Mercurial > repos > galaxyp > openms_openswathconfidencescoring

comparison OpenSwathConfidenceScoring.xml @ 9:401b29d0f88c draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 19:49:07 -0400
parents b1cacc7586e2
children fa73919cc97e
comparison
equal deleted inserted replaced
8:3d24698daa6e 9:401b29d0f88c
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="2.3.0"> 4 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Compute confidence scores for OpenSwath results</description> 5 <description>Compute confidence scores for OpenSwath results</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token> 7 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[OpenSwathConfidenceScoring 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir lib &&
22 ln -s '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' &&
23 mkdir out &&
24 #if $trafo:
25 mkdir trafo &&
26 ln -s '$trafo' 'trafo/${re.sub("[^\w\-_]", "_", $trafo.element_identifier)}.$gxy2omsext($trafo.ext)' &&
17 #end if 27 #end if
18 #if $param_lib: 28
19 -lib $param_lib 29 ## Main program call
30
31 set -o pipefail &&
32 @EXECUTABLE@ -write_ctd ./ &&
33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
35 -in
36 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
37 -lib
38 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)'
39 -out
40 'out/output.${gxy2omsext("featurexml")}'
41 #if $trafo:
42 -trafo
43 'trafo/${re.sub("[^\w\-_]", "_", $trafo.element_identifier)}.$gxy2omsext($trafo.ext)'
20 #end if 44 #end if
21 #if $param_out: 45
22 -out $param_out 46 ## Postprocessing
23 #end if 47 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
24 #if $param_trafo: 48 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
25 -trafo $param_trafo 49 && mv '@EXECUTABLE@.ctd' '$ctd_out'
26 #end if 50 #end if]]></command>
27 #if $param_decoys: 51 <configfiles>
28 -decoys $param_decoys 52 <inputs name="args_json" data_style="paths"/>
29 #end if 53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
30 #if $param_transitions: 54 </configfiles>
31 -transitions $param_transitions
32 #end if
33 #if $adv_opts.adv_opts_selector=='advanced':
34 #if $adv_opts.param_force:
35 -force
36 #end if
37 #if $adv_opts.param_GLM_intercept:
38 -GLM:intercept $adv_opts.param_GLM_intercept
39 #end if
40 #if $adv_opts.param_GLM_delta_rt:
41 -GLM:delta_rt $adv_opts.param_GLM_delta_rt
42 #end if
43 #if $adv_opts.param_GLM_dist_int:
44 -GLM:dist_int $adv_opts.param_GLM_dist_int
45 #end if
46 #end if
47 ]]></command>
48 <inputs> 55 <inputs>
49 <param name="param_in" type="data" format="featurexml" optional="False" label="Input file (OpenSwath results)" help="(-in) "/> 56 <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input file (OpenSwath results)" help=" select featurexml data sets(s)"/>
50 <param name="param_lib" type="data" format="traml" optional="False" label="Assay library" help="(-lib) "/> 57 <param name="lib" argument="-lib" type="data" format="traml" optional="false" label="Assay library" help=" select traml data sets(s)"/>
51 <param name="param_trafo" type="data" format="trafoxml" optional="True" label="Retention time transformation" help="(-trafo) "/> 58 <param name="trafo" argument="-trafo" type="data" format="trafoxml" optional="true" label="Retention time transformation" help=" select trafoxml data sets(s)"/>
52 <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) "/> 59 <param name="decoys" argument="-decoys" type="integer" optional="true" min="0" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" help=""/>
53 <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) "/> 60 <param name="transitions" argument="-transitions" type="integer" optional="true" min="0" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" help=""/>
54 <expand macro="advanced_options"> 61 <section name="GLM" title="Parameters of the binomial GLM" help="" expanded="false">
55 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 62 <param name="intercept" argument="-GLM:intercept" type="float" optional="true" value="3.87333466" label="Intercept term" help=""/>
56 <param name="param_GLM_intercept" type="float" value="3.87333466" label="Intercept term" help="(-intercept) "/> 63 <param name="delta_rt" argument="-GLM:delta_rt" type="float" optional="true" value="-0.02898629" label="Coefficient of retention time difference" help=""/>
57 <param name="param_GLM_delta_rt" type="float" value="-0.02898629" label="Coefficient of retention time difference" help="(-delta_rt) "/> 64 <param name="dist_int" argument="-GLM:dist_int" type="float" optional="true" value="-7.75880768" label="Coefficient of intensity distance" help=""/>
58 <param name="param_GLM_dist_int" type="float" value="-7.75880768" label="Coefficient of intensity distance" help="(-dist_int) "/> 65 </section>
66 <expand macro="adv_opts_macro">
67 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
68 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
69 <expand macro="list_string_san"/>
70 </param>
59 </expand> 71 </expand>
72 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
73 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
74 </param>
60 </inputs> 75 </inputs>
61 <outputs> 76 <outputs>
62 <data name="param_out" format="featurexml"/> 77 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
78 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
79 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
80 </data>
63 </outputs> 81 </outputs>
64 <help>Compute confidence scores for OpenSwath results 82 <tests>
83 <expand macro="autotest_OpenSwathConfidenceScoring"/>
84 <expand macro="manutest_OpenSwathConfidenceScoring"/>
85 </tests>
86 <help><![CDATA[Compute confidence scores for OpenSwath results
65 87
66 88
67 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_OpenSwathConfidenceScoring.html</help> 89 For more information, visit http://www.openms.de/documentation/TOPP_OpenSwathConfidenceScoring.html]]></help>
90 <expand macro="references"/>
68 </tool> 91 </tool>