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comparison OpenSwathDIAPreScoring.xml @ 12:986d14ec9394 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 21:34:43 +0000
parents c99d5004b74f
children
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11:c99d5004b74f 12:986d14ec9394
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="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Scoring spectra using the DIA scores.</description> 4 <description>Scoring spectra using the DIA scores</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</token> 6 <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</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 tr && 16 mkdir tr &&
18 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && 17 cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
19 mkdir swath_files_cond.swath_files && 18 mkdir swath_files_cond.swath_files &&
20 #if $swath_files_cond.swath_files_select == "no" 19 #if $swath_files_cond.swath_files_select == "no"
21 mkdir ${' '.join(["'swath_files_cond.swath_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} && 20 mkdir ${' '.join(["'swath_files_cond.swath_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} &&
22 ${' '.join(["ln -s '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])} 21 ${' '.join(["cp '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])}
23 #else 22 #else
24 ln -s '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' && 23 cp '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' &&
25 #end if 24 #end if
26 mkdir output_files && 25 mkdir output_files &&
27 mkdir ${' '.join(["'output_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} && 26 mkdir ${' '.join(["'output_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} &&
28 27
29 ## Main program call 28 ## Main program call
51 <configfiles> 50 <configfiles>
52 <inputs name="args_json" data_style="paths"/> 51 <inputs name="args_json" data_style="paths"/>
53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 52 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
54 </configfiles> 53 </configfiles>
55 <inputs> 54 <inputs>
56 <param argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/> 55 <param argument="-tr" type="data" format="traml" label="transition file" help=" select traml data sets(s)"/>
57 <conditional name="swath_files_cond"> 56 <conditional name="swath_files_cond">
58 <param name="swath_files_select" type="select" label="Run tool in batch mode for -swath_files"> 57 <param name="swath_files_select" type="select" label="Run tool in batch mode for -swath_files">
59 <option value="no">No: process all datasets jointly</option> 58 <option value="no">No: process all datasets jointly</option>
60 <option value="yes">Yes: process each dataset in an independent job</option> 59 <option value="yes">Yes: process each dataset in an independent job</option>
61 </param> 60 </param>
62 <when value="no"> 61 <when value="no">
63 <param argument="-swath_files" type="data" format="mzml" multiple="true" optional="false" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/> 62 <param argument="-swath_files" type="data" format="mzml" multiple="true" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/>
64 </when> 63 </when>
65 <when value="yes"> 64 <when value="yes">
66 <param argument="-swath_files" type="data" format="mzml" multiple="false" optional="false" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/> 65 <param argument="-swath_files" type="data" format="mzml" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/>
67 </when> 66 </when>
68 </conditional> 67 </conditional>
69 <param argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help=""/> 68 <param argument="-min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help=""/>
70 <expand macro="adv_opts_macro"> 69 <expand macro="adv_opts_macro">
71 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 70 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
72 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 71 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
73 <expand macro="list_string_san" name="test"/> 72 <expand macro="list_string_san" name="test"/>
74 </param> 73 </param>
75 </expand> 74 </expand>
76 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 75 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
77 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 76 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
83 </collection> 82 </collection>
84 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 83 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
85 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 84 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
86 </data> 85 </data>
87 </outputs> 86 </outputs>
88 <tests><!-- data from a test that included all the needed test files --> 87 <tests>
89 <test> 88 <!-- data from a test that included all the needed test files -->
90 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> 89 <test expect_num_outputs="1">
91 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> 90 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
92 <output_collection name="output_files" count="1"> 91 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
93 <element name="OpenSwathAnalyzer_2_swathfile_mzML" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> 92 <output_collection name="output_files" count="1">
94 </output_collection> 93 <element name="OpenSwathAnalyzer_2_swathfile_mzML" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
95 </test> 94 </output_collection>
96 <!-- test with two inputs (actually the same file .. symlinked) --> 95 </test>
97 <test> 96 <!-- test with two inputs (actually the same file .. symlinked) -->
98 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> 97 <test expect_num_outputs="1">
99 <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/> 98 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
100 <output_collection name="output_files" count="2"> 99 <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>
101 <element name="OpenSwathDIAPreScoring_in1_mzML" file="OpenSwathDIAPreScoring_2_1.tsv" ftype="tabular"/> 100 <output_collection name="output_files" count="2">
102 <element name="OpenSwathDIAPreScoring_in2_mzML" file="OpenSwathDIAPreScoring_2_2.tsv" ftype="tabular"/> 101 <element name="OpenSwathDIAPreScoring_in1_mzML" file="OpenSwathDIAPreScoring_2_1.tsv" ftype="tabular"/>
103 </output_collection> 102 <element name="OpenSwathDIAPreScoring_in2_mzML" file="OpenSwathDIAPreScoring_2_2.tsv" ftype="tabular"/>
104 </test> 103 </output_collection>
105 </tests> 104 </test>
105 </tests>
106 <help><![CDATA[Scoring spectra using the DIA scores. 106 <help><![CDATA[Scoring spectra using the DIA scores.
107 107
108 108
109 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathDIAPreScoring.html]]></help> 109 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathDIAPreScoring.html]]></help>
110 <expand macro="references"/> 110 <expand macro="references"/>
111 </tool> 111 </tool>