exit_code"> + <![CDATA[ + + + #if $input.format == "data_collection" + mkdir "temp" + && + cd "temp" + && + #for $fn in $input.source + #if str( $fn ).endswith(".dat") + ln -s '$fn' '$fn.name' + && + #end if + #end for + cd .. + && + #end if + + #if $metadata + ln -s '$metadata' 'metadata.json' && + #end if + + mzml2isa -s $name_of_study -o . -i + + #if $input.format == "zip_file" + "zip://$input.source" + #else if $input.format == "tar_file" + "tar://$input.source" + #else if $input.format == "data_collection" + "temp" + #end if + + #if $metadata + -m "metadata.json" + #end if + + && zip isa.zip i_* a_* s_* && mv isa.zip "$ISA_zip"; + ]]> + </command> + + <inputs> + <param name="name_of_study" type="text" label="Name study" help="This should not contain any spaces as the name will be used a prefix for ISA-tab file names" /> + <conditional name="input"> + <param name="format" type="select" label="Choose the source for the dataset (zip, tar or data collection)" > + <option value="zip_file" selected="true">Zip file from your History containing a folder of *.mzML files</option> + <option value="tar_file">TAR file from your history containing a folder of *.mzML files</option> + <option value="data_collection">Data collection (*.mzML files)</option> + </param> + <when value="zip_file"> + <param name="source" type="data" format="zip" label="Zip file from your History containing *.mzml files"> + </param> + </when> + <when value="tar_file"> + <param name="source" type="data" format="tar" label="TAR file from your History containing *.mzml files"/> + </when> + <when value="data_collection"> + <param name="source" type="data_collection" format="mzml" label="Data collection of *.mzml" > + </param> + </when> + </conditional> + + <param optional="true" format="json" name="metadata" type="data" label="Additional user Metadata in json" help="A user can add additional metadata directory through a json file"/> + + </inputs> + <outputs> + + <data name="ISA_zip" format="zip" label="ISA Zip file"/> + <collection type="list" label="Assay files" name="a_files"> + <discover_datasets pattern="(?P<designation>a_.+)\.txt" directory="." format="tabular"/> + </collection> + <collection type="list" label="Study files" name="s_files"> + <discover_datasets pattern="(?P<designation>s_.+)\.txt" directory="." format="tabular"/> + </collection> + <data name="i_file" format="tabular" label="Investigation file" from_work_dir="i_Investigation.txt"/> + </outputs> + + <tests> + <test> + <param name="name_of_study" value="test" /> + <param name="input|format" value="zip_file" /> + <param name="input|source" value="metabolomics_study.zip" ftype="zip" /> + <output name="i_file" value="i_Investigation.txt" /> + <output_collection name="a_files" type="list" count="1"> + <element name="a_test_metabolite_profiling_mass_spectrometry"> + <assert_contents> + <has_n_columns n="80" /> + </assert_contents> + </element> + </output_collection> + <output_collection name="s_files" type="list" count="1"> + <element name="s_test"> + <assert_contents> + <has_n_columns n="12" /> + </assert_contents> + </element> + </output_collection> + </test> + <test> + <param name="name_of_study" value="test" /> + <param name="input|format" value="data_collection" /> + <param name="input|source" > + <collection type="list"> + <element name="1_samp" value="1_samp.mzML" /> + <element name="2_samp" value="2_samp.mzML" /> + <element name="3_samp" value="3_samp.mzML" /> + <element name="4_samp" value="4_samp.mzML" /> + <element name="5_samp" value="5_samp.mzML" /> + <element name="6_samp" value="6_samp.mzML" /> + </collection> + </param > + <output name="i_file" value="i_Investigation.txt" /> + <output_collection name="a_files" type="list" count="1"> + <element name="a_test_metabolite_profiling_mass_spectrometry"> + <assert_contents> + <has_n_columns n="80" /> + </assert_contents> + </element> + </output_collection> + <output_collection name="s_files" type="list" count="1"> + <element name="s_test"> + <assert_contents> + <has_n_columns n="12" /> + </assert_contents> + </element> + </output_collection> + </test> + </tests> + <help><![CDATA[ +**Overview** + A program to automatically generate ISA-Tab metadata files from metabolomics raw XML (mzML and imzML) data files. + + Additional meta-information not found within the mzML file can be added through a JSON file. + However, it is recommended that the mzML2ISA tool is used to create a semi-completed ISA-Tab file structure + that is further annotated using ISAcreator https://github.com/ISA-tools/ISAcreator or via the ISA-API. + +.. image::mzml2isa.png + ]]></help> + <citations> + <citation type="doi">10.1002/0471250953.bi1413s53</citation> + <citation type="doi">10.1007/s11306-015-0879-3</citation> + <citation type="doi">10.1038/ng.1054</citation> + </citations> +</tool> + + + +