Mercurial > repos > tomnl > mzml2isa
changeset 3:7f958f54468e draft default tip
planemo upload for repository https://github.com/ISA-tools/mzml2isa commit 16f55e636c7d9c2be748cb8212184164e57e4b95
| author | computational-metabolomics |
|---|---|
| date | Wed, 07 Dec 2022 17:31:40 +0000 |
| parents | 26b1c61f7b4c |
| children | |
| files | mzml2isa.xml |
| diffstat | 1 files changed, 11 insertions(+), 23 deletions(-) [+] |
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--- a/mzml2isa.xml Wed Dec 07 14:54:23 2022 +0000 +++ b/mzml2isa.xml Wed Dec 07 17:31:40 2022 +0000 @@ -1,18 +1,15 @@ -<tool id="mzml2isa" name="mzml2isa" version="1.1.1+galaxy0"> +<tool id="mzml2isa" name="mzml2isa" version="1.1.1+galaxy1"> <description>Parser to get meta information from mzML files and create an ISA-Tab structure</description> - <requirements> + <requirement type="package">zip</requirement> <requirement type="package" version="1.1.1">mzml2isa</requirement> </requirements> - <stdio> <exit_code range="1:" /> </stdio> - <command detect_errors="exit_code"> <![CDATA[ - #if $input.format == "data_collection" mkdir "temp" && @@ -49,7 +46,6 @@ && zip isa.zip i_* a_* s_* && mv isa.zip "$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"> @@ -70,22 +66,18 @@ </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"/> + <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" /> @@ -152,8 +144,4 @@ <citation type="doi">10.1007/s11306-015-0879-3</citation> <citation type="doi">10.1038/ng.1054</citation> </citations> -</tool> - - - - +</tool> \ No newline at end of file