Mercurial > repos > galaxyp > openms_openswathdiaprescoring

comparison OpenSwathDIAPreScoring.xml @ 9:e6ba7a995b35 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:25:20 +0000
parents 9bf5470fb0bc
children c99d5004b74f
comparison
equal deleted inserted replaced
8:0bddef8d144e 9:e6ba7a995b35
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: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="2.3.0"> 4 <tool id="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Scoring spectra using the DIA scores.</description> 5 <description>Scoring spectra using the DIA scores.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</token> 7 <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</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[OpenSwathDIAPreScoring 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_tr: 18 ## Preprocessing
16 -tr $param_tr 19 mkdir tr &&
17 #end if 20 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
18 #if $param_out: 21 mkdir swath_files &&
19 -out $param_out 22 ${ ' '.join(["ln -s '%s' 'swath_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _]) }
20 #end if 23 mkdir output_files &&
24
25 ## Main program call
26
27 set -o pipefail &&
28 @EXECUTABLE@ -write_ctd ./ &&
29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
31 -tr
32 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
21 -swath_files 33 -swath_files
22 #for token in $param_swath_files: 34 ${' '.join(["'swath_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $swath_files if _])}
23 $token 35 -output_files
24 #end for 36 ${' '.join(["'output_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("tabular")) for _ in $swath_files if _])}
25 #if $param_min_upper_edge_dist: 37
26 -min_upper_edge_dist $param_min_upper_edge_dist 38 ## Postprocessing
27 #end if 39 ${' '.join(["&& mv -n 'swath_files/%(id)s.%(gext)s' 'output_files/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("tabular")} for _ in $output_files if _])}
28 #if $adv_opts.adv_opts_selector=='advanced': 40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
29 #if $adv_opts.param_force: 41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
30 -force 42 #end if]]></command>
31 #end if 43 <configfiles>
32 #end if 44 <inputs name="args_json" data_style="paths"/>
33 ]]></command> 45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles>
34 <inputs> 47 <inputs>
35 <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/> 48 <param name="tr" argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/>
36 <param name="param_swath_files" type="data" format="mzml" multiple="true" optional="True" size="30" label="Swath files that were used to extract the transitions" help="(-swath_files) If present, SWATH specific scoring will be applied"> 49 <param name="swath_files" argument="-swath_files" type="data" format="mzml" multiple="true" optional="false" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/>
37 <sanitizer> 50 <param name="min_upper_edge_dist" argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help=""/>
38 <valid initial="string.printable"> 51 <expand macro="adv_opts_macro">
39 <remove value="'"/> 52 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
40 <remove value="&quot;"/> 53 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
41 </valid> 54 <expand macro="list_string_san"/>
42 </sanitizer> 55 </param>
56 </expand>
57 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
58 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
43 </param> 59 </param>
44 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help="(-min_upper_edge_dist) "/>
45 <expand macro="advanced_options">
46 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
47 </expand>
48 </inputs> 60 </inputs>
49 <outputs> 61 <outputs>
50 <data name="param_out" format="tabular"/> 62 <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files">
63 <discover_datasets directory="output_files" format="tabular" pattern="__name__"/>
64 </collection>
65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
67 </data>
51 </outputs> 68 </outputs>
52 <help>Scoring spectra using the DIA scores. 69 <tests>
70 <expand macro="autotest_OpenSwathDIAPreScoring"/>
71 <expand macro="manutest_OpenSwathDIAPreScoring"/>
72 </tests>
73 <help><![CDATA[Scoring spectra using the DIA scores.
53 74
54 75
55 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_OpenSwathDIAPreScoring.html</help> 76 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_OpenSwathDIAPreScoring.html]]></help>
77 <expand macro="references"/>
56 </tool> 78 </tool>