Mercurial > repos > galaxyp > openms_clustermasstracesbyprecursor
comparison ClusterMassTracesByPrecursor.xml @ 4:75480fff2586 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:22:18 +0000 |
parents | f61e132c4536 |
children | f0c018228cec |
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3:dedbf43ccfb5 | 4:75480fff2586 |
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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="ClusterMassTracesByPrecursor" name="ClusterMassTracesByPrecursor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="ClusterMassTracesByPrecursor" name="ClusterMassTracesByPrecursor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile.</description> | 5 <description>Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">ClusterMassTracesByPrecursor</token> | 7 <token name="@EXECUTABLE@">ClusterMassTracesByPrecursor</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
11 </macros> | 9 </macros> |
12 <expand macro="requirements"/> | 10 <expand macro="requirements"/> |
13 <expand macro="stdio"/> | 11 <expand macro="stdio"/> |
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
15 @EXT_FOO@ | 13 @EXT_FOO@ |
43 <configfiles> | 41 <configfiles> |
44 <inputs name="args_json" data_style="paths"/> | 42 <inputs name="args_json" data_style="paths"/> |
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
46 </configfiles> | 44 </configfiles> |
47 <inputs> | 45 <inputs> |
48 <param name="in_ms1" argument="-in_ms1" type="data" format="consensusxml" optional="false" label="MS1 mass traces" help=" select consensusxml data sets(s)"/> | 46 <param argument="-in_ms1" type="data" format="consensusxml" optional="false" label="MS1 mass traces" help=" select consensusxml data sets(s)"/> |
49 <param name="in_swath" argument="-in_swath" type="data" format="consensusxml" optional="false" label="MS2 / SWATH mass traces" help=" select consensusxml data sets(s)"/> | 47 <param argument="-in_swath" type="data" format="consensusxml" optional="false" label="MS2 / SWATH mass traces" help=" select consensusxml data sets(s)"/> |
50 <param name="assign_unassigned_to_all" argument="-assign_unassigned_to_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assign unassigned MS2 fragments to all precursors (only for ms1_centrif)" help=""/> | 48 <param argument="-assign_unassigned_to_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assign unassigned MS2 fragments to all precursors (only for ms1_centrif)" help=""/> |
51 <param name="min_pearson_correlation" argument="-min_pearson_correlation" type="float" optional="true" value="0.7" label="Minimal pearson correlation score to match elution profiles to each othe" help=""/> | 49 <param argument="-min_pearson_correlation" type="float" optional="true" value="0.7" label="Minimal pearson correlation score to match elution profiles to each othe" help=""/> |
52 <param name="max_lag" argument="-max_lag" type="integer" optional="true" value="1" label="Maximal lag" help="(e.g. by how many spectra the peak may be shifted at most). This parameter will depend on your chromatographic setup but a number between 1 and 3 is usually sensible"/> | 50 <param argument="-max_lag" type="integer" optional="true" value="1" label="Maximal lag" help="(e.g. by how many spectra the peak may be shifted at most). This parameter will depend on your chromatographic setup but a number between 1 and 3 is usually sensible"/> |
53 <param name="min_nr_ions" argument="-min_nr_ions" type="integer" optional="true" value="3" label="Minimal number of ions to report a spectrum" help=""/> | 51 <param argument="-min_nr_ions" type="integer" optional="true" value="3" label="Minimal number of ions to report a spectrum" help=""/> |
54 <param name="max_rt_apex_difference" argument="-max_rt_apex_difference" type="float" optional="true" value="5.0" label="Maximal difference of the apex in retention time (in seconds)" help="This is a hard parameter, all profiles further away will not be considered at all"/> | 52 <param argument="-max_rt_apex_difference" type="float" optional="true" value="5.0" label="Maximal difference of the apex in retention time (in seconds)" help="This is a hard parameter, all profiles further away will not be considered at all"/> |
55 <param name="swath_lower" argument="-swath_lower" type="float" optional="true" value="0.0" label="Swath lower isolation window" help=""/> | 53 <param argument="-swath_lower" type="float" optional="true" value="0.0" label="Swath lower isolation window" help=""/> |
56 <param name="swath_upper" argument="-swath_upper" type="float" optional="true" value="0.0" label="Swath upper isolation window" help=""/> | 54 <param argument="-swath_upper" type="float" optional="true" value="0.0" label="Swath upper isolation window" help=""/> |
57 <expand macro="adv_opts_macro"> | 55 <expand macro="adv_opts_macro"> |
58 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 56 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
59 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 57 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
60 <expand macro="list_string_san"/> | 58 <expand macro="list_string_san" name="test"/> |
61 </param> | 59 </param> |
62 </expand> | 60 </expand> |
63 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 61 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 62 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
65 </param> | 63 </param> |
68 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> | 66 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 67 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 68 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
71 </data> | 69 </data> |
72 </outputs> | 70 </outputs> |
73 <tests> | 71 <tests><test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML --> |
74 <expand macro="autotest_ClusterMassTracesByPrecursor"/> | 72 <param name="adv_opts|test" value="true"/> |
75 <expand macro="manutest_ClusterMassTracesByPrecursor"/> | 73 <param name="in_ms1" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> |
76 </tests> | 74 <param name="in_swath" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> |
75 <output name="out" ftype="mzml" value="ClusterMassTracesByPrecursor.mzml"/> | |
76 </test> | |
77 </tests> | |
77 <help><![CDATA[Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile. | 78 <help><![CDATA[Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile. |
78 | 79 |
79 | 80 |
80 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_ClusterMassTracesByPrecursor.html]]></help> | 81 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_ClusterMassTracesByPrecursor.html]]></help> |
81 <expand macro="references"/> | 82 <expand macro="references"/> |
82 </tool> | 83 </tool> |