Mercurial > repos > galaxyp > openms_rnpxlxicfilter

comparison RNPxlXICFilter.xml @ 8:8a2e37503e3e 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 19:48:37 -0400
parents 397b489a4f8d
children c2827f0ca312
comparison
equal deleted inserted replaced
7:397b489a4f8d 8:8a2e37503e3e
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="RNPxlXICFilter" name="RNPxlXICFilter" version="2.3.0"> 4 <tool id="RNPxlXICFilter" name="RNPxlXICFilter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Remove MS2 spectra from treatment based on the fold change between control and treatment.</description> 5 <description>Remove MS2 spectra from treatment based on the fold change between control and treatment.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">RNPxlXICFilter</token> 7 <token name="@EXECUTABLE@">RNPxlXICFilter</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[RNPxlXICFilter 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_control: 18 ## Preprocessing
16 -control $param_control 19 mkdir control &&
17 #end if 20 ln -s '$control' 'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)' &&
18 #if $param_treatment: 21 mkdir treatment &&
19 -treatment $param_treatment 22 ln -s '$treatment' 'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)' &&
20 #end if 23 mkdir out &&
21 #if $param_fold_change: 24
22 -fold_change $param_fold_change 25 ## Main program call
23 #end if 26
24 #if $param_rt_tol: 27 set -o pipefail &&
25 -rt_tol $param_rt_tol 28 @EXECUTABLE@ -write_ctd ./ &&
26 #end if 29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
27 #if $param_mz_tol: 30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
28 -mz_tol $param_mz_tol 31 -control
29 #end if 32 'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)'
30 #if $param_out: 33 -treatment
31 -out $param_out 34 'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)'
32 #end if 35 -out
33 #if $adv_opts.adv_opts_selector=='advanced': 36 'out/output.${gxy2omsext("mzml")}'
34 #if $adv_opts.param_force: 37
35 -force 38 ## Postprocessing
36 #end if 39 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
37 #end if 40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
38 ]]></command> 41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
42 #end if]]></command>
43 <configfiles>
44 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles>
39 <inputs> 47 <inputs>
40 <param name="param_control" type="data" format="mzml" optional="False" label="input mzML file" help="(-control) "/> 48 <param name="control" argument="-control" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/>
41 <param name="param_treatment" type="data" format="mzml" optional="False" label="input mzML file" help="(-treatment) "/> 49 <param name="treatment" argument="-treatment" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/>
42 <param name="param_fold_change" type="float" value="2.0" label="fold change between XICs" help="(-fold_change) "/> 50 <param name="fold_change" argument="-fold_change" type="float" optional="true" value="2.0" label="fold change between XICs" help=""/>
43 <param name="param_rt_tol" type="float" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help="(-rt_tol) "/> 51 <param name="rt_tol" argument="-rt_tol" type="float" optional="true" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/>
44 <param name="param_mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help="(-mz_tol) "/> 52 <param name="mz_tol" argument="-mz_tol" type="float" optional="true" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/>
45 <expand macro="advanced_options"> 53 <expand macro="adv_opts_macro">
46 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 54 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
55 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
56 <expand macro="list_string_san"/>
57 </param>
47 </expand> 58 </expand>
59 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
61 </param>
48 </inputs> 62 </inputs>
49 <outputs> 63 <outputs>
50 <data name="param_out" format="mzml"/> 64 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
67 </data>
51 </outputs> 68 </outputs>
52 <help>Remove MS2 spectra from treatment based on the fold change between control and treatment. 69 <tests>
70 <expand macro="autotest_RNPxlXICFilter"/>
71 <expand macro="manutest_RNPxlXICFilter"/>
72 </tests>
73 <help><![CDATA[Remove MS2 spectra from treatment based on the fold change between control and treatment.
53 74
54 75
55 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_RNPxlXICFilter.html</help> 76 For more information, visit http://www.openms.de/documentation/UTILS_RNPxlXICFilter.html]]></help>
77 <expand macro="references"/>
56 </tool> 78 </tool>