Mercurial > repos > galaxyp > openms_idscoreswitcher

comparison IDScoreSwitcher.xml @ 9:ee6cc162893a draft

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 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:11:56 +0000
parents 7bcbee002e9d
children ec0d05b20eed
comparison
equal deleted inserted replaced
8:0e52c85f3b15 9:ee6cc162893a
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="IDScoreSwitcher" name="IDScoreSwitcher" version="2.3.0"> 4 <tool id="IDScoreSwitcher" name="IDScoreSwitcher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Switches between different scores of peptide or protein hits in identification data</description> 5 <description>Switches between different scores of peptide or protein hits in identification data</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IDScoreSwitcher</token> 7 <token name="@EXECUTABLE@">IDScoreSwitcher</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[IDScoreSwitcher 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 &&
19 -out $param_out 22
20 #end if 23 ## Main program call
21 #if $param_new_score: 24
22 -new_score "$param_new_score" 25 set -o pipefail &&
23 #end if 26 @EXECUTABLE@ -write_ctd ./ &&
24 #if $param_new_score_orientation: 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 -new_score_orientation 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 #if " " in str($param_new_score_orientation): 29 -in
27 "$param_new_score_orientation" 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 #else 31 -out
29 $param_new_score_orientation 32 'out/output.${gxy2omsext("idxml")}'
30 #end if 33
31 #end if 34 ## Postprocessing
32 #if $param_new_score_type: 35 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
33 -new_score_type "$param_new_score_type" 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 #end if 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
35 #if $param_old_score: 38 #end if]]></command>
36 -old_score "$param_old_score" 39 <configfiles>
37 #end if 40 <inputs name="args_json" data_style="paths"/>
38 #if $param_proteins: 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
39 -proteins 42 </configfiles>
40 #end if
41 #if $adv_opts.adv_opts_selector=='advanced':
42 #if $adv_opts.param_force:
43 -force
44 #end if
45 #end if
46 ]]></command>
47 <inputs> 43 <inputs>
48 <param name="param_in" type="data" format="idxml" optional="False" label="Input file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/>
49 <param name="param_new_score" type="text" size="30" label="Name of the meta value to use as the new score" help="(-new_score) "> 45 <param name="new_score" argument="-new_score" type="text" optional="false" value="" label="Name of the meta value to use as the new score" help="">
50 <sanitizer> 46 <expand macro="list_string_san"/>
51 <valid initial="string.printable">
52 <remove value="'"/>
53 <remove value="&quot;"/>
54 </valid>
55 </sanitizer>
56 </param> 47 </param>
57 <param name="param_new_score_orientation" display="radio" type="select" optional="False" label="Orientation of the new score (are higher or lower values better?)" help="(-new_score_orientation) "> 48 <param name="new_score_orientation" argument="-new_score_orientation" display="radio" type="select" optional="false" label="Orientation of the new score (are higher or lower values better?)" help="">
58 <option value="lower_better">lower_better</option> 49 <option value="lower_better">lower_better</option>
59 <option value="higher_better">higher_better</option> 50 <option value="higher_better">higher_better</option>
51 <expand macro="list_string_san"/>
60 </param> 52 </param>
61 <param name="param_new_score_type" type="text" size="30" label="Name to use as the type of the new score (default: same as 'new_score')" help="(-new_score_type) "> 53 <param name="new_score_type" argument="-new_score_type" type="text" optional="true" value="" label="Name to use as the type of the new score (default: same as 'new_score')" help="">
62 <sanitizer> 54 <expand macro="list_string_san"/>
63 <valid initial="string.printable">
64 <remove value="'"/>
65 <remove value="&quot;"/>
66 </valid>
67 </sanitizer>
68 </param> 55 </param>
69 <param name="param_old_score" type="text" size="30" label="Name to use for the meta value storing the old score (default: old score type)" help="(-old_score) "> 56 <param name="old_score" argument="-old_score" type="text" optional="true" value="" label="Name to use for the meta value storing the old score (default: old score type)" help="">
70 <sanitizer> 57 <expand macro="list_string_san"/>
71 <valid initial="string.printable">
72 <remove value="'"/>
73 <remove value="&quot;"/>
74 </valid>
75 </sanitizer>
76 </param> 58 </param>
77 <param name="param_proteins" display="radio" type="boolean" truevalue="-proteins" falsevalue="" checked="false" optional="True" label="Apply to protein scores instead of PSM scores" help="(-proteins) "/> 59 <param name="proteins" argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/>
78 <expand macro="advanced_options"> 60 <expand macro="adv_opts_macro">
79 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 61 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
62 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
63 <expand macro="list_string_san"/>
64 </param>
80 </expand> 65 </expand>
66 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
67 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
68 </param>
81 </inputs> 69 </inputs>
82 <outputs> 70 <outputs>
83 <data name="param_out" format="idxml"/> 71 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
72 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
73 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
74 </data>
84 </outputs> 75 </outputs>
85 <help>Switches between different scores of peptide or protein hits in identification data 76 <tests>
77 <expand macro="autotest_IDScoreSwitcher"/>
78 <expand macro="manutest_IDScoreSwitcher"/>
79 </tests>
80 <help><![CDATA[Switches between different scores of peptide or protein hits in identification data
86 81
87 82
88 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_IDScoreSwitcher.html</help> 83 For more information, visit http://www.openms.de/documentation/UTILS_IDScoreSwitcher.html]]></help>
84 <expand macro="references"/>
89 </tool> 85 </tool>