Mercurial > repos > galaxyp > openms_mrmpairfinder

comparison MRMPairFinder.xml @ 8:a040e1ed8736 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:15:23 +0000
parents 0369ed5ff70e
children 482de0c17531
comparison
equal deleted inserted replaced
7:0369ed5ff70e 8:a040e1ed8736
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MRMPairFinder" name="MRMPairFinder" version="2.3.0"> 4 <tool id="MRMPairFinder" name="MRMPairFinder" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Util which can be used to evaluate labeled pair ratios on MRM features.</description> 5 <description>Util which can be used to evaluate labeled pair ratios on MRM features.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MRMPairFinder</token> 7 <token name="@EXECUTABLE@">MRMPairFinder</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[MRMPairFinder 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($in.ext)' &&
21 mkdir pair_in &&
22 ln -s '$pair_in' 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)' &&
23 mkdir out &&
24 #if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
25 mkdir feature_out &&
17 #end if 26 #end if
18 #if $param_pair_in: 27
19 -pair_in $param_pair_in 28 ## Main program call
29
30 set -o pipefail &&
31 @EXECUTABLE@ -write_ctd ./ &&
32 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
33 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
34 -in
35 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
36 -pair_in
37 'pair_in/${re.sub("[^\w\-_]", "_", $pair_in.element_identifier)}.$gxy2omsext($pair_in.ext)'
38 -out
39 'out/output.${gxy2omsext("consensusxml")}'
40 #if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
41 -feature_out
42 'feature_out/output.${gxy2omsext("featurexml")}'
20 #end if 43 #end if
21 #if $param_out: 44 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
22 -out $param_out 45 | tee '$stdout'
23 #end if 46 #end if
24 #if $param_feature_out: 47
25 -feature_out $param_feature_out 48 ## Postprocessing
49 && mv 'out/output.${gxy2omsext("consensusxml")}' '$out'
50 #if "feature_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
51 && mv 'feature_out/output.${gxy2omsext("featurexml")}' '$feature_out'
26 #end if 52 #end if
27 #if $adv_opts.adv_opts_selector=='advanced': 53 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
28 #if $adv_opts.param_mass_tolerance: 54 && mv '@EXECUTABLE@.ctd' '$ctd_out'
29 -mass_tolerance $adv_opts.param_mass_tolerance 55 #end if]]></command>
30 #end if 56 <configfiles>
31 #if $adv_opts.param_RT_tolerance: 57 <inputs name="args_json" data_style="paths"/>
32 -RT_tolerance $adv_opts.param_RT_tolerance 58 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
33 #end if 59 </configfiles>
34 #if $adv_opts.param_RT_pair_tolerance:
35 -RT_pair_tolerance $adv_opts.param_RT_pair_tolerance
36 #end if
37 #if $adv_opts.param_force:
38 -force
39 #end if
40 #end if
41 ]]></command>
42 <inputs> 60 <inputs>
43 <param name="param_in" type="data" format="featurexml" optional="False" label="Input featureXML file containing the features of the MRM experiment spectra" help="(-in) "/> 61 <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input featureXML file containing the features of the MRM experiment spectra" help=" select featurexml data sets(s)"/>
44 <param name="param_pair_in" type="data" format="tabular" optional="False" label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" help="(-pair_in) "/> 62 <param name="pair_in" argument="-pair_in" type="data" format="csv" optional="false" label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" help=" select csv data sets(s)"/>
45 <expand macro="advanced_options"> 63 <expand macro="adv_opts_macro">
46 <param name="param_mass_tolerance" type="float" min="0.0" optional="True" value="0.01" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help="(-mass_tolerance) "/> 64 <param name="mass_tolerance" argument="-mass_tolerance" type="float" optional="true" min="0.0" value="0.01" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help=""/>
47 <param name="param_RT_tolerance" type="float" min="0.0" optional="True" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help="(-RT_tolerance) "/> 65 <param name="RT_tolerance" argument="-RT_tolerance" type="float" optional="true" min="0.0" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help=""/>
48 <param name="param_RT_pair_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have" help="(-RT_pair_tolerance) "/> 66 <param name="RT_pair_tolerance" argument="-RT_pair_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have" help=""/>
49 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 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>
50 </expand> 71 </expand>
72 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
73 <option value="feature_out_FLAG">feature_out (Enables the test mode (needed for internal use only))</option>
74 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
75 </param>
51 </inputs> 76 </inputs>
52 <outputs> 77 <outputs>
53 <data name="param_out" format="consensusxml"/> 78 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
54 <data name="param_feature_out" format="featurexml"/> 79 <data name="feature_out" label="${tool.name} on ${on_string}: feature_out" format="featurexml">
80 <filter>OPTIONAL_OUTPUTS is not None and "feature_out_FLAG" in OPTIONAL_OUTPUTS</filter>
81 </data>
82 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
83 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
84 </data>
55 </outputs> 85 </outputs>
56 <help>Util which can be used to evaluate labeled pair ratios on MRM features. 86 <tests>
87 <expand macro="autotest_MRMPairFinder"/>
88 <expand macro="manutest_MRMPairFinder"/>
89 </tests>
90 <help><![CDATA[Util which can be used to evaluate labeled pair ratios on MRM features.
57 91
58 92
59 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MRMPairFinder.html</help> 93 For more information, visit http://www.openms.de/documentation/UTILS_MRMPairFinder.html]]></help>
94 <expand macro="references"/>
60 </tool> 95 </tool>