Mercurial > repos > galaxyp > openms_rtevaluation
comparison RTEvaluation.xml @ 11:b08e0ac606a4 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 20:01:20 +0000 |
parents | 0cf2a9047a17 |
children | 062fcf33f18d |
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10:ece8b8f33a60 | 11:b08e0ac606a4 |
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35 #if $sequences_file: | 35 #if $sequences_file: |
36 -sequences_file | 36 -sequences_file |
37 'sequences_file/${re.sub("[^\w\-_]", "_", $sequences_file.element_identifier)}.$gxy2omsext($sequences_file.ext)' | 37 'sequences_file/${re.sub("[^\w\-_]", "_", $sequences_file.element_identifier)}.$gxy2omsext($sequences_file.ext)' |
38 #end if | 38 #end if |
39 -out | 39 -out |
40 'out/output.${gxy2omsext("csv")}' | 40 'out/output.${gxy2omsext("tabular")}' |
41 | 41 |
42 ## Postprocessing | 42 ## Postprocessing |
43 && mv 'out/output.${gxy2omsext("csv")}' '$out' | 43 && mv 'out/output.${gxy2omsext("tabular")}' '$out' |
44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS | 44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
45 && mv '@EXECUTABLE@.ctd' '$ctd_out' | 45 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
46 #end if]]></command> | 46 #end if]]></command> |
47 <configfiles> | 47 <configfiles> |
48 <inputs name="args_json" data_style="paths"/> | 48 <inputs name="args_json" data_style="paths"/> |
49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
50 </configfiles> | 50 </configfiles> |
51 <inputs> | 51 <inputs> |
52 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/> | 52 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/> |
53 <param name="sequences_file" argument="-sequences_file" type="data" format="fasta" optional="true" label="Fasta File" help=" select fasta data sets(s)"/> | 53 <param name="sequences_file" argument="-sequences_file" type="data" format="fasta" optional="true" label="Fasta File" help=" select fasta data sets(s)"/> |
54 <param name="latex" argument="-latex" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Indicates whether the output file format of the table should be LaTeX or CSV (default)" help=""/> | 54 <param name="latex" argument="-latex" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Indicates whether the output file format of the table should be LaTeX or TSV (default)" help=""/> |
55 <param name="p_value_dim_1" argument="-p_value_dim_1" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Significance level of first dimension RT filte" help=""/> | 55 <param name="p_value_dim_1" argument="-p_value_dim_1" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Significance level of first dimension RT filte" help=""/> |
56 <param name="p_value_dim_2" argument="-p_value_dim_2" type="float" optional="true" min="0.0" max="1.0" value="0.05" label="Significance level of second dimension RT filte" help=""/> | 56 <param name="p_value_dim_2" argument="-p_value_dim_2" type="float" optional="true" min="0.0" max="1.0" value="0.05" label="Significance level of second dimension RT filte" help=""/> |
57 <expand macro="adv_opts_macro"> | 57 <expand macro="adv_opts_macro"> |
58 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> | 58 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
59 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 59 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
60 <expand macro="list_string_san"/> | 60 <expand macro="list_string_san"/> |
61 </param> | 61 </param> |
62 </expand> | 62 </expand> |
63 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | 63 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
65 </param> | 65 </param> |
66 </inputs> | 66 </inputs> |
67 <outputs> | 67 <outputs> |
68 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/> | 68 <data name="out" label="${tool.name} on ${on_string}: out" format="tabular"/> |
69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
71 </data> | 71 </data> |
72 </outputs> | 72 </outputs> |
73 <tests> | 73 <tests> |
75 <expand macro="manutest_RTEvaluation"/> | 75 <expand macro="manutest_RTEvaluation"/> |
76 </tests> | 76 </tests> |
77 <help><![CDATA[Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs. | 77 <help><![CDATA[Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs. |
78 | 78 |
79 | 79 |
80 For more information, visit http://www.openms.de/documentation/UTILS_RTEvaluation.html]]></help> | 80 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_RTEvaluation.html]]></help> |
81 <expand macro="references"/> | 81 <expand macro="references"/> |
82 </tool> | 82 </tool> |