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comparison SeedListGenerator.xml @ 3:bff2e0548994 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:53:30 +0000
parents b7c51c9a8fa2
children f840d8e8099a
comparison
equal deleted inserted replaced
2:b7c51c9a8fa2 3:bff2e0548994
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: [Quantitation]--> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="SeedListGenerator" name="SeedListGenerator" version="2.3.0"> 4 <tool id="SeedListGenerator" name="SeedListGenerator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Generates seed lists for feature detection.</description> 5 <description>Generates seed lists for feature detection.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">SeedListGenerator</token> 7 <token name="@EXECUTABLE@">SeedListGenerator</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[SeedListGenerator 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)' &&
21 mkdir out &&
18 22
19 #if $rep_param_out: 23 ## Main program call
24
25 set -o pipefail &&
26 @EXECUTABLE@ -write_ctd ./ &&
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
29 -in
30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
20 -out 31 -out
21 #for token in $rep_param_out: 32 'out/output.${gxy2omsext("featurexml")}'
22 #if " " in str(token): 33
23 "$token.param_out" 34 ## Postprocessing
24 #else 35 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
25 $token.param_out 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
26 #end if 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
27 #end for 38 #end if]]></command>
28 #end if 39 <configfiles>
29 #if $param_use_peptide_mass: 40 <inputs name="args_json" data_style="paths"/>
30 -use_peptide_mass 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
31 #end if 42 </configfiles>
32 #if $adv_opts.adv_opts_selector=='advanced':
33 #if $adv_opts.param_force:
34 -force
35 #end if
36 #end if
37 ]]></command>
38 <inputs> 43 <inputs>
39 <param name="param_in" type="data" format="mzml,idxml,featurexml,consensusxml" optional="False" label="Input file (see below for details)" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="featurexml,idxml,mzml" optional="false" label="Input file (see below for details)" help=" select featurexml,idxml,mzml data sets(s)"/>
40 <param name="param_use_peptide_mass" display="radio" type="boolean" truevalue="-use_peptide_mass" falsevalue="" checked="false" optional="True" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help="(-use_peptide_mass) "/> 45 <param name="use_peptide_mass" argument="-use_peptide_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help=""/>
41 <expand macro="advanced_options"> 46 <expand macro="adv_opts_macro">
42 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 47 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
48 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
49 <expand macro="list_string_san"/>
50 </param>
43 </expand> 51 </expand>
52 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
53 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
54 </param>
44 </inputs> 55 </inputs>
45 <outputs> 56 <outputs>
46 <data name="param_out" format="featurexml"/> 57 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
58 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
59 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
60 </data>
47 </outputs> 61 </outputs>
48 <help>Generates seed lists for feature detection. 62 <tests>
63 <expand macro="autotest_SeedListGenerator"/>
64 <expand macro="manutest_SeedListGenerator"/>
65 </tests>
66 <help><![CDATA[Generates seed lists for feature detection.
49 67
50 68
51 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_SeedListGenerator.html</help> 69 For more information, visit http://www.openms.de/documentation/TOPP_SeedListGenerator.html]]></help>
70 <expand macro="references"/>
52 </tool> 71 </tool>