Mercurial > repos > galaxyp > openms_openswathrewritetofeaturexml
comparison OpenSwathRewriteToFeatureXML.xml @ 13:b956337a7473 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 19:23:47 +0000 |
parents | 5ad2d341fb2f |
children | 77f01ffce2b7 |
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12:1f7cf69e180c | 13:b956337a7473 |
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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: [Targeted Experiments]--> | 3 <!--Proposed Tool Section: [Targeted Experiments]--> |
4 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description> | 5 <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token> | 7 <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</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@ |
47 <configfiles> | 45 <configfiles> |
48 <inputs name="args_json" data_style="paths"/> | 46 <inputs name="args_json" data_style="paths"/> |
49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 47 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
50 </configfiles> | 48 </configfiles> |
51 <inputs> | 49 <inputs> |
52 <param name="csv" argument="-csv" type="data" format="csv" optional="true" label="mProphet tsv output file: "all_peakgroups.xls"" help=" select csv data sets(s)"/> | 50 <param argument="-csv" type="data" format="csv" optional="true" label="mProphet tsv output file: "all_peakgroups.xls"" help=" select csv data sets(s)"/> |
53 <param name="featureXML" argument="-featureXML" type="data" format="featurexml" optional="false" label="input featureXML file" help=" select featurexml data sets(s)"/> | 51 <param argument="-featureXML" type="data" format="featurexml" optional="false" label="input featureXML file" help=" select featurexml data sets(s)"/> |
54 <param name="FDR_cutoff" argument="-FDR_cutoff" type="float" optional="true" value="-1.0" label="FDR cutoff" help="(e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/> | 52 <param argument="-FDR_cutoff" type="float" optional="true" value="-1.0" label="FDR cutoff" help="(e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/> |
55 <expand macro="adv_opts_macro"> | 53 <expand macro="adv_opts_macro"> |
56 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
57 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 55 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
58 <expand macro="list_string_san"/> | 56 <expand macro="list_string_san" name="test"/> |
59 </param> | 57 </param> |
60 </expand> | 58 </expand> |
61 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
62 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
63 </param> | 61 </param> |
66 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> | 64 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> |
67 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
68 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
69 </data> | 67 </data> |
70 </outputs> | 68 </outputs> |
71 <tests> | 69 <tests><test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> |
72 <expand macro="autotest_OpenSwathRewriteToFeatureXML"/> | 70 <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> |
73 <expand macro="manutest_OpenSwathRewriteToFeatureXML"/> | 71 <param name="adv_opts|test" value="true"/> |
74 </tests> | 72 <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/> |
73 </test> | |
74 </tests> | |
75 <help><![CDATA[Combines featureXML and mProphet tsv to FDR filtered featureXML. | 75 <help><![CDATA[Combines featureXML and mProphet tsv to FDR filtered featureXML. |
76 | 76 |
77 | 77 |
78 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_OpenSwathRewriteToFeatureXML.html]]></help> | 78 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathRewriteToFeatureXML.html]]></help> |
79 <expand macro="references"/> | 79 <expand macro="references"/> |
80 </tool> | 80 </tool> |