Mercurial > repos > bgruening > openms

comparison OpenSwathConfidenceScoring.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
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="1.12.0"> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <description>Compute confidence scores for OpenSwath results</description> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <macros> 4 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="2.0.0">
5 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token> 5 <description>Compute confidence scores for OpenSwath results</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>OpenSwathConfidenceScoring 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathConfidenceScoring
11 14
12 -in ${param_in} 15 #if $param_in:
13 -lib ${param_lib} 16 -in $param_in
14 -out ${param_out} 17 #end if
15 -trafo ${param_trafo} 18 #if $param_lib:
16 -decoys ${param_decoys} 19 -lib $param_lib
17 -transitions ${param_transitions} 20 #end if
18 -threads \${GALAXY_SLOTS:-24} 21 #if $param_out:
22 -out $param_out
23 #end if
24 #if $param_trafo:
25 -trafo $param_trafo
26 #end if
27 #if $param_decoys:
28 -decoys $param_decoys
29 #end if
30 #if $param_transitions:
31 -transitions $param_transitions
32 #end if
33 -threads \${GALAXY_SLOTS:-24}
19 #if $adv_opts.adv_opts_selector=='advanced': 34 #if $adv_opts.adv_opts_selector=='advanced':
20 -GLM:intercept ${adv_opts.param_intercept} 35 #if $adv_opts.param_force:
21 -GLM:delta_rt ${adv_opts.param_delta_rt} 36 -force
22 -GLM:dist_int ${adv_opts.param_dist_int} 37 #end if
38 #if $adv_opts.param_GLM_intercept:
39 -GLM:intercept $adv_opts.param_GLM_intercept
40 #end if
41 #if $adv_opts.param_GLM_delta_rt:
42 -GLM:delta_rt $adv_opts.param_GLM_delta_rt
43 #end if
44 #if $adv_opts.param_GLM_dist_int:
45 -GLM:dist_int $adv_opts.param_GLM_dist_int
46 #end if
23 #end if 47 #end if
24 </command> 48 </command>
25 <inputs> 49 <inputs>
26 <param name="param_in" type="data" format="featureXML" optional="False" label="Input file (OpenSwath results)" help="(-in)"/> 50 <param format="xml" help="(-in) " label="Input file (OpenSwath results)" name="param_in" optional="False" type="data"/>
27 <param name="param_lib" type="data" format="" optional="False" label="Assay library" help="(-lib)"/> 51 <param format="traml" help="(-lib) " label="Assay library" name="param_lib" optional="False" type="data"/>
28 <param name="param_trafo" type="data" format="" optional="True" label="Retention time transformation" help="(-trafo)"/> 52 <param format="trafoxml" help="(-trafo) " label="Retention time transformation" name="param_trafo" optional="True" type="data"/>
29 <param name="param_decoys" type="integer" min="0" optional="True" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help="(-decoys)"/> 53 <param help="(-decoys) " label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" min="0" name="param_decoys" optional="True" type="integer" value="1000"/>
30 <param name="param_transitions" type="integer" min="0" optional="True" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help="(-transitions)"/> 54 <param help="(-transitions) " label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" min="0" name="param_transitions" optional="True" type="integer" value="6"/>
31 <expand macro="advanced_options"> 55 <expand macro="advanced_options">
32 <param name="param_intercept" type="float" value="3.87333466" label="Intercept term" help="(-intercept)"/> 56 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
33 <param name="param_delta_rt" type="float" value="-0.02898629" label="Coefficient of retention time difference" help="(-delta_rt)"/> 57 <param help="(-intercept) " label="Intercept term" name="param_GLM_intercept" type="float" value="3.87333466"/>
34 <param name="param_dist_int" type="float" value="-7.75880768" label="Coefficient of intensity distance" help="(-dist_int)"/> 58 <param help="(-delta_rt) " label="Coefficient of retention time difference" name="param_GLM_delta_rt" type="float" value="-0.02898629"/>
35 </expand> 59 <param help="(-dist_int) " label="Coefficient of intensity distance" name="param_GLM_dist_int" type="float" value="-7.75880768"/>
36 </inputs> 60 </expand>
37 <outputs> 61 </inputs>
38 <data name="param_out" label="Output file (results with confidence scores)" format="featureXML"/> 62 <outputs>
39 </outputs> 63 <data format="xml" name="param_out"/>
40 <help>**What it does** 64 </outputs>
41 65 <help>Compute confidence scores for OpenSwath results
42 Compute confidence scores for OpenSwath results
43 66
44 67
45 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathConfidenceScoring.html 68 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathConfidenceScoring.html</help>
46 69 </tool>
47 @REFERENCES@
48 </help>
49 </tool>