ProteoRE tool 'get_unique_peptide_srm_method' #591
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yvandenb
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combesf
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@bgruening we are all set on our side for this PR. |
| --features='$protein_features' | ||
| --output='$output' | ||
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| #if "SRM_atlas" in str($srm_file).split("/") |
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you could do a string search with if "/SRM_atlas/" in $srm_file I guess
tools/proteore_get_unique_peptide_srm_method/proteore_get_unique_peptide_SRM-MRM_method.xml
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| <tests> | ||
| <test> | ||
| <conditional name="input" > | ||
| <param name="ids" value="file"/> |
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can we have a second test for the text input?
tools/proteore_get_unique_peptide_srm_method/proteore_get_unique_peptide_SRM-MRM_method.xml
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tools/proteore_get_unique_peptide_srm_method/proteore_get_unique_peptide_SRM-MRM_method.xml
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…ake compressed ref file as input
Thanks Björn, this file does not change over time. I gziped it and lade modifications in the wrapper (loc file) and Python script to take gzip csv file as input. |
| <param name="header" value="true" /> | ||
| <param name="ncol" value="c1"/> | ||
| </conditional> | ||
| <param name="srm_file" value="tool-data/Human_SRM_atlas_2016-04.csv.gz" /> |
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This is wired. I would assume the value needs to be the key/id from the datatable. E.g. 9979839599?
| </conditional> | ||
| <param name="srm_file" type="select" label="Release" > | ||
| <options from_data_table="proteore_human_srm_atlas"> | ||
| <filter type="sort_by" column="0"/> |
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Do we realy want to sort for the ID column? E.g. 9979839599 ... what is this number? Should we sort for column 1?
Another ProteoRE tool ; this one is 'get_unique_peptide_srm_method'
Thanks for the review !
Still 16 tools to come ...