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comparison QCImporter.xml @ 14:988ae4cfb522 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 21:38:55 +0000
parents d29c4c46e057
children
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13:d29c4c46e057 14:988ae4cfb522
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="QCImporter" name="QCImporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Imports tables with quality control parameters into qcml files</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">QCImporter</token> 6 <token name="@EXECUTABLE@">QCImporter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 #if $in: 16 #if $in:
18 mkdir in && 17 mkdir in &&
19 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 18 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
20 #end if 19 #end if
21 mkdir table && 20 mkdir table &&
22 ln -s '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' && 21 cp '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' &&
23 mkdir mapping && 22 mkdir mapping &&
24 ln -s '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' && 23 cp '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' &&
25 mkdir out && 24 mkdir out &&
26 25
27 ## Main program call 26 ## Main program call
28 27
29 set -o pipefail && 28 set -o pipefail &&
50 <inputs name="args_json" data_style="paths"/> 49 <inputs name="args_json" data_style="paths"/>
51 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 50 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
52 </configfiles> 51 </configfiles>
53 <inputs> 52 <inputs>
54 <param argument="-in" type="data" format="qcml" optional="true" label="Input qcml file" help=" select qcml data sets(s)"/> 53 <param argument="-in" type="data" format="qcml" optional="true" label="Input qcml file" help=" select qcml 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 &quot;raw data file&quot;, so each row after the header will contain the values of qps for that run. (csv without &quot;!) select csv data sets(s)"/> 54 <param argument="-table" type="data" format="csv" 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 &quot;raw data file&quot;, so each row after the header will contain the values of qps for that run. (csv without &quot;!) 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 &quot;!) select csv data sets(s)"/> 55 <param argument="-mapping" type="data" format="csv" 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 &quot;!) select csv data sets(s)"/>
57 <expand macro="adv_opts_macro"> 56 <expand macro="adv_opts_macro">
58 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 57 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
59 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 58 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
60 <expand macro="list_string_san" name="test"/> 59 <expand macro="list_string_san" name="test"/>
61 </param> 60 </param>
62 </expand> 61 </expand>
63 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 62 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 63 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
68 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/> 67 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/>
69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 68 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 69 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
71 </data> 70 </data>
72 </outputs> 71 </outputs>
73 <tests><!--TODO--> 72 <tests>
74 </tests> 73 <!--TODO-->
74 </tests>
75 <help><![CDATA[Imports tables with quality control parameters into qcml files. 75 <help><![CDATA[Imports tables with quality control parameters into qcml files.
76 76
77 77
78 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCImporter.html]]></help> 78 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCImporter.html]]></help>
79 <expand macro="references"/> 79 <expand macro="references"/>
80 </tool> 80 </tool>