Mercurial > repos > galaxyp > openms_phosphoscoring

comparison PhosphoScoring.xml @ 14:af4a55cbf5b6 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:36:07 +0000
parents 996ca7c1d45e
children
comparison
equal deleted inserted replaced
13:996ca7c1d45e 14:af4a55cbf5b6
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.--> 1 <!--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: [ID Processing]--> 2 <!--Proposed Tool Section: [Identification Processing]-->
4 <tool id="PhosphoScoring" name="PhosphoScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="PhosphoScoring" name="PhosphoScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Scores potential phosphorylation sites in order to localize the most probable sites.</description> 4 <description>Scores potential phosphorylation sites in order to localize the most probable sites</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">PhosphoScoring</token> 6 <token name="@EXECUTABLE@">PhosphoScoring</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir id && 18 mkdir id &&
20 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && 19 cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
21 mkdir out && 20 mkdir out &&
22 21
23 ## Main program call 22 ## Main program call
24 23
25 set -o pipefail && 24 set -o pipefail &&
41 <configfiles> 40 <configfiles>
42 <inputs name="args_json" data_style="paths"/> 41 <inputs name="args_json" data_style="paths"/>
43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 42 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
44 </configfiles> 43 </configfiles>
45 <inputs> 44 <inputs>
46 <param argument="-in" type="data" format="mzml" optional="false" label="Input file with MS/MS spectra" help=" select mzml data sets(s)"/> 45 <param argument="-in" type="data" format="mzml" label="Input file with MS/MS spectra" help=" select mzml data sets(s)"/>
47 <param argument="-id" type="data" format="idxml" optional="false" label="Identification input file which contains a search against a concatenated sequence database" help=" select idxml data sets(s)"/> 46 <param argument="-id" type="data" format="idxml" label="Identification input file which contains a search against a concatenated sequence database" help=" select idxml data sets(s)"/>
48 <param argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0" value="0.05" label="Fragment mass tolerance for spectrum comparisons" help=""/> 47 <param argument="-fragment_mass_tolerance" type="float" min="0.0" value="0.05" label="Fragment mass tolerance for spectrum comparisons" help=""/>
49 <param argument="-fragment_mass_unit" type="select" optional="true" label="Unit of fragment mass tolerance" help=""> 48 <param argument="-fragment_mass_unit" type="select" label="Unit of fragment mass tolerance" help="">
50 <option value="Da" selected="true">Da</option> 49 <option value="Da" selected="true">Da</option>
51 <option value="ppm">ppm</option> 50 <option value="ppm">ppm</option>
52 <expand macro="list_string_san" name="fragment_mass_unit"/> 51 <expand macro="list_string_san" name="fragment_mass_unit"/>
53 </param> 52 </param>
54 <expand macro="adv_opts_macro"> 53 <expand macro="adv_opts_macro">
55 <param 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=""/> 54 <param argument="-max_peptide_length" type="integer" min="0" value="40" label="Restrict scoring to peptides with a length no greater than this value ('0' for 'no restriction')" help=""/>
56 <param 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=""/> 55 <param argument="-max_num_perm" type="integer" min="0" value="16384" label="Maximum number of permutations a sequence can have to be processed ('0' for 'no restriction')" help=""/>
57 <param 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'.)"/> 56 <param argument="-unambiguous_score" type="integer" 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'.)"/>
58 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 57 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
59 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 58 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
60 <expand macro="list_string_san" name="test"/> 59 <expand macro="list_string_san" name="test"/>
61 </param> 60 </param>
62 </expand> 61 </expand>
63 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 62 <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> 63 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
68 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 67 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 68 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 69 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
71 </data> 70 </data>
72 </outputs> 71 </outputs>
73 <tests><test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> 72 <tests>
74 <param name="adv_opts|test" value="true"/> 73 <test expect_num_outputs="1">
75 <param name="in" ftype="mzml" value="spectra.mzML"/> 74 <!-- same input as used in the MSGF+Adapter -->
76 <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/> 75 <param name="adv_opts|test" value="true"/>
77 <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/> 76 <param name="in" ftype="mzml" value="spectra.mzML"/>
78 </test> 77 <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/>
79 </tests> 78 <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
79 </test>
80 </tests>
80 <help><![CDATA[Scores potential phosphorylation sites in order to localize the most probable sites. 81 <help><![CDATA[Scores potential phosphorylation sites in order to localize the most probable sites.
81 82
82 83
83 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PhosphoScoring.html]]></help> 84 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PhosphoScoring.html]]></help>
84 <expand macro="references"/> 85 <expand macro="references"/>
85 </tool> 86 </tool>