Mercurial > repos > galaxyp > openms_openswathdiaprescoring
comparison OpenSwathDIAPreScoring.xml @ 9:e6ba7a995b35 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author | galaxyp |
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date | Tue, 13 Oct 2020 20:25:20 +0000 |
parents | 9bf5470fb0bc |
children | c99d5004b74f |
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8:0bddef8d144e | 9:e6ba7a995b35 |
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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: [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="""/> | 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> |