Mercurial > repos > galaxyp > openms_openswathrewritetofeaturexml

comparison OpenSwathRewriteToFeatureXML.xml @ 13:fecccb4b673b 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, 27 Aug 2020 22:56:01 +0000
parents 2c6c9e743075
children f46b54789f6f
comparison
equal deleted inserted replaced
12:2c6c9e743075 13:fecccb4b673b
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: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="2.3.0"> 4 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description> 5 <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token> 7 <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</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[OpenSwathRewriteToFeatureXML 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_csv: 18 ## Preprocessing
16 -csv $param_csv 19 #if $csv:
20 mkdir csv &&
21 ln -s '$csv' 'csv/${re.sub("[^\w\-_]", "_", $csv.element_identifier)}.$gxy2omsext($csv.ext)' &&
17 #end if 22 #end if
18 #if $param_featureXML: 23 mkdir featureXML &&
19 -featureXML $param_featureXML 24 ln -s '$featureXML' 'featureXML/${re.sub("[^\w\-_]", "_", $featureXML.element_identifier)}.$gxy2omsext($featureXML.ext)' &&
25 mkdir out &&
26
27 ## Main program call
28
29 set -o pipefail &&
30 @EXECUTABLE@ -write_ctd ./ &&
31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
33 #if $csv:
34 -csv
35 'csv/${re.sub("[^\w\-_]", "_", $csv.element_identifier)}.$gxy2omsext($csv.ext)'
20 #end if 36 #end if
21 #if $param_out: 37 -featureXML
22 -out $param_out 38 'featureXML/${re.sub("[^\w\-_]", "_", $featureXML.element_identifier)}.$gxy2omsext($featureXML.ext)'
23 #end if 39 -out
24 #if $param_FDR_cutoff: 40 'out/output.${gxy2omsext("featurexml")}'
25 -FDR_cutoff $param_FDR_cutoff 41
26 #end if 42 ## Postprocessing
27 #if $adv_opts.adv_opts_selector=='advanced': 43 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
28 #if $adv_opts.param_force: 44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
29 -force 45 && mv '@EXECUTABLE@.ctd' '$ctd_out'
30 #end if 46 #end if]]></command>
31 #end if 47 <configfiles>
32 ]]></command> 48 <inputs name="args_json" data_style="paths"/>
49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
50 </configfiles>
33 <inputs> 51 <inputs>
34 <param name="param_csv" type="data" format="tabular" optional="True" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help="(-csv) "/> 52 <param name="csv" argument="-csv" type="data" format="csv" optional="true" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help=" select csv data sets(s)"/>
35 <param name="param_featureXML" type="data" format="featurexml" optional="False" label="input featureXML file" help="(-featureXML) "/> 53 <param name="featureXML" argument="-featureXML" type="data" format="featurexml" optional="false" label="input featureXML file" help=" select featurexml data sets(s)"/>
36 <param name="param_FDR_cutoff" type="float" value="-1.0" label="FDR cutoff (" help="(-FDR_cutoff) e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/> 54 <param name="FDR_cutoff" argument="-FDR_cutoff" type="float" optional="true" value="-1.0" label="FDR cutoff" help="(e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/>
37 <expand macro="advanced_options"> 55 <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) "/> 56 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
57 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
58 <expand macro="list_string_san"/>
59 </param>
39 </expand> 60 </expand>
61 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
62 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
63 </param>
40 </inputs> 64 </inputs>
41 <outputs> 65 <outputs>
42 <data name="param_out" format="featurexml"/> 66 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
67 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
68 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
69 </data>
43 </outputs> 70 </outputs>
44 <help>Combines featureXML and mProphet tsv to FDR filtered featureXML. 71 <tests>
72 <expand macro="autotest_OpenSwathRewriteToFeatureXML"/>
73 <expand macro="manutest_OpenSwathRewriteToFeatureXML"/>
74 </tests>
75 <help><![CDATA[Combines featureXML and mProphet tsv to FDR filtered featureXML.
45 76
46 77
47 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_OpenSwathRewriteToFeatureXML.html</help> 78 For more information, visit http://www.openms.de/documentation/UTILS_OpenSwathRewriteToFeatureXML.html]]></help>
79 <expand macro="references"/>
48 </tool> 80 </tool>