Mercurial > repos > galaxyp > peptideshaker
changeset 41:3634c90301af draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit dea56622eb32b82c87dc87567dc89db3a787033d
| author | galaxyp |
|---|---|
| date | Sat, 28 Oct 2017 04:16:50 -0400 |
| parents | a72c48001f7c |
| children | 9e20c34298e3 |
| files | macros.xml searchgui.xml |
| diffstat | 2 files changed, 13 insertions(+), 8 deletions(-) [+] |
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--- a/macros.xml Wed Sep 27 08:59:54 2017 -0400 +++ b/macros.xml Sat Oct 28 04:16:50 2017 -0400 @@ -8,10 +8,10 @@ </stdio> </xml> <token name="@GENERAL_PARAMETERS@"> - -frag_tol "${precursor_options.fragment_tol}" - ### -frag_ppm - -prec_tol "${precursor_options.precursor_ion_tol}" - -prec_ppm "${precursor_options.precursor_ion_tol_units}" + -frag_tol '${precursor_options.fragment_tol}' + -frag_ppm '${precursor_options.fragment_tol_units}' + -prec_tol '${precursor_options.precursor_ion_tol}' + -prec_ppm '${precursor_options.precursor_ion_tol_units}' -min_charge $precursor_options.min_charge -max_charge $precursor_options.max_charge @@ -126,7 +126,12 @@ </param> <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance" help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/> - <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" + <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units" + help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> + <option value="1">Parts per million (ppm)</option> + <option value="2">Daltons</option> + </param> + <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance" help="Provide error value for fragment ions, based on instrument used"/> <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/> <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
--- a/searchgui.xml Wed Sep 27 08:59:54 2017 -0400 +++ b/searchgui.xml Sat Oct 28 04:16:50 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@"> +<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1"> <description> Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> @@ -537,7 +537,7 @@ label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" /> <param name="xtandem_output_spectra" help="Controls output of spectrum information" label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" /> - <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="text" help="Path to a spectrum data file for use by skyline." --> + <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" help="Path to a spectrum data file for use by skyline." --> <conditional name="xtandem_refine"><!-- -xtandem_refine --> <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> @@ -676,7 +676,7 @@ label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> <param name="msgf_max_pep_length" type="integer" value="30" label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> - <param name="msgf_termini" type="select" format="text" + <param name="msgf_termini" type="select" format="txt" label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2"> <option value="0">0 (ie non-specific cleavage)</option> <option value="1">1 (ie semi-tryptic cleavage)</option>