Mercurial > repos > galaxyp > openms_databasesuitability

comparison DatabaseSuitability.xml @ 0:d994c72a91fc 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 19:54:23 +0000
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children 4890f50ae1a2
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-1:000000000000 0:d994c72a91fc
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.-->
3 <!--Proposed Tool Section: []-->
4 <tool id="DatabaseSuitability" name="DatabaseSuitability" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra.</description>
6 <macros>
7 <token name="@EXECUTABLE@">DatabaseSuitability</token>
8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros>
12 <expand macro="requirements"/>
13 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@
16 #import re
17
18 ## Preprocessing
19 mkdir in_id &&
20 ln -s '$in_id' 'in_id/${re.sub("[^\w\-_]", "_", $in_id.element_identifier)}.$gxy2omsext($in_id.ext)' &&
21 mkdir in_spec &&
22 ln -s '$in_spec' 'in_spec/${re.sub("[^\w\-_]", "_", $in_spec.element_identifier)}.$gxy2omsext($in_spec.ext)' &&
23 mkdir in_novo &&
24 ln -s '$in_novo' 'in_novo/${re.sub("[^\w\-_]", "_", $in_novo.element_identifier)}.$gxy2omsext($in_novo.ext)' &&
25 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
26 mkdir out &&
27 #end if
28
29 ## Main program call
30
31 set -o pipefail &&
32 @EXECUTABLE@ -write_ctd ./ &&
33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
35 -in_id
36 'in_id/${re.sub("[^\w\-_]", "_", $in_id.element_identifier)}.$gxy2omsext($in_id.ext)'
37 -in_spec
38 'in_spec/${re.sub("[^\w\-_]", "_", $in_spec.element_identifier)}.$gxy2omsext($in_spec.ext)'
39 -in_novo
40 'in_novo/${re.sub("[^\w\-_]", "_", $in_novo.element_identifier)}.$gxy2omsext($in_novo.ext)'
41 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
42 -out
43 'out/output.${gxy2omsext("tabular")}'
44 #end if
45 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
46 | tee '$stdout'
47 #end if
48
49 ## Postprocessing
50 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
51 && mv 'out/output.${gxy2omsext("tabular")}' '$out'
52 #end if
53 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
54 && mv '@EXECUTABLE@.ctd' '$ctd_out'
55 #end if]]></command>
56 <configfiles>
57 <inputs name="args_json" data_style="paths"/>
58 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
59 </configfiles>
60 <inputs>
61 <param name="in_id" argument="-in_id" type="data" format="idxml" optional="false" label="Input idXML file from peptide search with combined database with added de novo peptide" help="PeptideIndexer is needed, FDR is forbidden select idxml data sets(s)"/>
62 <param name="in_spec" argument="-in_spec" type="data" format="mzml" optional="false" label="Input MzML file used for the peptide identification" help=" select mzml data sets(s)"/>
63 <param name="in_novo" argument="-in_novo" type="data" format="idxml" optional="false" label="Input idXML file containing de novo peptides (unfiltered)" help=" select idxml data sets(s)"/>
64 <section name="algorithm" title="Parameter section for the suitability calculation algorithm" help="" expanded="false">
65 <param name="no_rerank" argument="-algorithm:no_rerank" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if you want to disable re-ranking" help="Cases, where a de novo peptide scores just higher than the database peptide, are overlooked and counted as a de novo hit. This might underestimate the database quality"/>
66 <param name="reranking_cutoff_percentile" argument="-algorithm:reranking_cutoff_percentile" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Swap a top-scoring deNovo hit with a lower scoring DB hit if their xcorr score difference is in the given percentile of all score differences between the first two decoy hits of a PSM" help="The lower the value the lower the decoy cut-off will be. Therefore it will be harder for a lower scoring DB hit to be re-ranked to the top"/>
67 <param name="FDR" argument="-algorithm:FDR" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Filter peptide hits based on this q-value" help="(e.g., 0.05 = 5 % FDR)"/>
68 </section>
69 <expand macro="adv_opts_macro">
70 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
71 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
72 <expand macro="list_string_san"/>
73 </param>
74 </expand>
75 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
76 <option value="out_FLAG">out (Optional tsv output containing database suitability information as well as spectral quality)</option>
77 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
78 </param>
79 </inputs>
80 <outputs>
81 <data name="out" label="${tool.name} on ${on_string}: out" format="tabular">
82 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
83 </data>
84 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
85 <filter>OPTIONAL_OUTPUTS is None</filter>
86 </data>
87 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
88 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
89 </data>
90 </outputs>
91 <tests>
92 <expand macro="autotest_DatabaseSuitability"/>
93 <expand macro="manutest_DatabaseSuitability"/>
94 </tests>
95 <help><![CDATA[Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra.
96
97 ]]></help>
98 <expand macro="references"/>
99 </tool>