Mercurial > repos > galaxyp > openms_qcmerger
comparison QCMerger.xml @ 9:aeb80a19bda0 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
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date | Thu, 27 Aug 2020 19:42:35 -0400 |
parents | 8c627b0c8276 |
children | 786873b9c3e3 |
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8:03e2e25c1e5b | 9:aeb80a19bda0 |
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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="QCMerger" name="QCMerger" version="2.3.0"> | 4 <tool id="QCMerger" name="QCMerger" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Merges two qcml files together.</description> | 5 <description>Merges two qcml files together.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">QCMerger</token> | 7 <token name="@EXECUTABLE@">QCMerger</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
9 </macros> | 11 </macros> |
10 <expand macro="references"/> | 12 <expand macro="requirements"/> |
11 <expand macro="stdio"/> | 13 <expand macro="stdio"/> |
12 <expand macro="requirements"/> | 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
13 <command detect_errors="aggressive"><![CDATA[QCMerger | 15 @EXT_FOO@ |
16 #import re | |
14 | 17 |
18 ## Preprocessing | |
19 mkdir in && | |
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } | |
21 mkdir out && | |
22 | |
23 ## Main program call | |
24 | |
25 set -o pipefail && | |
26 @EXECUTABLE@ -write_ctd ./ && | |
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | |
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | |
15 -in | 29 -in |
16 #for token in $param_in: | 30 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} |
17 $token | 31 -out |
18 #end for | 32 'out/output.${gxy2omsext("qcml")}' |
19 #if $param_out: | 33 |
20 -out $param_out | 34 ## Postprocessing |
21 #end if | 35 && mv 'out/output.${gxy2omsext("qcml")}' '$out' |
22 #if $param_setname: | 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
23 -setname "$param_setname" | 37 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
24 #end if | 38 #end if]]></command> |
25 #if $adv_opts.adv_opts_selector=='advanced': | 39 <configfiles> |
26 #if $adv_opts.param_force: | 40 <inputs name="args_json" data_style="paths"/> |
27 -force | 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
28 #end if | 42 </configfiles> |
29 #end if | |
30 ]]></command> | |
31 <inputs> | 43 <inputs> |
32 <param name="param_in" type="data" format="qcml" multiple="true" optional="False" size="30" label="List of qcml files to be merged" help="(-in) "> | 44 <param name="in" argument="-in" type="data" format="qcml" multiple="true" optional="false" label="List of qcml files to be merged" help=" select qcml data sets(s)"/> |
33 <sanitizer> | 45 <param name="setname" argument="-setname" type="text" optional="true" value="" label="Use only when all given qcml files belong to one set, which will be held under the given name" help=""> |
34 <valid initial="string.printable"> | 46 <expand macro="list_string_san"/> |
35 <remove value="'"/> | |
36 <remove value="""/> | |
37 </valid> | |
38 </sanitizer> | |
39 </param> | 47 </param> |
40 <param name="param_setname" type="text" size="30" label="Use only when all given qcml files belong to one set, which will be held under the given name" help="(-setname) "> | 48 <expand macro="adv_opts_macro"> |
41 <sanitizer> | 49 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> |
42 <valid initial="string.printable"> | 50 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
43 <remove value="'"/> | 51 <expand macro="list_string_san"/> |
44 <remove value="""/> | 52 </param> |
45 </valid> | 53 </expand> |
46 </sanitizer> | 54 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> |
55 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
47 </param> | 56 </param> |
48 <expand macro="advanced_options"> | |
49 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
50 </expand> | |
51 </inputs> | 57 </inputs> |
52 <outputs> | 58 <outputs> |
53 <data name="param_out" format="qcml"/> | 59 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/> |
60 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
61 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
62 </data> | |
54 </outputs> | 63 </outputs> |
55 <help>Merges two qcml files together. | 64 <tests> |
65 <expand macro="autotest_QCMerger"/> | |
66 <expand macro="manutest_QCMerger"/> | |
67 </tests> | |
68 <help><![CDATA[Merges two qcml files together. | |
56 | 69 |
57 | 70 |
58 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_QCMerger.html</help> | 71 For more information, visit http://www.openms.de/documentation/UTILS_QCMerger.html]]></help> |
72 <expand macro="references"/> | |
59 </tool> | 73 </tool> |