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comparison macros.xml @ 32:ff592231f118 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
author galaxyp
date Wed, 25 Jan 2017 15:37:43 -0500
parents ad60446b1e93
children bce45e9e6d70
comparison
equal deleted inserted replaced
31:f3f67aa3123b 32:ff592231f118
14 -prec_ppm "${precursor_ion_tol_units}" 14 -prec_ppm "${precursor_ion_tol_units}"
15 ### -digestion 15 ### -digestion
16 ### multiple enzymes? 16 ### multiple enzymes?
17 -enzyme "${enzyme}" 17 -enzyme "${enzyme}"
18 ### -specificity 18 ### -specificity
19 ### value per enzyme
20 -mc $missed_cleavages
19 #set $fixed_mods_str = $fixed_modifications or '' 21 #set $fixed_mods_str = $fixed_modifications or ''
20 #set $variable_mods_str = $variable_modifications or '' 22 #set $variable_mods_str = $variable_modifications or ''
21 #if $fixed_mods_str 23 #if $fixed_mods_str
22 -fixed_mods "$fixed_mods_str" 24 -fixed_mods "$fixed_mods_str"
23 #end if 25 #end if
24 #if $variable_mods_str 26 #if $variable_mods_str
25 -variable_mods "$variable_mods_str" 27 -variable_mods "$variable_mods_str"
26 #end if 28 #end if
27 -min_charge $min_charge 29 -min_charge $min_charge
28 -max_charge $max_charge 30 -max_charge $max_charge
29 ### value per enzyme
30 -mc $missed_cleavages
31 -fi $forward_ion 31 -fi $forward_ion
32 -ri $reverse_ion 32 -ri $reverse_ion
33 -min_isotope ${min_isotope}
34 -max_isotope ${max_isotope}
35
33 </token> 36 </token>
34 <token name="@SEARCHGUI_MAJOR_VERSION@">3</token> 37 <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
35 <token name="@SEARCHGUI_VERSION@">3.1.4</token> 38 <token name="@SEARCHGUI_VERSION@">3.1.4</token>
36 <xml name="general_options"> 39 <xml name="general_options">
37 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" 40 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
104 <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"> 107 <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">
105 <option value="x">x</option> 108 <option value="x">x</option>
106 <option value="y" selected="true">y</option> 109 <option value="y" selected="true">y</option>
107 <option value="z">z</option> 110 <option value="z">z</option>
108 </param> 111 </param>
112 <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
113 <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
109 </xml> 114 </xml>
110 115
111 <xml name="citations"> 116 <xml name="citations">
112 <citations> 117 <citations>
113 <citation type="doi">10.1186/1471-2105-12-70</citation> 118 <citation type="doi">10.1186/1471-2105-12-70</citation>