Mercurial > repos > galaxyp > peptideshaker
changeset 30:49f8c1b05425 draft
Uploaded
| author | galaxyp |
|---|---|
| date | Wed, 10 May 2017 09:22:58 -0400 |
| parents | 84dcffe17895 |
| children | ed6c90ef5b82 |
| files | peptide_shaker.xml |
| diffstat | 1 files changed, 9 insertions(+), 1 deletions(-) [+] |
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--- a/peptide_shaker.xml Fri Apr 21 15:14:41 2017 -0400 +++ b/peptide_shaker.xml Wed May 10 09:22:58 2017 -0400 @@ -51,8 +51,9 @@ -ptm_threshold "${processing_options.ptm_score.ptm_threshold}" #end if #end if + -ptm_alignment "${processing_options.ptm_alignment}" + -ptm_sequence_matching_type "${processing_options.ptm_sequence_matching_type}" -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" - -ptm_alignment "${processing_options.ptm_alignment}" #end if ##Optional filtering parameters: @@ -205,6 +206,7 @@ <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization"> <option value="0" selected="True">A-score</option> <option value="1">PhosphoRS</option> + <option value="2">None</option> </param> <when value="0" /> <when value="1"> @@ -212,7 +214,13 @@ <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float" help="Automatic mode will be used if not set" /> </when> + <when value="2" /> </conditional> + <param name="ptm_sequence_matching_type" type="select" label="The PTM to peptide sequence matching type"> + <option value="0">Character Sequence</option> + <option value="1" selected="true">Amino Acids</option> + <option value="2">Indistinguishable Amino Acids</option> + </param> <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/> <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> </when>