Mercurial > repos > galaxyp > openms_erpairfinder

comparison ERPairFinder.xml @ 11:919d5280d1db 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 19:48:03 -0400
parents 5fd5f1d02251
children e5e2b0d57f1d
comparison
equal deleted inserted replaced
10:3414b014f3b2 11:919d5280d1db
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="ERPairFinder" name="ERPairFinder" version="2.3.0"> 4 <tool id="ERPairFinder" name="ERPairFinder" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description> 5 <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">ERPairFinder</token> 7 <token name="@EXECUTABLE@">ERPairFinder</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[ERPairFinder 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 $param_precursor_mass_tolerance: 53 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
28 -precursor_mass_tolerance $param_precursor_mass_tolerance 54 && mv '@EXECUTABLE@.ctd' '$ctd_out'
29 #end if 55 #end if]]></command>
30 #if $adv_opts.adv_opts_selector=='advanced': 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_max_charge:
35 -max_charge $adv_opts.param_max_charge
36 #end if
37 #if $adv_opts.param_intensity_threshold:
38 -intensity_threshold $adv_opts.param_intensity_threshold
39 #end if
40 #if $adv_opts.param_max_isotope:
41 -max_isotope $adv_opts.param_max_isotope
42 #end if
43 #if $adv_opts.param_expansion_range:
44 -expansion_range $adv_opts.param_expansion_range
45 #end if
46 #if $adv_opts.param_force:
47 -force
48 #end if
49 #end if
50 ]]></command>
51 <inputs> 60 <inputs>
52 <param name="param_in" type="data" format="mzml" optional="False" label="Input mzML file containing the ER spectra" help="(-in) "/> 61 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input mzML file containing the ER spectra" help=" select mzml data sets(s)"/>
53 <param name="param_pair_in" type="data" format="txt" optional="False" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help="(-pair_in) "/> 62 <param name="pair_in" argument="-pair_in" type="data" format="txt" optional="false" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help=" select txt data sets(s)"/>
54 <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="0.3" 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="(-precursor_mass_tolerance) "/> 63 <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" min="0.0" value="0.3" 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=""/>
55 <expand macro="advanced_options"> 64 <expand macro="adv_opts_macro">
56 <param name="param_RT_tolerance" type="float" min="1.0" 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="1.0" 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=""/>
57 <param name="param_max_charge" type="integer" min="1" optional="True" value="3" label="Maximal charge state features should be search fo" help="(-max_charge) "/> 66 <param name="max_charge" argument="-max_charge" type="integer" optional="true" min="1" value="3" label="Maximal charge state features should be search fo" help=""/>
58 <param name="param_intensity_threshold" type="float" min="-1.0" optional="True" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" help="(-intensity_threshold) "/> 67 <param name="intensity_threshold" argument="-intensity_threshold" type="float" optional="true" min="-1.0" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" help=""/>
59 <param name="param_max_isotope" type="integer" min="2" optional="True" value="3" label="Max isotope of the isotope distribution to be considered" help="(-max_isotope) "/> 68 <param name="max_isotope" argument="-max_isotope" type="integer" optional="true" min="2" value="3" label="Max isotope of the isotope distribution to be considered" help=""/>
60 <param name="param_expansion_range" type="float" min="0.0" optional="True" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th" help="(-expansion_range) "/> 69 <param name="expansion_range" argument="-expansion_range" type="float" optional="true" min="0.0" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th" help=""/>
61 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 70 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
71 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
72 <expand macro="list_string_san"/>
73 </param>
62 </expand> 74 </expand>
75 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
76 <option value="feature_out_FLAG">feature_out (Enables the test mode (needed for internal use only))</option>
77 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
78 </param>
63 </inputs> 79 </inputs>
64 <outputs> 80 <outputs>
65 <data name="param_out" format="consensusxml"/> 81 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
66 <data name="param_feature_out" format="featurexml"/> 82 <data name="feature_out" label="${tool.name} on ${on_string}: feature_out" format="featurexml">
83 <filter>OPTIONAL_OUTPUTS is not None and "feature_out_FLAG" in OPTIONAL_OUTPUTS</filter>
84 </data>
85 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
86 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
87 </data>
67 </outputs> 88 </outputs>
68 <help>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans. 89 <tests>
90 <expand macro="autotest_ERPairFinder"/>
91 <expand macro="manutest_ERPairFinder"/>
92 </tests>
93 <help><![CDATA[Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
69 94
70 95
71 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_ERPairFinder.html</help> 96 For more information, visit http://www.openms.de/documentation/UTILS_ERPairFinder.html]]></help>
97 <expand macro="references"/>
72 </tool> 98 </tool>