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comparison msgfplus_search.xml @ 1:d3994c3ec487 draft

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author iracooke
date Mon, 03 Mar 2014 19:31:53 -0500
parents a84952540969
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0:a84952540969 1:d3994c3ec487
24 $fixed_mods 24 $fixed_mods
25 #for $custom_fix_mod in $custom_fix_mods: 25 #for $custom_fix_mod in $custom_fix_mods:
26 ,${custom_fix_mod.custom_mod} 26 ,${custom_fix_mod.custom_mod}
27 #end for 27 #end for
28 ' 28 '
29
29 $input_file 30 $input_file
30 -o $output 31 -o $output
31 -r 32 -r
32 --enzyme=$enzyme 33 --enzyme=$enzyme
33 --precursor-ion-tol-units=$precursor_tolu 34 --precursor-ion-tol-units=$precursor_tolu
42 --max-pep-len=$max_pep_len 43 --max-pep-len=$max_pep_len
43 --max-pep-charge=$max_pep_charge 44 --max-pep-charge=$max_pep_charge
44 --min-pep-charge=$min_pep_charge 45 --min-pep-charge=$min_pep_charge
45 --num-reported-matches=$num_reported_matches 46 --num-reported-matches=$num_reported_matches
46 --java-mem=$java_mem 47 --java-mem=$java_mem
47 #if $pepxml_output_use 48 #if $pepxml_output_use:
48 #else 49 #else
49 --no-pepxml 50 --no-pepxml
50 #end if 51 #end if
51 </command> 52 </command>
52 53