Mercurial > repos > galaxyp > openms_phosphoscoring
comparison PhosphoScoring.xml @ 15:ad6553691b65 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 18:10:56 +0000 |
parents | 0d8d62c95d15 |
children |
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14:2dfb21c1c7b8 | 15:ad6553691b65 |
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55 </param> | 55 </param> |
56 <expand macro="adv_opts_macro"> | 56 <expand macro="adv_opts_macro"> |
57 <param name="max_peptide_length" argument="-max_peptide_length" type="integer" optional="true" min="0" value="40" label="Restrict scoring to peptides with a length no greater than this value ('0' for 'no restriction')" help=""/> | 57 <param name="max_peptide_length" argument="-max_peptide_length" type="integer" optional="true" min="0" value="40" label="Restrict scoring to peptides with a length no greater than this value ('0' for 'no restriction')" help=""/> |
58 <param name="max_num_perm" argument="-max_num_perm" type="integer" optional="true" min="0" value="16384" label="Maximum number of permutations a sequence can have to be processed ('0' for 'no restriction')" help=""/> | 58 <param name="max_num_perm" argument="-max_num_perm" type="integer" optional="true" min="0" value="16384" label="Maximum number of permutations a sequence can have to be processed ('0' for 'no restriction')" help=""/> |
59 <param name="unambiguous_score" argument="-unambiguous_score" type="integer" optional="true" value="1000" label="Score to use for unambiguous assignments, where all sites on a peptide are phosphorylated" help="(Note: If a peptide is not phosphorylated at all, its score is set to '-1'.)"/> | 59 <param name="unambiguous_score" argument="-unambiguous_score" type="integer" optional="true" value="1000" label="Score to use for unambiguous assignments, where all sites on a peptide are phosphorylated" help="(Note: If a peptide is not phosphorylated at all, its score is set to '-1'.)"/> |
60 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> | 60 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
61 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 61 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
62 <expand macro="list_string_san"/> | 62 <expand macro="list_string_san"/> |
63 </param> | 63 </param> |
64 </expand> | 64 </expand> |
65 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | 65 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
66 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 66 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
67 </param> | 67 </param> |
68 </inputs> | 68 </inputs> |
69 <outputs> | 69 <outputs> |
70 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> | 70 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> |
77 <expand macro="manutest_PhosphoScoring"/> | 77 <expand macro="manutest_PhosphoScoring"/> |
78 </tests> | 78 </tests> |
79 <help><![CDATA[Scores potential phosphorylation sites in order to localize the most probable sites. | 79 <help><![CDATA[Scores potential phosphorylation sites in order to localize the most probable sites. |
80 | 80 |
81 | 81 |
82 For more information, visit http://www.openms.de/documentation/TOPP_PhosphoScoring.html]]></help> | 82 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PhosphoScoring.html]]></help> |
83 <expand macro="references"/> | 83 <expand macro="references"/> |
84 </tool> | 84 </tool> |