Mercurial > repos > galaxyp > openms_qcimporter
comparison QCImporter.xml @ 13:d29c4c46e057 draft default tip
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 19:23:03 +0000 |
parents | 0cfaedd90c2b |
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12:dd0a6ad39f0e | 13:d29c4c46e057 |
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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="QCImporter" name="QCImporter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="QCImporter" name="QCImporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Imports tables with quality control parameters into qcml files.</description> | 5 <description>Imports tables with quality control parameters into qcml files.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">QCImporter</token> | 7 <token name="@EXECUTABLE@">QCImporter</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@ |
51 <configfiles> | 49 <configfiles> |
52 <inputs name="args_json" data_style="paths"/> | 50 <inputs name="args_json" data_style="paths"/> |
53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 51 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
54 </configfiles> | 52 </configfiles> |
55 <inputs> | 53 <inputs> |
56 <param name="in" argument="-in" type="data" format="qcml" optional="true" label="Input qcml file" help=" select qcml data sets(s)"/> | 54 <param argument="-in" type="data" format="qcml" optional="true" label="Input qcml file" help=" select qcml data sets(s)"/> |
57 <param name="table" argument="-table" type="data" format="csv" optional="false" label="The table containing the additional qp values in the columns" help="First row is considered containing the header. The target run or set names/ids are indicated by column "raw data file", so each row after the header will contain the values of qps for that run. (csv without "!) select csv data sets(s)"/> | 55 <param argument="-table" type="data" format="csv" optional="false" label="The table containing the additional qp values in the columns" help="First row is considered containing the header. The target run or set names/ids are indicated by column "raw data file", so each row after the header will contain the values of qps for that run. (csv without "!) select csv data sets(s)"/> |
58 <param name="mapping" argument="-mapping" type="data" format="csv" optional="false" label="The mapping of the table header to the according qp cvs, also in csv format" help="The first row is considered containing the headers as in the table. The second row is considered the according qp cv accessions. (csv without "!) select csv data sets(s)"/> | 56 <param argument="-mapping" type="data" format="csv" optional="false" label="The mapping of the table header to the according qp cvs, also in csv format" help="The first row is considered containing the headers as in the table. The second row is considered the according qp cv accessions. (csv without "!) select csv data sets(s)"/> |
59 <expand macro="adv_opts_macro"> | 57 <expand macro="adv_opts_macro"> |
60 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 58 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
61 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 59 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
62 <expand macro="list_string_san"/> | 60 <expand macro="list_string_san" name="test"/> |
63 </param> | 61 </param> |
64 </expand> | 62 </expand> |
65 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 63 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
66 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
67 </param> | 65 </param> |
70 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/> | 68 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/> |
71 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
72 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
73 </data> | 71 </data> |
74 </outputs> | 72 </outputs> |
75 <tests> | 73 <tests><!--TODO--> |
76 <expand macro="autotest_QCImporter"/> | 74 </tests> |
77 <expand macro="manutest_QCImporter"/> | |
78 </tests> | |
79 <help><![CDATA[Imports tables with quality control parameters into qcml files. | 75 <help><![CDATA[Imports tables with quality control parameters into qcml files. |
80 | 76 |
81 | 77 |
82 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_QCImporter.html]]></help> | 78 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCImporter.html]]></help> |
83 <expand macro="references"/> | 79 <expand macro="references"/> |
84 </tool> | 80 </tool> |