Mercurial > repos > galaxyp > openms_rnpxlxicfilter
comparison RNPxlXICFilter.xml @ 13:8ee87d58ed48 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author | galaxyp |
---|---|
date | Fri, 14 Jun 2024 21:30:53 +0000 |
parents | 81d5ef72ef9d |
children |
comparison
equal
deleted
inserted
replaced
12:81d5ef72ef9d | 13:8ee87d58ed48 |
---|---|
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: [Utilities]--> | 2 <!--Proposed Tool Section: [Cross-Linking]--> |
4 <tool id="RNPxlXICFilter" name="RNPxlXICFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | 3 <tool id="RNPxlXICFilter" name="RNPxlXICFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Remove MS2 spectra from treatment based on the fold change between control and treatment.</description> | 4 <description>Remove MS2 spectra from treatment based on the fold change between control and treatment</description> |
6 <macros> | 5 <macros> |
7 <token name="@EXECUTABLE@">RNPxlXICFilter</token> | 6 <token name="@EXECUTABLE@">RNPxlXICFilter</token> |
8 <import>macros.xml</import> | 7 <import>macros.xml</import> |
9 </macros> | 8 </macros> |
10 <expand macro="requirements"/> | 9 <expand macro="requirements"/> |
13 @EXT_FOO@ | 12 @EXT_FOO@ |
14 #import re | 13 #import re |
15 | 14 |
16 ## Preprocessing | 15 ## Preprocessing |
17 mkdir control && | 16 mkdir control && |
18 ln -s '$control' 'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)' && | 17 cp '$control' 'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)' && |
19 mkdir treatment && | 18 mkdir treatment && |
20 ln -s '$treatment' 'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)' && | 19 cp '$treatment' 'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)' && |
21 mkdir out && | 20 mkdir out && |
22 | 21 |
23 ## Main program call | 22 ## Main program call |
24 | 23 |
25 set -o pipefail && | 24 set -o pipefail && |
41 <configfiles> | 40 <configfiles> |
42 <inputs name="args_json" data_style="paths"/> | 41 <inputs name="args_json" data_style="paths"/> |
43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 42 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
44 </configfiles> | 43 </configfiles> |
45 <inputs> | 44 <inputs> |
46 <param argument="-control" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/> | 45 <param argument="-control" type="data" format="mzml" label="input mzML file" help=" select mzml data sets(s)"/> |
47 <param argument="-treatment" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/> | 46 <param argument="-treatment" type="data" format="mzml" label="input mzML file" help=" select mzml data sets(s)"/> |
48 <param argument="-fold_change" type="float" optional="true" value="2.0" label="fold change between XICs" help=""/> | 47 <param argument="-fold_change" type="float" value="2.0" label="fold change between XICs" help=""/> |
49 <param 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=""/> | 48 <param argument="-rt_tol" type="float" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/> |
50 <param argument="-mz_tol" type="float" optional="true" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/> | 49 <param argument="-mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/> |
51 <expand macro="adv_opts_macro"> | 50 <expand macro="adv_opts_macro"> |
52 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 51 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
53 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 52 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> |
54 <expand macro="list_string_san" name="test"/> | 53 <expand macro="list_string_san" name="test"/> |
55 </param> | 54 </param> |
56 </expand> | 55 </expand> |
57 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 56 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
58 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 57 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
62 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> | 61 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
63 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 62 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
64 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 63 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
65 </data> | 64 </data> |
66 </outputs> | 65 </outputs> |
67 <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input (2x the same which is likely nonsense, but sufficient for the test) and autgenerated output--> | 66 <tests> |
68 <param name="adv_opts|test" value="true"/> | 67 <test expect_num_outputs="1"> |
69 <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/> | 68 <!-- just chosen an arbitrary input (2x the same which is likely nonsense, but sufficient for the test) and autgenerated output--> |
70 <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/> | 69 <param name="adv_opts|test" value="true"/> |
71 <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/> | 70 <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/> |
72 </test> | 71 <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/> |
73 </tests> | 72 <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/> |
73 </test> | |
74 </tests> | |
74 <help><![CDATA[Remove MS2 spectra from treatment based on the fold change between control and treatment. | 75 <help><![CDATA[Remove MS2 spectra from treatment based on the fold change between control and treatment. |
75 | 76 |
76 | 77 |
77 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RNPxlXICFilter.html]]></help> | 78 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_RNPxlXICFilter.html]]></help> |
78 <expand macro="references"/> | 79 <expand macro="references"/> |
79 </tool> | 80 </tool> |