Mercurial > repos > galaxyp > openms_qcembedder

comparison QCEmbedder.xml @ 13:f9e709333234 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 19:04:55 +0000
parents 2c6f5858e89a
children 815e502a2288
comparison
equal deleted inserted replaced
12:df711389fe7f 13:f9e709333234
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="QCEmbedder" name="QCEmbedder" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="QCEmbedder" name="QCEmbedder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Attaches a table or an image to a given qc parameter.</description> 5 <description>Attaches a table or an image to a given qc parameter.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">QCEmbedder</token> 7 <token name="@EXECUTABLE@">QCEmbedder</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@
67 <configfiles> 65 <configfiles>
68 <inputs name="args_json" data_style="paths"/> 66 <inputs name="args_json" data_style="paths"/>
69 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 67 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
70 </configfiles> 68 </configfiles>
71 <inputs> 69 <inputs>
72 <param name="in" argument="-in" type="data" format="qcml" optional="true" label="Input qcml file" help=" select qcml data sets(s)"/> 70 <param argument="-in" type="data" format="qcml" optional="true" label="Input qcml file" help=" select qcml data sets(s)"/>
73 <param name="qp_att_acc" argument="-qp_att_acc" type="text" optional="true" value="" label="Defines the qp cv accession of the qp to which the table/image is attached" help=""> 71 <param argument="-qp_att_acc" type="text" optional="true" value="" label="Defines the qp cv accession of the qp to which the table/image is attached" help="">
74 <expand macro="list_string_san"/> 72 <expand macro="list_string_san" name="qp_att_acc"/>
75 </param> 73 </param>
76 <param name="cv_acc" argument="-cv_acc" type="text" optional="false" value="" label="Defines the cv accession of the attachment" help=""> 74 <param argument="-cv_acc" type="text" optional="false" value="" label="Defines the cv accession of the attachment" help="">
77 <expand macro="list_string_san"/> 75 <expand macro="list_string_san" name="cv_acc"/>
78 </param> 76 </param>
79 <param name="run" argument="-run" type="data" format="mzml" optional="true" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="The file is only used to extract the run name from the file name select mzml data sets(s)"/> 77 <param argument="-run" type="data" format="mzml" optional="true" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="The file is only used to extract the run name from the file name select mzml data sets(s)"/>
80 <param name="name" argument="-name" type="text" optional="true" value="" label="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given" help=""> 78 <param argument="-name" type="text" optional="true" value="" label="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given" help="">
81 <expand macro="list_string_san"/> 79 <expand macro="list_string_san" name="name"/>
82 </param> 80 </param>
83 <param name="plot" argument="-plot" type="data" format="png" optional="true" label="If a plot image is to be attached to a qp, this has to be specified here" help=" select png data sets(s)"/> 81 <param argument="-plot" type="data" format="png" optional="true" label="If a plot image is to be attached to a qp, this has to be specified here" help=" select png data sets(s)"/>
84 <param name="table" argument="-table" type="data" format="csv" optional="true" label="If a table is to be attached to a qp, this has to be specified here" help=" select csv data sets(s)"/> 82 <param argument="-table" type="data" format="csv" optional="true" label="If a table is to be attached to a qp, this has to be specified here" help=" select csv data sets(s)"/>
85 <expand macro="adv_opts_macro"> 83 <expand macro="adv_opts_macro">
86 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 84 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
87 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 85 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
88 <expand macro="list_string_san"/> 86 <expand macro="list_string_san" name="test"/>
89 </param> 87 </param>
90 </expand> 88 </expand>
91 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 89 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
92 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 90 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
93 </param> 91 </param>
96 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/> 94 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/>
97 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 95 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
98 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 96 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
99 </data> 97 </data>
100 </outputs> 98 </outputs>
101 <tests> 99 <tests><!--TODO-->
102 <expand macro="autotest_QCEmbedder"/> 100 </tests>
103 <expand macro="manutest_QCEmbedder"/>
104 </tests>
105 <help><![CDATA[Attaches a table or an image to a given qc parameter. 101 <help><![CDATA[Attaches a table or an image to a given qc parameter.
106 102
107 103
108 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_QCEmbedder.html]]></help> 104 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCEmbedder.html]]></help>
109 <expand macro="references"/> 105 <expand macro="references"/>
110 </tool> 106 </tool>