Mercurial > repos > galaxyp > openms_ffeval
comparison FFEval.xml @ 11:12513e823fd0 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
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date | Wed, 09 Sep 2020 20:08:15 +0000 |
parents | ff14c17ee29c |
children | a02af506fe40 |
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10:fb30da3d8514 | 11:12513e823fd0 |
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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="FFEval" name="FFEval" version="2.3.0"> | 4 <tool id="FFEval" name="FFEval" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Evaluation tool for feature detection algorithms.</description> | 5 <description>Evaluation tool for feature detection algorithms.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">FFEval</token> | 7 <token name="@EXECUTABLE@">FFEval</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[FFEval | 15 @EXT_FOO@ |
16 #import re | |
14 | 17 |
15 #if $param_in: | 18 ## Preprocessing |
16 -in $param_in | 19 mkdir in && |
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && | |
21 mkdir truth && | |
22 ln -s '$truth' 'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)' && | |
23 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
24 mkdir out && | |
17 #end if | 25 #end if |
18 #if $param_truth: | 26 #if $abort_reasons: |
19 -truth $param_truth | 27 mkdir abort_reasons && |
28 ln -s '$abort_reasons' 'abort_reasons/${re.sub("[^\w\-_]", "_", $abort_reasons.element_identifier)}.$gxy2omsext($abort_reasons.ext)' && | |
20 #end if | 29 #end if |
21 #if $param_rt_tol: | 30 #if "out_roc_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
22 -rt_tol $param_rt_tol | 31 mkdir out_roc && |
23 #end if | 32 #end if |
24 #if $param_rt_tol_abs: | 33 |
25 -rt_tol_abs $param_rt_tol_abs | 34 ## Main program call |
35 | |
36 set -o pipefail && | |
37 @EXECUTABLE@ -write_ctd ./ && | |
38 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | |
39 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | |
40 -in | |
41 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' | |
42 -truth | |
43 'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)' | |
44 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
45 -out | |
46 'out/output.${gxy2omsext("featurexml")}' | |
26 #end if | 47 #end if |
27 #if $param_mz_tol: | 48 #if $abort_reasons: |
28 -mz_tol $param_mz_tol | 49 -abort_reasons |
50 'abort_reasons/${re.sub("[^\w\-_]", "_", $abort_reasons.element_identifier)}.$gxy2omsext($abort_reasons.ext)' | |
29 #end if | 51 #end if |
30 #if $param_out: | 52 #if "out_roc_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
31 -out $param_out | 53 -out_roc |
54 'out_roc/output.${gxy2omsext("csv")}' | |
32 #end if | 55 #end if |
33 #if $param_abort_reasons: | 56 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 |
34 -abort_reasons $param_abort_reasons | 57 | tee '$stdout' |
35 #end if | 58 #end if |
36 #if $param_out_roc: | 59 |
37 -out_roc $param_out_roc | 60 ## Postprocessing |
61 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
62 && mv 'out/output.${gxy2omsext("featurexml")}' '$out' | |
38 #end if | 63 #end if |
39 #if $adv_opts.adv_opts_selector=='advanced': | 64 #if "out_roc_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
40 #if $adv_opts.param_force: | 65 && mv 'out_roc/output.${gxy2omsext("csv")}' '$out_roc' |
41 -force | |
42 #end if | 66 #end if |
43 #end if | 67 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
44 ]]></command> | 68 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
69 #end if]]></command> | |
70 <configfiles> | |
71 <inputs name="args_json" data_style="paths"/> | |
72 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | |
73 </configfiles> | |
45 <inputs> | 74 <inputs> |
46 <param name="param_in" type="data" format="featurexml" optional="False" label="Feature input file, which contains the data to be tested against the truth file" help="(-in) "/> | 75 <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Feature input file, which contains the data to be tested against the truth file" help=" select featurexml data sets(s)"/> |
47 <param name="param_truth" type="data" format="featurexml" optional="False" label="Truth feature file that defines what features should be found" help="(-truth) "/> | 76 <param name="truth" argument="-truth" type="data" format="featurexml" optional="false" label="Truth feature file that defines what features should be found" help=" select featurexml data sets(s)"/> |
48 <param name="param_rt_tol" type="float" min="0.0" optional="True" value="0.3" label="Allowed tolerance of RT relative to average feature RT span" help="(-rt_tol) "/> | 77 <param name="rt_tol" argument="-rt_tol" type="float" optional="true" min="0.0" value="0.3" label="Allowed tolerance of RT relative to average feature RT span" help=""/> |
49 <param name="param_rt_tol_abs" type="float" min="-1.0" optional="True" value="-1.0" label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)" help="(-rt_tol_abs) "/> | 78 <param name="rt_tol_abs" argument="-rt_tol_abs" type="float" optional="true" min="-1.0" value="-1.0" label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)" help=""/> |
50 <param name="param_mz_tol" type="float" min="0.0" optional="True" value="0.25" label="Allowed tolerance in m/z (is divided by charge)" help="(-mz_tol) "/> | 79 <param name="mz_tol" argument="-mz_tol" type="float" optional="true" min="0.0" value="0.25" label="Allowed tolerance in m/z (is divided by charge)" help=""/> |
51 <param name="param_abort_reasons" type="data" format="featurexml" optional="True" label="Feature file containing seeds with abort reasons" help="(-abort_reasons) "/> | 80 <param name="abort_reasons" argument="-abort_reasons" type="data" format="featurexml" optional="true" label="Feature file containing seeds with abort reasons" help=" select featurexml data sets(s)"/> |
52 <expand macro="advanced_options"> | 81 <expand macro="adv_opts_macro"> |
53 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | 82 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> |
83 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | |
84 <expand macro="list_string_san"/> | |
85 </param> | |
54 </expand> | 86 </expand> |
87 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> | |
88 <option value="out_FLAG">out (Enables the test mode (needed for internal use only))</option> | |
89 <option value="out_roc_FLAG">out_roc (Enables the test mode (needed for internal use only))</option> | |
90 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
91 </param> | |
55 </inputs> | 92 </inputs> |
56 <outputs> | 93 <outputs> |
57 <data name="param_out" format="featurexml"/> | 94 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"> |
58 <data name="param_out_roc" format="tabular"/> | 95 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter> |
96 </data> | |
97 <data name="out_roc" label="${tool.name} on ${on_string}: out_roc" format="csv"> | |
98 <filter>OPTIONAL_OUTPUTS is not None and "out_roc_FLAG" in OPTIONAL_OUTPUTS</filter> | |
99 </data> | |
100 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> | |
101 <filter>OPTIONAL_OUTPUTS is None</filter> | |
102 </data> | |
103 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
104 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
105 </data> | |
59 </outputs> | 106 </outputs> |
60 <help>Evaluation tool for feature detection algorithms. | 107 <tests> |
108 <expand macro="autotest_FFEval"/> | |
109 <expand macro="manutest_FFEval"/> | |
110 </tests> | |
111 <help><![CDATA[Evaluation tool for feature detection algorithms. | |
61 | 112 |
62 | 113 |
63 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_FFEval.html</help> | 114 For more information, visit http://www.openms.de/documentation/UTILS_FFEval.html]]></help> |
115 <expand macro="references"/> | |
64 </tool> | 116 </tool> |