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comparison QCExporter.xml @ 9:7e8a254ef96d draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:24:22 +0000
parents bb52c480a74a
children adf7f5301284
comparison
equal deleted inserted replaced
8:d02e46f6c54a 9:7e8a254ef96d
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="QCExporter" name="QCExporter" version="2.3.0"> 4 <tool id="QCExporter" name="QCExporter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Will extract several qp from several run/sets in a tabular format.</description> 5 <description>Will extract several qp from several run/sets in a tabular format.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">QCExporter</token> 7 <token name="@EXECUTABLE@">QCExporter</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[QCExporter 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir mapping &&
22 ln -s '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' &&
23 mkdir out_csv &&
18 24
19 #if $rep_param_names: 25 ## Main program call
20 -names 26
21 #for token in $rep_param_names: 27 set -o pipefail &&
22 #if " " in str(token): 28 @EXECUTABLE@ -write_ctd ./ &&
23 "$token.param_names" 29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
24 #else 30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
25 $token.param_names 31 -in
26 #end if 32 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
27 #end for 33 -mapping
28 #end if 34 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)'
29 #if $param_mapping: 35 -out_csv
30 -mapping $param_mapping 36 'out_csv/output.${gxy2omsext("csv")}'
31 #end if 37
32 #if $param_out_csv: 38 ## Postprocessing
33 -out_csv $param_out_csv 39 && mv 'out_csv/output.${gxy2omsext("csv")}' '$out_csv'
34 #end if 40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
35 #if $adv_opts.adv_opts_selector=='advanced': 41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
36 #if $adv_opts.param_force: 42 #end if]]></command>
37 -force 43 <configfiles>
38 #end if 44 <inputs name="args_json" data_style="paths"/>
39 #end if 45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
40 ]]></command> 46 </configfiles>
41 <inputs> 47 <inputs>
42 <param name="param_in" type="data" format="qcml" optional="False" label="Input qcml file" help="(-in) "/> 48 <param name="in" argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/>
43 <repeat name="rep_param_names" min="0" title="param_names"> 49 <param name="names" 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)">
44 <param name="param_names" type="text" size="30" label="The name of the target runs or sets to be exported from" help="(-names) If empty, from all will be exported"> 50 <expand macro="list_string_val"/>
45 <sanitizer> 51 <expand macro="list_string_san"/>
46 <valid initial="string.printable"> 52 </param>
47 <remove value="'"/> 53 <param name="mapping" 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)"/>
48 <remove value="&quot;"/> 54 <expand macro="adv_opts_macro">
49 </valid> 55 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
50 </sanitizer> 56 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
57 <expand macro="list_string_san"/>
51 </param> 58 </param>
52 </repeat>
53 <param name="param_mapping" type="data" format="tabular" optional="False" label="The mapping of the exported table's headers to the according qp cvs" help="(-mapping) 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"/>
54 <expand macro="advanced_options">
55 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
56 </expand> 59 </expand>
60 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
61 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
62 </param>
57 </inputs> 63 </inputs>
58 <outputs> 64 <outputs>
59 <data name="param_out_csv" format="tabular"/> 65 <data name="out_csv" label="${tool.name} on ${on_string}: out_csv" format="csv"/>
66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
68 </data>
60 </outputs> 69 </outputs>
61 <help>Will extract several qp from several run/sets in a tabular format. 70 <tests>
71 <expand macro="autotest_QCExporter"/>
72 <expand macro="manutest_QCExporter"/>
73 </tests>
74 <help><![CDATA[Will extract several qp from several run/sets in a tabular format.
62 75
63 76
64 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_QCExporter.html</help> 77 For more information, visit http://www.openms.de/documentation/UTILS_QCExporter.html]]></help>
78 <expand macro="references"/>
65 </tool> 79 </tool>