Mercurial > repos > galaxyp > peptideshaker
diff macros.xml @ 33:bce45e9e6d70 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
| author | galaxyp |
|---|---|
| date | Mon, 06 Feb 2017 21:53:07 -0500 |
| parents | ff592231f118 |
| children | 0ebf3d3e4c90 |
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--- a/macros.xml Wed Jan 25 15:37:43 2017 -0500 +++ b/macros.xml Mon Feb 06 21:53:07 2017 -0500 @@ -8,109 +8,159 @@ </stdio> </xml> <token name="@GENERAL_PARAMETERS@"> - -frag_tol "${fragment_tol}" + -frag_tol "${precursor_options.fragment_tol}" ### -frag_ppm - -prec_tol "${precursor_ion_tol}" - -prec_ppm "${precursor_ion_tol_units}" - ### -digestion - ### multiple enzymes? - -enzyme "${enzyme}" - ### -specificity - ### value per enzyme - -mc $missed_cleavages - #set $fixed_mods_str = $fixed_modifications or '' - #set $variable_mods_str = $variable_modifications or '' + -prec_tol "${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 + -fi $precursor_options.forward_ion + -ri $precursor_options.reverse_ion + -min_isotope ${precursor_options.min_isotope} + -max_isotope ${precursor_options.max_isotope} + #if $protein_digest_options.digestion.cleavage == 'default': + ## -enzyme "Trysin" + -mc $protein_digest_options.digestion.missed_cleavages + #elif $protein_digest_options.digestion.cleavage == '0' and len($protein_digest_options.digestion.digests) > 0: + #set $enzymes = [] + #set $missed_cleavages = [] + ## #set $specificities = [] + #for $i, $digest in enumerate($protein_digest_options.digestion.digests): + #silent $enzymes.append(str($digest.enzyme)) + #silent $missed_cleavages.append(str($digest.missed_cleavages)) + ## #silent $specificities.append(str($digest.specificity)) + #end for + -enzyme "#echo ','.join($enzymes)#" + -mc "#echo ','.join($missed_cleavages)#" + ## -specificity "#echo ','.join($specificities)#" + #else: + -digestion $protein_digest_options.digestion.cleavage + #end if + + #set $fixed_mods_str = $protein_modification_options.fixed_modifications or '' + #set $variable_mods_str = $protein_modification_options.variable_modifications or '' #if $fixed_mods_str -fixed_mods "$fixed_mods_str" #end if #if $variable_mods_str -variable_mods "$variable_mods_str" #end if - -min_charge $min_charge - -max_charge $max_charge - -fi $forward_ion - -ri $reverse_ion - -min_isotope ${min_isotope} - -max_isotope ${max_isotope} </token> <token name="@SEARCHGUI_MAJOR_VERSION@">3</token> - <token name="@SEARCHGUI_VERSION@">3.1.4</token> + <token name="@SEARCHGUI_VERSION@">3.2.5</token> <xml name="general_options"> - <param name="precursor_ion_tol_units" type="select" label="Precursor Ion 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="precursor_ion_tol" type="float" value="10" label="Percursor 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)" - help="Provide error value for fragment ions, based on instrument used"/> - <param name="enzyme" type="select" label="Enzyme" - help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> - <option value="Trypsin">Trypsin</option> - <option value="Arg-C">Arg-C</option> - <option value="CNBr">CNBr</option> - <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> - <option value="Formic Acid">Formic Acid</option> - <option value="Lys-C">Lys-C</option> - <option value="Lys-C, no P rule">Lys-C, no P rule</option> - <option value="Pepsin A">Pepsin A</option> - <option value="Trypsin + CNBr">Trypsin + CNBr</option> - <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> - <option value="Trypsin, no P rule">Trypsin, no P rule</option> - <option value="Whole Protein">Whole Protein</option> - <option value="Asp-N">Asp-N</option> - <option value="Glu-C">Glu-C</option> - <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> - <option value="Top-Down">Top-Down</option> - <option value="Semi-Tryptic">Semi-Tryptic</option> - <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! --> - <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option> - <option value="Asp-N (DE)">Asp-N (DE)</option> - <option value="Glu-C (DE)">Glu-C (DE)</option> - <option value="Lys-N (K)">Lys-N (K)</option> - <option value="Thermolysin, no P rule">Thermolysin, no P rule</option> - <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> - <option value="Semi-Glu-C">Semi-Glu-C</option> - <option value="LysargiNase">LysargiNase</option> - <option value="Semi-LysargiNase">Semi-LysargiNase</option> - <option value="Trypsin + Glu-C">Trypsin + Glu-C</option> - <option value="Semi-Arg-C">Semi-Arg-C</option> - <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option> - <option value="Arg-N">Arg-N</option> - <option value="Semi-Arg-N">Semi-Arg-N</option> - </param> - <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" - help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> - <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" - help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> - <options from_file="searchgui_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="0" /> - </options> - </param> - <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" - help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> - <options