Mercurial > repos > galaxyp > openms_databasefilter

comparison DatabaseFilter.xml @ 15:2f7a8b58314e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:44:52 +0000
parents 0878a55de9e7
children
comparison
equal deleted inserted replaced
14:0878a55de9e7 15:2f7a8b58314e
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: [File Filtering / Extraction / Merging]-->
4 <tool id="DatabaseFilter" name="DatabaseFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Filters a protein database (FASTA format) based on identified proteins</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">DatabaseFilter</token> 6 <token name="@EXECUTABLE@">DatabaseFilter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir id && 18 mkdir id &&
20 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && 19 cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.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="-in" type="data" format="fasta" optional="false" label="Input FASTA file, containing a database" help=" select fasta data sets(s)"/> 45 <param argument="-in" type="data" format="fasta" label="Input FASTA file, containing a database" help=" select fasta 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)"/> 46 <param argument="-id" type="data" format="idxml,mzid" label="Input file containing identified peptides and proteins" help=" select idxml,mzid data sets(s)"/>
48 <param argument="-method" type="select" optional="true" label="Switch between white-/blacklisting" help=""> 47 <param argument="-method" type="select" label="Switch between white-/blacklisting" help="">
49 <option value="whitelist" selected="true">whitelist</option> 48 <option value="whitelist" selected="true">whitelist</option>
50 <option value="blacklist">blacklist</option> 49 <option value="blacklist">blacklist</option>
51 <expand macro="list_string_san" name="method"/> 50 <expand macro="list_string_san" name="method"/>
52 </param> 51 </param>
53 <expand macro="adv_opts_macro"> 52 <expand macro="adv_opts_macro">
54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 53 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
55 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 54 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
56 <expand macro="list_string_san" name="test"/> 55 <expand macro="list_string_san" name="test"/>
57 </param> 56 </param>
58 </expand> 57 </expand>
59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
64 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta"/> 63 <data name="out" label="${tool.name} on ${on_string}: out" format="fasta"/>
65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
67 </data> 66 </data>
68 </outputs> 67 </outputs>
69 <tests><!-- UTILS_DatabaseFilter_1 --> 68 <tests>
69 <!-- TOPP_DatabaseFilter_1 -->
70 <test expect_num_outputs="2"> 70 <test expect_num_outputs="2">
71 <section name="adv_opts"> 71 <section name="adv_opts">
72 <param name="force" value="false"/> 72 <param name="force" value="false"/>
73 <param name="test" value="true"/> 73 <param name="test" value="true"/>
74 </section> 74 </section>
75 <param name="in" value="DatabaseFilter_1.fasta"/> 75 <param name="in" value="DatabaseFilter_1.fasta"/>
76 <param name="id" value="DatabaseFilter_1.idXML"/> 76 <param name="id" value="DatabaseFilter_1.idXML"/>
77 <param name="method" value="whitelist"/> 77 <param name="method" value="whitelist"/>
78 <output name="out" file="DatabaseFilter_1_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> 78 <output name="out" value="DatabaseFilter_1_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
79 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 79 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
80 <output name="ctd_out" ftype="xml"> 80 <output name="ctd_out" ftype="xml">
81 <assert_contents> 81 <assert_contents>
82 <is_valid_xml/> 82 <is_valid_xml/>
83 </assert_contents> 83 </assert_contents>
84 </output> 84 </output>
85 <assert_stdout>
86 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
87 </assert_stdout>
85 </test> 88 </test>
86 <!-- UTILS_DatabaseFilter_2 --> 89 <!-- TOPP_DatabaseFilter_2 -->
87 <test expect_num_outputs="2"> 90 <test expect_num_outputs="2">
88 <section name="adv_opts"> 91 <section name="adv_opts">
89 <param name="force" value="false"/> 92 <param name="force" value="false"/>
