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comparison DatabaseFilter.xml @ 10:d589c931720d draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:16:22 +0000
parents 27b22fc937b8
children 0c98acedb17a
comparison
equal deleted inserted replaced
9:9a03d0e71155 10:d589c931720d
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="2.3.0"> 4 <tool id="DatabaseFilter" name="DatabaseFilter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[DatabaseFilter 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_id: 21 mkdir id &&
19 -id $param_id 22 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
20 #end if 23 mkdir out &&
21 #if $param_method: 24
22 -method 25 ## Main program call
23 #if " " in str($param_method): 26
24 "$param_method" 27 set -o pipefail &&
25 #else 28 @EXECUTABLE@ -write_ctd ./ &&
26 $param_method 29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
27 #end if 30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
28 #end if 31 -in
29 #if $param_out: 32 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
30 -out $param_out 33 -id
31 #end if 34 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
32 #if $adv_opts.adv_opts_selector=='advanced': 35 -out
33 #if $adv_opts.param_force: 36 'out/output.${gxy2omsext("fasta")}'
34 -force 37
35 #end if 38 ## Postprocessing
36 #end if 39 && mv 'out/output.${gxy2omsext("fasta")}' '$out'
37 ]]></command> 40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
42 #end if]]></command>
43 <configfiles>
44 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles>
38 <inputs> 47 <inputs>
39 <param name="param_in" type="data" format="fasta" optional="False" label="Input FASTA file, containing a database" help="(-in) "/> 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)"/>
40 <param name="param_id" type="data" format="idxml,mzid" optional="False" label="Input file containing identified peptides and proteins" help="(-id) "/> 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)"/>
41 <param name="param_method" display="radio" type="select" optional="False" value="whitelist" label="Switch between white-/blacklisting" help="(-method) "> 50 <param name="method" argument="-method" display="radio" type="select" optional="false" label="Switch between white-/blacklisting" help="">
42 <option value="whitelist" selected="true">whitelist</option> 51 <option value="whitelist" selected="true">whitelist</option>
43 <option value="blacklist">blacklist</option> 52 <option value="blacklist">blacklist</option>
53 <expand macro="list_string_san"/>
44 </param> 54 </param>
45 <expand macro="advanced_options"> 55 <expand macro="adv_opts_macro">
46 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 56 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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="">
58 <expand macro="list_string_san"/>
59 </param>
47 </expand> 60 </expand>
61 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
62 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
63 </param>
48 </inputs> 64 </inputs>
49 <outputs> 65 <outputs>
50 <data name="param_out" format="fasta"/> 66 <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">
68 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
69 </data>
51 </outputs> 70 </outputs>
52 <help>Filters a protein database (FASTA format) based on identified proteins 71 <tests>
72 <expand macro="autotest_DatabaseFilter"/>
73 <expand macro="manutest_DatabaseFilter"/>
74 </tests>
75 <help><![CDATA[Filters a protein database (FASTA format) based on identified proteins
53 76
54 77
55 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_DatabaseFilter.html</help> 78 For more information, visit http://www.openms.de/documentation/UTILS_DatabaseFilter.html]]></help>
79 <expand macro="references"/>
56 </tool> 80 </tool>