Mercurial > repos > galaxyp > openms_labeledeval
annotate LabeledEval.xml @ 16:a501c0193c9c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author | galaxyp |
---|---|
date | Tue, 13 Oct 2020 19:15:40 +0000 |
parents | 785f5e8022a4 |
children |
rev | line source |
---|---|
0
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
1 <?xml version='1.0' encoding='UTF-8'?> |
13
81b5149b41a9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
parents:
6
diff
changeset
|
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
0
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
3 <!--Proposed Tool Section: [Utilities]--> |
14
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
4 <tool id="LabeledEval" name="LabeledEval" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
0
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
5 <description> Evaluation tool for isotope-labeled quantitation experiments.</description> |
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
6 <macros> |
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
7 <token name="@EXECUTABLE@">LabeledEval</token> |
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
8 <import>macros.xml</import> |
14
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
9 <import>macros_autotest.xml</import> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
10 <import>macros_test.xml</import> |
0
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
11 </macros> |
14
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
12 <expand macro="requirements"/> |
0
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
13 <expand macro="stdio"/> |
14
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
15 @EXT_FOO@ |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
16 #import re |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
17 |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
18 ## Preprocessing |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
19 mkdir in && |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
21 mkdir truth && |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
22 ln -s '$truth' 'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)' && |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
23 |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
24 ## Main program call |
0
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
25 |
14
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
26 set -o pipefail && |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
27 @EXECUTABLE@ -write_ctd ./ && |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
28 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
29 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
30 -in |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
31 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
32 -truth |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
33 'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)' |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
34 | tee '$stdout' |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
35 |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
36 ## Postprocessing |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
37 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
38 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
39 #end if]]></command> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
40 <configfiles> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
41 <inputs name="args_json" data_style="paths"/> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
42 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
43 </configfiles> |
0
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
44 <inputs> |
14
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
45 <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Feature result file" help=" select featurexml data sets(s)"/> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
46 <param name="truth" argument="-truth" type="data" format="consensusxml" optional="false" label="Expected result file" help=" select consensusxml data sets(s)"/> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
47 <param name="rt_tol" argument="-rt_tol" type="float" optional="true" value="20.0" label="Maximum allowed retention time deviation" help=""/> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
48 <param name="mz_tol" argument="-mz_tol" type="float" optional="true" value="0.25" label="Maximum allowed m/z deviation (divided by charge)" help=""/> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
49 <expand macro="adv_opts_macro"> |
16
a501c0193c9c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents:
14
diff
changeset
|
50 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
14
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
51 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
52 <expand macro="list_string_san"/> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
53 </param> |
0
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
54 </expand> |
16
a501c0193c9c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents:
14
diff
changeset
|
55 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
14
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
56 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
57 </param> |
0
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
58 </inputs> |
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
59 <outputs> |
14
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
60 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
61 <filter>OPTIONAL_OUTPUTS is None</filter> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
62 </data> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
63 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
64 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
65 </data> |
0
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
66 </outputs> |
14
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
67 <tests> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
68 <expand macro="autotest_LabeledEval"/> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
69 <expand macro="manutest_LabeledEval"/> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
70 </tests> |
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
71 <help><![CDATA[ Evaluation tool for isotope-labeled quantitation experiments. |
0
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
72 |
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
73 |
16
a501c0193c9c
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents:
14
diff
changeset
|
74 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_LabeledEval.html]]></help> |
14
785f5e8022a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
13
diff
changeset
|
75 <expand macro="references"/> |
0
426f8f977c0a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
76 </tool> |