Mercurial > repos > galaxyp > openms_openswathrewritetofeaturexml

comparison OpenSwathRewriteToFeatureXML.xml @ 14:77f01ffce2b7 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 21:34:21 +0000
parents b956337a7473
children
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13:b956337a7473 14:77f01ffce2b7
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
4 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description> 4 <description>Combines featureXML and mProphet tsv to FDR filtered featureXML</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token> 6 <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 #if $csv: 16 #if $csv:
18 mkdir csv && 17 mkdir csv &&
19 ln -s '$csv' 'csv/${re.sub("[^\w\-_]", "_", $csv.element_identifier)}.$gxy2omsext($csv.ext)' && 18 cp '$csv' 'csv/${re.sub("[^\w\-_]", "_", $csv.element_identifier)}.$gxy2omsext($csv.ext)' &&
20 #end if 19 #end if
21 mkdir featureXML && 20 mkdir featureXML &&
22 ln -s '$featureXML' 'featureXML/${re.sub("[^\w\-_]", "_", $featureXML.element_identifier)}.$gxy2omsext($featureXML.ext)' && 21 cp '$featureXML' 'featureXML/${re.sub("[^\w\-_]", "_", $featureXML.element_identifier)}.$gxy2omsext($featureXML.ext)' &&
23 mkdir out && 22 mkdir out &&
24 23
25 ## Main program call 24 ## Main program call
26 25
27 set -o pipefail && 26 set -o pipefail &&
46 <inputs name="args_json" data_style="paths"/> 45 <inputs name="args_json" data_style="paths"/>
47 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 46 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
48 </configfiles> 47 </configfiles>
49 <inputs> 48 <inputs>
50 <param argument="-csv" type="data" format="csv" optional="true" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help=" select csv data sets(s)"/> 49 <param argument="-csv" type="data" format="csv" optional="true" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help=" select csv data sets(s)"/>
51 <param argument="-featureXML" type="data" format="featurexml" optional="false" label="input featureXML file" help=" select featurexml data sets(s)"/> 50 <param argument="-featureXML" type="data" format="featurexml" label="input featureXML file" help=" select featurexml data sets(s)"/>
52 <param 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)"/> 51 <param argument="-FDR_cutoff" type="float" 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)"/>
53 <expand macro="adv_opts_macro"> 52 <expand macro="adv_opts_macro">
54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 53 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
55 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 54 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
56 <expand macro="list_string_san" name="test"/> 55 <expand macro="list_string_san" name="test"/>
57 </param> 56 </param>
58 </expand> 57 </expand>
59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
64 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> 63 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
67 </data> 66 </data>
68 </outputs> 67 </outputs>
69 <tests><test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> 68 <tests>
70 <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> 69 <test expect_num_outputs="1">
71 <param name="adv_opts|test" value="true"/> 70 <!-- same input as used in the MSGF+Adapter -->
72 <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/> 71 <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
73 </test> 72 <param name="adv_opts|test" value="true"/>
74 </tests> 73 <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/>
74 </test>
75 </tests>
75 <help><![CDATA[Combines featureXML and mProphet tsv to FDR filtered featureXML. 76 <help><![CDATA[Combines featureXML and mProphet tsv to FDR filtered featureXML.
76 77
77 78
78 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathRewriteToFeatureXML.html]]></help> 79 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathRewriteToFeatureXML.html]]></help>
79 <expand macro="references"/> 80 <expand macro="references"/>
80 </tool> 81 </tool>