Mercurial > repos > galaxyp > openms_idrtcalibration
comparison IDRTCalibration.xml @ 10:8bd1fe67a9b1 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 12:48:03 +0000 |
parents | cb8dd15e2a51 |
children | 28805cf9b024 |
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9:fdc8d37ea52c | 10:8bd1fe67a9b1 |
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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: [ID Processing]--> | 3 <!--Proposed Tool Section: [ID Processing]--> |
4 <tool id="IDRTCalibration" name="IDRTCalibration" version="2.3.0"> | 4 <tool id="IDRTCalibration" name="IDRTCalibration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Can be used to calibrate RTs of peptide hits linearly to standards.</description> | 5 <description>Can be used to calibrate RTs of peptide hits linearly to standards.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">IDRTCalibration</token> | 7 <token name="@EXECUTABLE@">IDRTCalibration</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[IDRTCalibration | 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_calibrant_1_reference: | 24 |
22 -calibrant_1_reference $param_calibrant_1_reference | 25 set -o pipefail && |
23 #end if | 26 @EXECUTABLE@ -write_ctd ./ && |
24 #if $param_calibrant_2_reference: | 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
25 -calibrant_2_reference $param_calibrant_2_reference | 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
26 #end if | 29 -in |
27 #if $param_calibrant_1_input: | 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
28 -calibrant_1_input $param_calibrant_1_input | 31 -out |
29 #end if | 32 'out/output.${gxy2omsext("idxml")}' |
30 #if $param_calibrant_2_input: | 33 |
31 -calibrant_2_input $param_calibrant_2_input | 34 ## Postprocessing |
32 #end if | 35 && mv 'out/output.${gxy2omsext("idxml")}' '$out' |
33 #if $adv_opts.adv_opts_selector=='advanced': | 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
34 #if $adv_opts.param_force: | 37 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
35 -force | 38 #end if]]></command> |
36 #end if | 39 <configfiles> |
37 #end if | 40 <inputs name="args_json" data_style="paths"/> |
38 ]]></command> | 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
42 </configfiles> | |
39 <inputs> | 43 <inputs> |
40 <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)"/> |
41 <param name="param_calibrant_1_reference" type="float" value="0.1" label="The RT of the first calibrant in the reference file" help="(-calibrant_1_reference) "/> | 45 <param name="calibrant_1_reference" argument="-calibrant_1_reference" type="float" optional="true" value="0.1" label="The RT of the first calibrant in the reference file" help=""/> |
42 <param name="param_calibrant_2_reference" type="float" value="0.9" label="The RT of the second calibrant in the reference file" help="(-calibrant_2_reference) "/> | 46 <param name="calibrant_2_reference" argument="-calibrant_2_reference" type="float" optional="true" value="0.9" label="The RT of the second calibrant in the reference file" help=""/> |
43 <param name="param_calibrant_1_input" type="float" value="-1.0" label="The RT of the first calibrant in the input file" help="(-calibrant_1_input) Please note that this value needs to be set. The default value -1.0 is not allowed"/> | 47 <param name="calibrant_1_input" argument="-calibrant_1_input" type="float" optional="true" value="-1.0" label="The RT of the first calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/> |
44 <param name="param_calibrant_2_input" type="float" value="-1.0" label="The RT of the second calibrant in the input file" help="(-calibrant_2_input) Please note that this value needs to be set. The default value -1.0 is not allowed"/> | 48 <param name="calibrant_2_input" argument="-calibrant_2_input" type="float" optional="true" value="-1.0" label="The RT of the second calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/> |
45 <expand macro="advanced_options"> | 49 <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) "/> | 50 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> |
51 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | |
52 <expand macro="list_string_san"/> | |
53 </param> | |
47 </expand> | 54 </expand> |
55 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | |
56 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
57 </param> | |
48 </inputs> | 58 </inputs> |
49 <outputs> | 59 <outputs> |
50 <data name="param_out" format="idxml"/> | 60 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> |
61 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
62 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
63 </data> | |
51 </outputs> | 64 </outputs> |
52 <help>Can be used to calibrate RTs of peptide hits linearly to standards. | 65 <tests> |
66 <expand macro="autotest_IDRTCalibration"/> | |
67 <expand macro="manutest_IDRTCalibration"/> | |
68 </tests> | |
69 <help><![CDATA[Can be used to calibrate RTs of peptide hits linearly to standards. | |
53 | 70 |
54 | 71 |
55 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_IDRTCalibration.html</help> | 72 For more information, visit http://www.openms.de/documentation/TOPP_IDRTCalibration.html]]></help> |
73 <expand macro="references"/> | |
56 </tool> | 74 </tool> |