Mercurial > repos > galaxyp > openms_databasefilter

comparison DatabaseFilter.xml @ 14:0878a55de9e7 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:17:07 +0000
parents 0c98acedb17a
children 2f7a8b58314e
comparison
equal deleted inserted replaced
13:56c9ad9cdb65 14:0878a55de9e7
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="DatabaseFilter" name="DatabaseFilter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="DatabaseFilter" name="DatabaseFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Filters a protein database (FASTA format) based on identified proteins</description> 5 <description>Filters a protein database (FASTA format) based on identified proteins</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">DatabaseFilter</token> 7 <token name="@EXECUTABLE@">DatabaseFilter</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@
43 <configfiles> 41 <configfiles>
44 <inputs name="args_json" data_style="paths"/> 42 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles> 44 </configfiles>
47 <inputs> 45 <inputs>
48 <param name="in" argument="-in" type="data" format="fasta" optional="false" label="Input FASTA file, containing a database" help=" select fasta data sets(s)"/> 46 <param argument="-in" type="data" format="fasta" optional="false" label="Input FASTA file, containing a database" help=" select fasta data sets(s)"/>
49 <param name="id" argument="-id" type="data" format="idxml,mzid" optional="false" label="Input file containing identified peptides and proteins" help=" select idxml,mzid data sets(s)"/> 47 <param argument="-id" type="data" format="idxml,mzid" optional="false" label="Input file containing identified peptides and proteins" help=" select idxml,mzid data sets(s)"/>
50 <param name="method" argument="-method" display="radio" type="select" optional="false" label="Switch between white-/blacklisting" help=""> 48 <param argument="-method" type="select" optional="true" label="Switch between white-/blacklisting" help="">
51 <option value="whitelist" selected="true">whitelist</option> 49 <option value="whitelist" selected="true">whitelist</option>
52 <option value="blacklist">blacklist</option> 50 <option value="blacklist">blacklist</option>
53 <expand macro="list_string_san"/> 51 <expand macro="list_string_san" name="method"/>
54 </param> 52 </param>
55 <expand macro="adv_opts_macro"> 53 <expand macro="adv_opts_macro">
56 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
57 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 55 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
58 <expand macro="list_string_san"/> 56 <expand macro="list_string_san" name="test"/>
59 </param> 57 </param>
60 </expand> 58 </expand>
61 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
62 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
63 </param> 61 </param>
66 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta"/> 64 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta"/>
67 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
68 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
69 </data> 67 </data>
70 </outputs> 68 </outputs>
71 <tests> 69 <tests><!-- UTILS_DatabaseFilter_1 -->
72 <expand macro="autotest_DatabaseFilter"/> 70 <test expect_num_outputs="2">
73 <expand macro="manutest_DatabaseFilter"/> 71 <section name="adv_opts">
72 <param name="force" value="false"/>
73 <param name="test" value="true"/>
74 </section>
75 <param name="in" value="DatabaseFilter_1.fasta"/>
76 <param name="id" value="DatabaseFilter_1.idXML"/>
77 <param name="method" value="whitelist"/>
78 <output name="out" file="DatabaseFilter_1_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
79 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
80 <output name="ctd_out" ftype="xml">
81 <assert_contents>
82 <is_valid_xml/>
83 </assert_contents>
84 </output>
85 </test>
86 <!-- UTILS_DatabaseFilter_2 -->
87 <test expect_num_outputs="2">
88 <section name="adv_opts">
89 <param name="force" value="false"/>
90 <param name="test" value="true"/>
91 </section>
92 <param name="in" value="DatabaseFilter_1.fasta"/>
93 <param name="id" value="DatabaseFilter_1.idXML"/>
94 <param name="method" value="blacklist"/>
95 <output name="out" file="DatabaseFilter_2_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
96 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
97 <output name="ctd_out" ftype="xml">
98 <assert_contents>
99 <is_valid_xml/>
100 </assert_contents>
101 </output>
102 </test>
103 <!-- UTILS_DatabaseFilter_3 -->
104 <test expect_num_outputs="2">
105 <section name="adv_opts">
106 <param name="force" value="false"/>
107 <param name="test" value="true"/>
108 </section>
109 <param name="in" value="DatabaseFilter_3.fasta"/>
110 <param name="id" value="DatabaseFilter_3.mzid"/>
111 <param name="method" value="whitelist"/>
112 <output name="out" file="DatabaseFilter_3_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
113 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
114 <output name="ctd_out" ftype="xml">
115 <assert_contents>
116 <is_valid_xml/>
117 </assert_contents>
118 </output>
119 </test>
120 <!-- UTILS_DatabaseFilter_4 -->
121 <test expect_num_outputs="2">
122 <section name="adv_opts">
123 <param name="force" value="false"/>
124 <param name="test" value="true"/>
125 </section>
126 <param name="in" value="DatabaseFilter_3.fasta"/>
127 <param name="id" value="DatabaseFilter_3.mzid"/>
128 <param name="method" value="blacklist"/>
129 <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
130 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
131 <output name="ctd_out" ftype="xml">
132 <assert_contents>
133 <is_valid_xml/>
134 </assert_contents>
135 </output>
136 </test>
74 </tests> 137 </tests>
75 <help><![CDATA[Filters a protein database (FASTA format) based on identified proteins 138 <help><![CDATA[Filters a protein database (FASTA format) based on identified proteins
76 139
77 140
78 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_DatabaseFilter.html]]></help> 141 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_DatabaseFilter.html]]></help>
79 <expand macro="references"/> 142 <expand macro="references"/>
80 </tool> 143 </tool>