Mercurial > repos > galaxyp > openms_qcshrinker

comparison QCShrinker.xml @ 13:a4b5b3c5df07 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:25:13 +0000
parents 910f1fdf039a
children 047c8ea82162
comparison
equal deleted inserted replaced
12:381abb197081 13:a4b5b3c5df07
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="QCShrinker" name="QCShrinker" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="QCShrinker" name="QCShrinker" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.</description> 5 <description>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">QCShrinker</token> 7 <token name="@EXECUTABLE@">QCShrinker</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="in" argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/> 50 <param argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/>
53 <param name="qp_accessions" argument="-qp_accessions" type="text" optional="true" value="" label="A list of cv accessions that should be removed" help="If empty, the usual suspects will be removed! (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 51 <param argument="-qp_accessions" type="text" optional="true" value="" label="A list of cv accessions that should be removed" help="If empty, the usual suspects will be removed! (space separated list, in order to allow for spaces in list items surround them by single quotes)">
54 <expand macro="list_string_val"/> 52 <expand macro="list_string_val" name="qp_accessions"/>
55 <expand macro="list_string_san"/> 53 <expand macro="list_string_san" name="qp_accessions"/>
56 </param> 54 </param>
57 <param name="name" argument="-name" type="text" optional="true" value="" label="The name of the target run or set that contains the requested quality paramete" help=""> 55 <param argument="-name" type="text" optional="true" value="" label="The name of the target run or set that contains the requested quality paramete" help="">
58 <expand macro="list_string_san"/> 56 <expand macro="list_string_san" name="name"/>
59 </param> 57 </param>
60 <param name="run" argument="-run" type="data" format="mzml" optional="true" label="The file from which the name of the target run that contains the requested quality parameter is taken" help="This overrides the name parameter! select mzml data sets(s)"/> 58 <param argument="-run" type="data" format="mzml" optional="true" label="The file from which the name of the target run that contains the requested quality parameter is taken" help="This overrides the name parameter! select mzml data sets(s)"/>
61 <expand macro="adv_opts_macro"> 59 <expand macro="adv_opts_macro">
62 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 60 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
63 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 61 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
64 <expand macro="list_string_san"/> 62 <expand macro="list_string_san" name="test"/>
65 </param> 63 </param>
66 </expand> 64 </expand>
67 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 65 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
68 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 66 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
69 </param> 67 </param>
72 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/> 70 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/>
73 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 71 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
74 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 72 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
75 </data> 73 </data>
76 </outputs> 74 </outputs>
77 <tests> 75 <tests><test expect_num_outputs="1"><!-- just using an output of QCCalculator as input -->
78 <expand macro="autotest_QCShrinker"/> 76 <param name="adv_opts|test" value="true"/>
79 <expand macro="manutest_QCShrinker"/> 77 <param name="in" ftype="qcml" value="QCCalculator1.qcML"/>
80 </tests> 78 <output name="out" ftype="qcml" value="QCShrinker.qcML"/>
79 </test>
80 </tests>
81 <help><![CDATA[This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report. 81 <help><![CDATA[This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.
82 82
83 83
84 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_QCShrinker.html]]></help> 84 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCShrinker.html]]></help>
85 <expand macro="references"/> 85 <expand macro="references"/>
86 </tool> 86 </tool>