Mercurial > repos > galaxyp > openms_idripper

comparison IDRipper.xml @ 9:b50cc9d1d1a9 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:19:09 +0000
parents 66abff058095
children b017e7bd2316
comparison
equal deleted inserted replaced
8:f6e7b89f7b94 9:b50cc9d1d1a9
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: [File Handling]--> 3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="IDRipper" name="IDRipper" version="2.3.0"> 4 <tool id="IDRipper" name="IDRipper" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Split protein/peptide identification file into several files according to annotated file origin.</description> 5 <description>Split protein/peptide identification file into several files according to annotated file origin.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IDRipper</token> 7 <token name="@EXECUTABLE@">IDRipper</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[IDRipper 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_out: 21 mkdir out_path &&
19 -out $param_out 22
20 #end if 23 ## Main program call
21 #if $param_out_path: 24
22 -out_path "$param_out_path" 25 set -o pipefail &&
23 #end if 26 @EXECUTABLE@ -write_ctd ./ &&
24 #if $adv_opts.adv_opts_selector=='advanced': 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 #if $adv_opts.param_force: 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 -force 29 -in
27 #end if 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 #end if 31 -out_path
29 ]]></command> 32 out_path/
33
34 ## Postprocessing
35 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
36 && mv '@EXECUTABLE@.ctd' '$ctd_out'
37 #end if]]></command>
38 <configfiles>
39 <inputs name="args_json" data_style="paths"/>
40 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
41 </configfiles>
30 <inputs> 42 <inputs>
31 <param name="param_in" type="data" format="idxml" optional="False" label="Input file, in which the protein/peptide identifications must be tagged with 'file_origin'" help="(-in) "/> 43 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input file, in which the protein/peptide identifications must be tagged with 'file_origin'" help=" select idxml data sets(s)"/>
32 <param name="param_out_path" type="text" size="30" label="Directory for the output files after ripping according to 'file_origin'" help="(-out_path) If 'out_path' is set, 'out' is ignored"> 44 <expand macro="adv_opts_macro">
33 <sanitizer> 45 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
34 <valid initial="string.printable"> 46 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
35 <remove value="'"/> 47 <expand macro="list_string_san"/>
36 <remove value="&quot;"/> 48 </param>
37 </valid> 49 </expand>
38 </sanitizer> 50 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
51 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
39 </param> 52 </param>
40 <expand macro="advanced_options">
41 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
42 </expand>
43 </inputs> 53 </inputs>
44 <outputs> 54 <outputs>
45 <data name="param_out" format="idxml"/> 55 <collection type="list" name="out_path" label="${tool.name} on ${on_string}: out_path">
56 <discover_datasets directory="out_path" format="idxml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
57 </collection>
58 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
59 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
60 </data>
46 </outputs> 61 </outputs>
47 <help>Split protein/peptide identification file into several files according to annotated file origin. 62 <tests>
63 <expand macro="autotest_IDRipper"/>
64 <expand macro="manutest_IDRipper"/>
65 </tests>
66 <help><![CDATA[Split protein/peptide identification file into several files according to annotated file origin.
48 67
49 68
50 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_IDRipper.html</help> 69 For more information, visit http://www.openms.de/documentation/TOPP_IDRipper.html]]></help>
70 <expand macro="references"/>
51 </tool> 71 </tool>