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comparison OpenMSInfo.xml @ 0:5da903bcd4f1 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 21:41:52 +0000
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-1:000000000000 0:5da903bcd4f1
1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
2 <!--Proposed Tool Section: [Misc / Helpers]-->
3 <tool id="OpenMSInfo" name="OpenMSInfo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
4 <description>Prints configurations details of OpenMS</description>
5 <macros>
6 <token name="@EXECUTABLE@">OpenMSInfo</token>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="requirements"/>
10 <expand macro="stdio"/>
11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
12 @EXT_FOO@
13 #import re
14
15 ## Preprocessing
16 ## advanced options
17 #if $adv_opts.dummy:
18 mkdir adv_opts.dummy &&
19 cp '$adv_opts.dummy' 'adv_opts.dummy/${re.sub("[^\w\-_]", "_", $adv_opts.dummy.element_identifier)}.$gxy2omsext($adv_opts.dummy.ext)' &&
20 #end if
21
22
23 ## Main program call
24
25 set -o pipefail &&
26 @EXECUTABLE@ -write_ctd ./ &&
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
29 ## advanced options
30 #if $adv_opts.dummy:
31 -dummy
32 'adv_opts.dummy/${re.sub("[^\w\-_]", "_", $adv_opts.dummy.element_identifier)}.$gxy2omsext($adv_opts.dummy.ext)'
33 #end if
34
35 | tee '$stdout'
36
37 ## Postprocessing
38 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
39 && mv '@EXECUTABLE@.ctd' '$ctd_out'
40 #end if]]></command>
41 <configfiles>
42 <inputs name="args_json" data_style="paths"/>
43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
44 </configfiles>
45 <inputs>
46 <param argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Print information (flag can also be omitted)" help=""/>
47 <expand macro="adv_opts_macro">
48 <param argument="-dummy" type="data" format="txt" optional="true" label="A fake input file, which is needed for some workflow systems to call this tool" help=" select txt data sets(s)"/>
49 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
50 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
51 <expand macro="list_string_san" name="test"/>
52 </param>
53 </expand>
54 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
55 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
56 </param>
57 </inputs>
58 <outputs>
59 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
60 <filter>OPTIONAL_OUTPUTS is None</filter>
61 </data>
62 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
63 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
64 </data>
65 </outputs>
66 <tests/>
67 <help><![CDATA[Prints configurations details of OpenMS.
68
69
70 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenMSInfo.html]]></help>
71 <expand macro="references"/>
72 </tool>