Mercurial > repos > galaxyp > openms_msgfplusadapter

comparison MSGFPlusAdapter.xml @ 1:06987761999d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author galaxyp
date Tue, 18 Apr 2017 15:40:51 -0400
parents 65a1b411e932
children b1b95a6933f9
comparison
equal deleted inserted replaced
0:65a1b411e932 1:06987761999d
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command><![CDATA[ 13 <command><![CDATA[
14 14
15 ## check input file type 15 ## check input file type
16 #set $in_type = $param_in.ext 16 #set $in_type = $param_in.ext
17 17
18 ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files 18 ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files
19 ln -s '$param_in' 'param_in.${in_type}' && 19 ln -s '$param_in' 'param_in.${in_type}' &&
20 ln -s '$param_database' param_database.fasta && 20 ln -s '$param_database' param_database.fasta &&
21 ## find location of the MSGFPlus.jar file of the msgf_plus conda package 21 ## find location of the MSGFPlus.jar file of the msgf_plus conda package
22 MSGF_JAR=\$(msgf_plus -get_jar_path) && 22 MSGF_JAR=\$(msgf_plus -get_jar_path) &&
23 23
24 MSGFPlusAdapter 24 MSGFPlusAdapter
25 -executable \$MSGF_JAR 25 -executable \$MSGF_JAR
26 #if $param_in: 26 #if $param_in:
27 -in 'param_in.${in_type}' 27 -in 'param_in.${in_type}'
28 #end if 28 #end if
29 #if $param_out: 29 #if $param_out:
30 -out $param_out 30 -out $param_out
31 #end if 31 #end if
32 #if $param_mzid_out: 32 #if $param_mzid_out:
33 -mzid_out $param_mzid_out 33 -mzid_out $param_mzid_out
34 #end if 34 #end if
35 #if $param_database: 35 #if $param_database:
36 -database param_database.fasta 36 -database param_database.fasta
37 #end if 37 #end if
38 #if $param_add_decoys: 38 #if $param_add_decoys:
39 -add_decoys 39 -add_decoys
40 #end if 40 #end if
41 #if $param_precursor_mass_tolerance: 41 #if $param_precursor_mass_tolerance:
42 -precursor_mass_tolerance $param_precursor_mass_tolerance 42 -precursor_mass_tolerance $param_precursor_mass_tolerance
43 #end if 43 #end if
44 #if $param_precursor_error_units: 44 #if $param_precursor_error_units:
45 -precursor_error_units $param_precursor_error_units 45 -precursor_error_units
46 #if " " in str($param_precursor_error_units):
47 "$param_precursor_error_units"
48 #else
49 $param_precursor_error_units
50 #end if
46 #end if 51 #end if
47 #if $param_isotope_error_range: 52 #if $param_isotope_error_range:
48 -isotope_error_range "$param_isotope_error_range" 53 -isotope_error_range "$param_isotope_error_range"
49 #end if 54 #end if
50 #if $param_fragment_method: 55 #if $param_fragment_method:
51 -fragment_method $param_fragment_method 56 -fragment_method
57 #if " " in str($param_fragment_method):
58 "$param_fragment_method"
59 #else
60 $param_fragment_method
61 #end if
52 #end if 62 #end if
53 #if $param_instrument: 63 #if $param_instrument:
54 -instrument $param_instrument 64 -instrument
65 #if " " in str($param_instrument):
66 "$param_instrument"
67 #else
68 $param_instrument
69 #end if
55 #end if 70 #end if
56 #if $param_enzyme: 71 #if $param_enzyme:
57 -enzyme $param_enzyme 72 -enzyme
73 #if " " in str($param_enzyme):
74 "$param_enzyme"
75 #else
76 $param_enzyme
77 #end if
58 #end if 78 #end if
59 #if $param_protocol: 79 #if $param_protocol:
60 -protocol $param_protocol 80 -protocol
81 #if " " in str($param_protocol):
82 "$param_protocol"
83 #else
84 $param_protocol
85 #end if
61 #end if 86 #end if
62 #if $param_tryptic: 87 #if $param_tryptic:
63 -tryptic $param_tryptic 88 -tryptic
89 #if " " in str($param_tryptic):
90 "$param_tryptic"
91 #else
92 $param_tryptic
93 #end if
64 #end if 94 #end if
65 #if $param_min_precursor_charge: 95 #if $param_min_precursor_charge:
66 -min_precursor_charge $param_min_precursor_charge 96 -min_precursor_charge $param_min_precursor_charge
67 #end if 97 #end if
68 #if $param_max_precursor_charge: 98 #if $param_max_precursor_charge:
111 #end if 141 #end if
112 #if $adv_opts.param_force: 142 #if $adv_opts.param_force:
113 -force 143 -force
114 #end if 144 #end if
115 #end if 145 #end if
116 ]]> 146 ]]>
117 </command> 147 </command>
118 <inputs> 148 <inputs>
119 <param name="param_in" type="data" format="mzxml,mgf,mzml" optional="False" label="Input file (MS-GF+ parameter '-s')" help="(-in) "/> 149 <param name="param_in" type="data" format="mzxml,mgf,mzml" optional="False" label="Input file (MS-GF+ parameter '-s')" help="(-in) "/>
120 <param name="param_database" type="data" format="fasta" optional="False" label="Protein sequence database (FASTA file; MS-GF+ parameter '-d')" help="(-database) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/> 150 <param name="param_database" type="data" format="fasta" optional="False" label="Protein sequence database (FASTA file; MS-GF+ parameter '-d')" help="(-database) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/>
121 <param name="param_add_decoys" display="radio" type="boolean" truevalue="-add_decoys" falsevalue="" checked="false" optional="True" label="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda')" help="(-add_decoys) This allows the calculation of FDRs, but should only be used if the database does not already contain decoys"/> 151 <param name="param_add_decoys" display="radio" type="boolean" truevalue="-add_decoys" falsevalue="" checked="false" optional="True" label="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda')" help="(-add_decoys) This allows the calculation of FDRs, but should only be used if the database does not already contain decoys"/>