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comparison QCImporter.xml @ 9:ddf8a08bbd91 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:00:11 +0000
parents 0798f2fa6c1f
children 0cfaedd90c2b
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equal deleted inserted replaced
8:6b6e7c5fb906 9:ddf8a08bbd91
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="QCImporter" name="QCImporter" version="2.3.0"> 4 <tool id="QCImporter" name="QCImporter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Imports tables with quality control parameters into qcml files.</description> 5 <description>Imports tables with quality control parameters into qcml files.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">QCImporter</token> 7 <token name="@EXECUTABLE@">QCImporter</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[QCImporter 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 #if $in:
20 mkdir in &&
21 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
17 #end if 22 #end if
18 #if $param_table: 23 mkdir table &&
19 -table $param_table 24 ln -s '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' &&
25 mkdir mapping &&
26 ln -s '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' &&
27 mkdir out &&
28
29 ## Main program call
30
31 set -o pipefail &&
32 @EXECUTABLE@ -write_ctd ./ &&
33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
35 #if $in:
36 -in
37 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
20 #end if 38 #end if
21 #if $param_mapping: 39 -table
22 -mapping $param_mapping 40 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)'
23 #end if 41 -mapping
24 #if $param_out: 42 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)'
25 -out $param_out 43 -out
26 #end if 44 'out/output.${gxy2omsext("qcml")}'
27 #if $adv_opts.adv_opts_selector=='advanced': 45
28 #if $adv_opts.param_force: 46 ## Postprocessing
29 -force 47 && mv 'out/output.${gxy2omsext("qcml")}' '$out'
30 #end if 48 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
31 #end if 49 && mv '@EXECUTABLE@.ctd' '$ctd_out'
32 ]]></command> 50 #end if]]></command>
51 <configfiles>
52 <inputs name="args_json" data_style="paths"/>
53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
54 </configfiles>
33 <inputs> 55 <inputs>
34 <param name="param_in" type="data" format="qcml" optional="True" label="Input qcml file" help="(-in) "/> 56 <param name="in" argument="-in" type="data" format="qcml" optional="true" label="Input qcml file" help=" select qcml data sets(s)"/>
35 <param name="param_table" type="data" format="tabular" optional="False" label="The table containing the additional qp values in the columns" help="(-table) 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;!)"/> 57 <param name="table" 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)"/>
36 <param name="param_mapping" type="data" format="tabular" optional="False" label="The mapping of the table header to the according qp cvs, also in csv format" help="(-mapping) 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;!)"/> 58 <param name="mapping" 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)"/>
37 <expand macro="advanced_options"> 59 <expand macro="adv_opts_macro">
38 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 60 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
61 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
62 <expand macro="list_string_san"/>
63 </param>
39 </expand> 64 </expand>
65 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
66 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
67 </param>
40 </inputs> 68 </inputs>
41 <outputs> 69 <outputs>
42 <data name="param_out" format="qcml"/> 70 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/>
71 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
72 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
73 </data>
43 </outputs> 74 </outputs>
44 <help>Imports tables with quality control parameters into qcml files. 75 <tests>
76 <expand macro="autotest_QCImporter"/>
77 <expand macro="manutest_QCImporter"/>
78 </tests>
79 <help><![CDATA[Imports tables with quality control parameters into qcml files.
45 80
46 81
47 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_QCImporter.html</help> 82 For more information, visit http://www.openms.de/documentation/UTILS_QCImporter.html]]></help>
83 <expand macro="references"/>
48 </tool> 84 </tool>