90 <param name="test" value="true"/> 93 <param name="test" value="true"/>
91 </section> 94 </section>
92 <param name="in" value="DatabaseFilter_1.fasta"/> 95 <param name="in" value="DatabaseFilter_1.fasta"/>
93 <param name="id" value="DatabaseFilter_1.idXML"/> 96 <param name="id" value="DatabaseFilter_1.idXML"/>
94 <param name="method" value="blacklist"/> 97 <param name="method" value="blacklist"/>
95 <output name="out" file="DatabaseFilter_2_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> 98 <output name="out" value="DatabaseFilter_2_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
96 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 99 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
97 <output name="ctd_out" ftype="xml"> 100 <output name="ctd_out" ftype="xml">
98 <assert_contents> 101 <assert_contents>
99 <is_valid_xml/> 102 <is_valid_xml/>
100 </assert_contents> 103 </assert_contents>
101 </output> 104 </output>
105 <assert_stdout>
106 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
107 </assert_stdout>
102 </test> 108 </test>
103 <!-- UTILS_DatabaseFilter_3 --> 109 <!-- TOPP_DatabaseFilter_3 -->
104 <test expect_num_outputs="2"> 110 <test expect_num_outputs="2">
105 <section name="adv_opts"> 111 <section name="adv_opts">
106 <param name="force" value="false"/> 112 <param name="force" value="false"/>
107 <param name="test" value="true"/> 113 <param name="test" value="true"/>
108 </section> 114 </section>
109 <param name="in" value="DatabaseFilter_3.fasta"/> 115 <param name="in" value="DatabaseFilter_3.fasta"/>
110 <param name="id" value="DatabaseFilter_3.mzid"/> 116 <param name="id" value="DatabaseFilter_3.mzid"/>
111 <param name="method" value="whitelist"/> 117 <param name="method" value="whitelist"/>
112 <output name="out" file="DatabaseFilter_3_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> 118 <output name="out" value="DatabaseFilter_3_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
113 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 119 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
114 <output name="ctd_out" ftype="xml"> 120 <output name="ctd_out" ftype="xml">
115 <assert_contents> 121 <assert_contents>
116 <is_valid_xml/> 122 <is_valid_xml/>
117 </assert_contents> 123 </assert_contents>
118 </output> 124 </output>
125 <assert_stdout>
126 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
127 </assert_stdout>
119 </test> 128 </test>
120 <!-- UTILS_DatabaseFilter_4 --> 129 <!-- TOPP_DatabaseFilter_4 -->
121 <test expect_num_outputs="2"> 130 <test expect_num_outputs="2">
122 <section name="adv_opts"> 131 <section name="adv_opts">
123 <param name="force" value="false"/> 132 <param name="force" value="false"/>
124 <param name="test" value="true"/> 133 <param name="test" value="true"/>
125 </section> 134 </section>
126 <param name="in" value="DatabaseFilter_3.fasta"/> 135 <param name="in" value="DatabaseFilter_3.fasta"/>
127 <param name="id" value="DatabaseFilter_3.mzid"/> 136 <param name="id" value="DatabaseFilter_3.mzid"/>
128 <param name="method" value="blacklist"/> 137 <param name="method" value="blacklist"/>
129 <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/> 138 <output name="out" value="DatabaseFilter_4_out.fasta" compare="sim_size" delta_frac="0.7" ftype="fasta"/>
130 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 139 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
131 <output name="ctd_out" ftype="xml"> 140 <output name="ctd_out" ftype="xml">
132 <assert_contents> 141 <assert_contents>
133 <is_valid_xml/> 142 <is_valid_xml/>
134 </assert_contents> 143 </assert_contents>
135 </output> 144 </output>
145 <assert_stdout>
146 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
147 </assert_stdout>
136 </test> 148 </test>
137 </tests> 149 </tests>
138 <help><![CDATA[Filters a protein database (FASTA format) based on identified proteins 150 <help><![CDATA[Filters a protein database (FASTA format) based on identified proteins
139 151
140 152
141 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_DatabaseFilter.html]]></help> 153 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DatabaseFilter.html]]></help>
142 <expand macro="references"/> 154 <expand macro="references"/>
143 </tool> 155 </tool>