Mercurial > repos > bgruening > openms

annotate FalseDiscoveryRate.xml @ 4:6ead64a594bd draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
3 <!--Proposed Tool Section: [ID Processing]-->
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
4 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.0.0">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
5 <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
6 <macros>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
7 <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
8 <import>macros.xml</import>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
9 </macros>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
10 <expand macro="references"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
11 <expand macro="stdio"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
12 <expand macro="requirements"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
13 <command>FalseDiscoveryRate
0
3d84209d3178 Uploaded
bgruening
parents:
diff changeset
14
4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
15 #if $param_in:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
16 -in $param_in
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
17 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
18 #if $param_in_target:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
19 -in_target $param_in_target
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
20 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
21 #if $param_in_decoy:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
22 -in_decoy $param_in_decoy
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
23 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
24 #if $param_out:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
25 -out $param_out
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
26 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
27 #if $param_proteins_only:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
28 -proteins_only
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
29 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
30 #if $param_peptides_only:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
31 -peptides_only
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
32 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
33 -threads \${GALAXY_SLOTS:-24}
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
34 #if $param_algorithm_no_qvalues:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
35 -algorithm:no_qvalues
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
36 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
37 #if $param_algorithm_use_all_hits:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
38 -algorithm:use_all_hits
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
39 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
40 #if $param_algorithm_split_charge_variants:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
41 -algorithm:split_charge_variants
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
42 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
43 #if $param_algorithm_treat_runs_separately:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
44 -algorithm:treat_runs_separately
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
45 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
46 #if $param_algorithm_add_decoy_peptides:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
47 -algorithm:add_decoy_peptides
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
48 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
49 #if $adv_opts.adv_opts_selector=='advanced':
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
50 #if $adv_opts.param_force:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
51 -force
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
52 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
53 #end if
0
3d84209d3178 Uploaded
bgruening
parents:
diff changeset
54 </command>
4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
55 <inputs>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
56 <param format="xml" help="(-in) Either specify '-in' alone or 'in_target' together with 'in_decoy' as input" label="Identification input file containing a search against a concatenated sequence database" name="param_in" optional="True" type="data"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
57 <param format="xml" help="(-in_target) " label="Identification input file containing a search against a target-only database" name="param_in_target" optional="True" type="data"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
58 <param format="xml" help="(-in_decoy) " label="Identification input file containing a search against a decoy-only database" name="param_in_decoy" optional="True" type="data"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
59 <param checked="false" falsevalue="" help="(-proteins_only) " label="If set only the FDR on protein level is calculated" name="param_proteins_only" optional="True" truevalue="-proteins_only" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
60 <param checked="false" falsevalue="" help="(-peptides_only) " label="If set only the FDR on peptide (PSM) level is calculated" name="param_peptides_only" optional="True" truevalue="-peptides_only" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
61 <param checked="false" falsevalue="" help="(-no_qvalues) " label="If 'true' strict FDRs will be calculated instead of q-values (the default)" name="param_algorithm_no_qvalues" optional="True" truevalue="-algorithm:no_qvalues" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
62 <param checked="false" falsevalue="" help="(-use_all_hits) " label="If 'true' not only the first hit, but all are used (peptides only)" name="param_algorithm_use_all_hits" optional="True" truevalue="-algorithm:use_all_hits" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
63 <param checked="false" falsevalue="" help="(-split_charge_variants) " label="If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)" name="param_algorithm_split_charge_variants" optional="True" truevalue="-algorithm:split_charge_variants" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
64 <param checked="false" falsevalue="" help="(-treat_runs_separately) " label="If 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)" name="param_algorithm_treat_runs_separately" optional="True" truevalue="-algorithm:treat_runs_separately" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
65 <param checked="false" falsevalue="" help="(-add_decoy_peptides) The q-value is set to the closest target score" label="If 'true' decoy peptides will be written to output file, too" name="param_algorithm_add_decoy_peptides" optional="True" truevalue="-algorithm:add_decoy_peptides" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
66 <expand macro="advanced_options">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
67 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
68 </expand>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
69 </inputs>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
70 <outputs>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
71 <data format="xml" name="param_out"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
72 </outputs>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
73 <help>Estimates the false discovery rate on peptide and protein level using decoy searches.
0
3d84209d3178 Uploaded
bgruening
parents:
diff changeset
74
3d84209d3178 Uploaded
bgruening
parents:
diff changeset
75
4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
76 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html</help>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
77 </tool>