from_file="searchgui_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="0" /> - </options> - </param> - <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"/> - <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment"> - <option value="a">a</option> - <option value="b" selected="true">b</option> - <option value="c">c</option> - </param> - <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment"> - <option value="x">x</option> - <option value="y" selected="true">y</option> - <option value="z">z</option> - </param> - <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" /> - <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" /> + + <section name="protein_digest_options" expanded="false" title="Protein Digestion Options"> + <conditional name="digestion"> + <param name="cleavage" type="select" label="Digestion"> + <option value="default" selected="true">Trypsin</option> + <option value="0">Select Enzymes</option> + <option value="1">Unspecific Cleavage</option> + <option value="2">Whole Protein</option> + </param> + <when value="default"> + <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" + help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> + </when> + <when value="0"> + <repeat name="digests" min="1" title="Enzymes"> + <param name="enzyme" type="select" label="Enzyme" + help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> + <option value="Trypsin">Trypsin</option> + <option value="Arg-C">Arg-C</option> + <option value="CNBr">CNBr</option> + <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> + <option value="Formic Acid">Formic Acid</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-C, no P rule">Lys-C, no P rule</option> + <option value="Pepsin A">Pepsin A</option> + <option value="Trypsin + CNBr">Trypsin + CNBr</option> + <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> + <option value="Trypsin, no P rule">Trypsin, no P rule</option> + <option value="Whole Protein">Whole Protein</option> + <option value="Asp-N">Asp-N</option> + <option value="Glu-C">Glu-C</option> + <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> + <option value="Top-Down">Top-Down</option> + <option value="Semi-Tryptic">Semi-Tryptic</option> + <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! --> + <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option> + <option value="Asp-N (DE)">Asp-N (DE)</option> + <option value="Glu-C (DE)">Glu-C (DE)</option> + <option value="Lys-N (K)">Lys-N (K)</option> + <option value="Thermolysin, no P rule">Thermolysin, no P rule</option> + <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> + <option value="Semi-Glu-C">Semi-Glu-C</option> + <option value="LysargiNase">LysargiNase</option> + <option value="Semi-LysargiNase">Semi-LysargiNase</option> + <option value="Trypsin + Glu-C">Trypsin + Glu-C</option> + <option value="Semi-Arg-C">Semi-Arg-C</option> + <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option> + <option value="Arg-N">Arg-N</option> + <option value="Semi-Arg-N">Semi-Arg-N</option> + </param> + <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" + help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> + <!-- + <param name="specificity" type="select" label="Specificity"> + <option value="0" selected="true">Specific at both termini</option> + <option value="1">Semi-Specific - one terminus</option> + <option value="2">Specific at the N-terminus only</option> + <option value="3">Specific at the C-terminus only</option> + </param> + --> + </repeat> + </when> + <when value="1"/> + <when value="2"/> + </conditional> + </section> + + <section name="precursor_options" expanded="false" title="Precursor Options"> + <param name="precursor_ion_tol_units" type="select" label="Precursor Ion 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="precursor_ion_tol" type="float" value="10" label="Percursor 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)" + 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"/> + <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment"> + <option value="a">a</option> + <option value="b" selected="true">b</option> + <option value="c">c</option> + </param> + <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment"> + <option value="x">x</option> + <option value="y" selected="true">y</option> + <option value="z">z</option> + </param> + <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" /> + <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" /> + </section> + + <section name="protein_modification_options" expanded="false" title="Protein Modification Options"> + <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" + help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> + <options from_file="searchgui_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" + help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> + <options from_file="searchgui_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + </section> + </xml> <xml name="citations">