Mercurial > repos > galaxyp > openms_rtevaluation

comparison RTEvaluation.xml @ 11:b08e0ac606a4 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 20:01:20 +0000
parents 0cf2a9047a17
children 062fcf33f18d
comparison
equal deleted inserted replaced
10:ece8b8f33a60 11:b08e0ac606a4
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>