Mercurial > repos > galaxyp > openms_idscoreswitcher

comparison IDScoreSwitcher.xml @ 15:eb0bc9c697ee 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 18:55:37 +0000
parents 19145c23a927
children
comparison
equal deleted inserted replaced
14:cecb51784c3a 15:eb0bc9c697ee
40 <inputs name="args_json" data_style="paths"/> 40 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 42 </configfiles>
43 <inputs> 43 <inputs>
44 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/> 44 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/>
45 <param name="new_score" argument="-new_score" type="text" optional="false" value="" label="Name of the meta value to use as the new score" help=""> 45 <param name="proteins" argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/>
46 <param name="new_score" argument="-new_score" type="text" optional="true" value="" label="Name of the meta value to use as the new score" help="">
46 <expand macro="list_string_san"/> 47 <expand macro="list_string_san"/>
47 </param> 48 </param>
48 <param name="new_score_orientation" argument="-new_score_orientation" display="radio" type="select" optional="false" label="Orientation of the new score (are higher or lower values better?)" help=""> 49 <param name="new_score_orientation" argument="-new_score_orientation" display="radio" type="select" optional="true" label="Orientation of the new score (are higher or lower values better?)" help="">
50 <option value="">default (nothing chosen)</option>
49 <option value="lower_better">lower_better</option> 51 <option value="lower_better">lower_better</option>
50 <option value="higher_better">higher_better</option> 52 <option value="higher_better">higher_better</option>
51 <expand macro="list_string_san"/> 53 <expand macro="list_string_san"/>
52 </param> 54 </param>
53 <param name="new_score_type" argument="-new_score_type" type="text" optional="true" value="" label="Name to use as the type of the new score (default: same as 'new_score')" help=""> 55 <param name="new_score_type" argument="-new_score_type" type="text" optional="true" value="" label="Name to use as the type of the new score (default: same as 'new_score')" help="">
54 <expand macro="list_string_san"/> 56 <expand macro="list_string_san"/>
55 </param> 57 </param>
56 <param name="old_score" argument="-old_score" type="text" optional="true" value="" label="Name to use for the meta value storing the old score (default: old score type)" help=""> 58 <param name="old_score" argument="-old_score" type="text" optional="true" value="" label="Name to use for the meta value storing the old score (default: old score type)" help="">
57 <expand macro="list_string_san"/> 59 <expand macro="list_string_san"/>
58 </param> 60 </param>
59 <param name="proteins" argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/>
60 <expand macro="adv_opts_macro"> 61 <expand macro="adv_opts_macro">
61 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 62 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
62 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 63 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
63 <expand macro="list_string_san"/> 64 <expand macro="list_string_san"/>
64 </param> 65 </param>
65 </expand> 66 </expand>
66 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 67 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
67 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 68 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
68 </param> 69 </param>
69 </inputs> 70 </inputs>
70 <outputs> 71 <outputs>
71 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 72 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
78 <expand macro="manutest_IDScoreSwitcher"/> 79 <expand macro="manutest_IDScoreSwitcher"/>
79 </tests> 80 </tests>
80 <help><![CDATA[Switches between different scores of peptide or protein hits in identification data 81 <help><![CDATA[Switches between different scores of peptide or protein hits in identification data
81 82
82 83
83 For more information, visit http://www.openms.de/documentation/UTILS_IDScoreSwitcher.html]]></help> 84 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_IDScoreSwitcher.html]]></help>
84 <expand macro="references"/> 85 <expand macro="references"/>
85 </tool> 86 </tool>