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comparison QCExporter.xml @ 14:bb22e965eb5a draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:31:54 +0000
parents 838b8e375587
children
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13:838b8e375587 14:bb22e965eb5a
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: []-->
4 <tool id="QCExporter" name="QCExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="QCExporter" name="QCExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Will extract several qp from several run/sets in a tabular format.</description> 4 <description>Will extract several qp from several run/sets in a tabular format</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">QCExporter</token> 6 <token name="@EXECUTABLE@">QCExporter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir mapping && 18 mkdir mapping &&
20 ln -s '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' && 19 cp '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' &&
21 mkdir out_csv && 20 mkdir out_csv &&
22 21
23 ## Main program call 22 ## Main program call
24 23
25 set -o pipefail && 24 set -o pipefail &&
41 <configfiles> 40 <configfiles>
42 <inputs name="args_json" data_style="paths"/> 41 <inputs name="args_json" data_style="paths"/>
43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 42 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
44 </configfiles> 43 </configfiles>
45 <inputs> 44 <inputs>
46 <param argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/> 45 <param argument="-in" type="data" format="qcml" label="Input qcml file" help=" select qcml data sets(s)"/>
47 <param argument="-names" type="text" optional="true" value="" label="The name of the target runs or sets to be exported from" help="If empty, from all will be exported (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 46 <param argument="-names" type="text" optional="true" value="" label="The name of the target runs or sets to be exported from" help="If empty, from all will be exported (space separated list, in order to allow for spaces in list items surround them by single quotes)">
48 <expand macro="list_string_val" name="names"/> 47 <expand macro="list_string_val" name="names"/>
49 <expand macro="list_string_san" name="names"/> 48 <expand macro="list_string_san" name="names"/>
50 </param> 49 </param>
51 <param argument="-mapping" type="data" format="csv" optional="false" label="The mapping of the exported table's headers to the according qp cvs" help="The first row is considered containing the headers as for the exported the table. The second row is considered the according qp cv accessions of the qp to be exported select csv data sets(s)"/> 50 <param argument="-mapping" type="data" format="csv" label="The mapping of the exported table's headers to the according qp cvs" help="The first row is considered containing the headers as for the exported the table. The second row is considered the according qp cv accessions of the qp to be exported select csv data sets(s)"/>
52 <expand macro="adv_opts_macro"> 51 <expand macro="adv_opts_macro">
53 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 52 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
54 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 53 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
55 <expand macro="list_string_san" name="test"/> 54 <expand macro="list_string_san" name="test"/>
56 </param> 55 </param>
57 </expand> 56 </expand>
58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 57 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 58 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
63 <data name="out_csv" label="${tool.name} on ${on_string}: out_csv" format="csv"/> 62 <data name="out_csv" label="${tool.name} on ${on_string}: out_csv" format="csv"/>
64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 63 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 64 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
66 </data> 65 </data>
67 </outputs> 66 </outputs>
68 <tests><!--TODO--> 67 <tests>
69 </tests> 68 <!--TODO-->
69 </tests>
70 <help><![CDATA[Will extract several qp from several run/sets in a tabular format. 70 <help><![CDATA[Will extract several qp from several run/sets in a tabular format.
71 71
72 72
73 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCExporter.html]]></help> 73 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCExporter.html]]></help>
74 <expand macro="references"/> 74 <expand macro="references"/>
75 </tool> 75 </tool>