Mercurial > repos > galaxyp > openms_seedlistgenerator
comparison SeedListGenerator.xml @ 7:f3c72f54b9eb draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:04:23 +0000 |
parents | f840d8e8099a |
children | f6076d07a33a |
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6:5227ade94537 | 7:f3c72f54b9eb |
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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: [Quantitation]--> | 3 <!--Proposed Tool Section: [Quantitation]--> |
4 <tool id="SeedListGenerator" name="SeedListGenerator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="SeedListGenerator" name="SeedListGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Generates seed lists for feature detection.</description> | 5 <description>Generates seed lists for feature detection.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">SeedListGenerator</token> | 7 <token name="@EXECUTABLE@">SeedListGenerator</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
11 </macros> | 9 </macros> |
12 <expand macro="requirements"/> | 10 <expand macro="requirements"/> |
13 <expand macro="stdio"/> | 11 <expand macro="stdio"/> |
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
15 @EXT_FOO@ | 13 @EXT_FOO@ |
16 #import re | 14 #import re |
17 | 15 |
18 ## Preprocessing | 16 ## Preprocessing |
19 mkdir in && | 17 mkdir in && |
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && | 18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
21 mkdir out && | 19 mkdir out_prefix && |
22 | 20 |
23 ## Main program call | 21 ## Main program call |
24 | 22 |
25 set -o pipefail && | 23 set -o pipefail && |
26 @EXECUTABLE@ -write_ctd ./ && | 24 @EXECUTABLE@ -write_ctd ./ && |
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | 25 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | 26 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
29 -in | 27 -in |
30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' | 28 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
31 -out | 29 -out_prefix |
32 'out/output.${gxy2omsext("featurexml")}' | 30 out_prefix/ |
33 | 31 |
34 ## Postprocessing | 32 ## Postprocessing |
35 && mv 'out/output.${gxy2omsext("featurexml")}' '$out' | |
36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS | 33 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
37 && mv '@EXECUTABLE@.ctd' '$ctd_out' | 34 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
38 #end if]]></command> | 35 #end if]]></command> |
39 <configfiles> | 36 <configfiles> |
40 <inputs name="args_json" data_style="paths"/> | 37 <inputs name="args_json" data_style="paths"/> |
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
42 </configfiles> | 39 </configfiles> |
43 <inputs> | 40 <inputs> |
44 <param name="in" argument="-in" type="data" format="featurexml,idxml,mzml" optional="false" label="Input file (see below for details)" help=" select featurexml,idxml,mzml data sets(s)"/> | 41 <param argument="-in" type="data" format="featurexml,idxml,mzml" optional="false" label="Input file (see below for details)" help=" select featurexml,idxml,mzml data sets(s)"/> |
45 <param name="use_peptide_mass" argument="-use_peptide_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help=""/> | 42 <param argument="-use_peptide_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help=""/> |
46 <expand macro="adv_opts_macro"> | 43 <expand macro="adv_opts_macro"> |
47 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 44 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
48 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 45 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
49 <expand macro="list_string_san"/> | 46 <expand macro="list_string_san" name="test"/> |
50 </param> | 47 </param> |
51 </expand> | 48 </expand> |
52 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 49 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
53 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 50 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
54 </param> | 51 </param> |
55 </inputs> | 52 </inputs> |
56 <outputs> | 53 <outputs> |
57 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> | 54 <collection type="list" name="out_prefix" label="${tool.name} on ${on_string}: out_prefix"> |
55 <discover_datasets directory="out_prefix" recurse="true" format="featurexml" pattern="_?(?P<designation>.*)\.[^.]*"/> | |
56 </collection> | |
58 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 57 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
59 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 58 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
60 </data> | 59 </data> |
61 </outputs> | 60 </outputs> |
62 <tests> | 61 <tests><!-- TOPP_SeedListGenerator_1 --> |
63 <expand macro="autotest_SeedListGenerator"/> | 62 <!-- TOPP_SeedListGenerator_2 --> |
64 <expand macro="manutest_SeedListGenerator"/> | 63 <!-- TOPP_SeedListGenerator_3 --> |
65 </tests> | 64 <test expect_num_outputs="2"> |
65 <section name="adv_opts"> | |
66 <param name="test" value="true"/> | |
67 </section> | |
68 <param name="in" value="PepXMLFile_test.mzML"/> | |
69 <output_collection name="out_prefix" count="1"> | |
70 <element name="0" file="SeedListGenerator_1_output_tmp_0.featureXML" ftype="featurexml"/> | |
71 </output_collection> | |
72 <param name="use_peptide_mass" value="false"/> | |
73 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
74 <output name="ctd_out" ftype="xml"> | |
75 <assert_contents> | |
76 <is_valid_xml/> | |
77 </assert_contents> | |
78 </output> | |
79 </test><test expect_num_outputs="2"> | |
80 <section name="adv_opts"> | |
81 <param name="test" value="true"/> | |
82 </section> | |
83 <param name="in" value="IDMapper_1_output.featureXML"/> | |
84 <output_collection name="out_prefix" count="1"> | |
85 <element name="0" file="SeedListGenerator_2_output_tmp_0.featureXML" ftype="featurexml"/> | |
86 </output_collection> | |
87 <param name="use_peptide_mass" value="false"/> | |
88 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
89 <output name="ctd_out" ftype="xml"> | |
90 <assert_contents> | |
91 <is_valid_xml/> | |
92 </assert_contents> | |
93 </output> | |
94 </test><test expect_num_outputs="2"> | |
95 <section name="adv_opts"> | |
96 <param name="test" value="true"/> | |
97 </section> | |
98 <param name="in" value="ConsensusXMLFile_1.consensusXML"/> | |
99 <output_collection name="out_prefix" count="2"> | |
100 <element name="0" file="SeedListGenerator_3_output_tmp_0.featureXML" ftype="featurexml"/> | |
101 <element name="1" file="SeedListGenerator_3_output_tmp_1.featureXML" ftype="featurexml"/> | |
102 </output_collection> | |
103 <param name="use_peptide_mass" value="false"/> | |
104 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
105 <output name="ctd_out" ftype="xml"> | |
106 <assert_contents> | |
107 <is_valid_xml/> | |
108 </assert_contents> | |
109 </output> | |
110 </test> | |
111 </tests> | |
66 <help><![CDATA[Generates seed lists for feature detection. | 112 <help><![CDATA[Generates seed lists for feature detection. |
67 | 113 |
68 | 114 |
69 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_SeedListGenerator.html]]></help> | 115 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SeedListGenerator.html]]></help> |
70 <expand macro="references"/> | 116 <expand macro="references"/> |
71 </tool> | 117 </tool> |