Mercurial > repos > galaxyp > openms_phosphoscoring

comparison PhosphoScoring.xml @ 9:4c583fde2a28 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 19:45:14 +0000
parents 3392cf4c19bb
children c04ff2777ed2
comparison
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8:8236ebbfc1b9 9:4c583fde2a28
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 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: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="PhosphoScoring" name="PhosphoScoring" version="2.3.0"> 4 <tool id="PhosphoScoring" name="PhosphoScoring" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Scores potential phosphorylation sites in order to localize the most probable sites.</description> 5 <description>Scores potential phosphorylation sites in order to localize the most probable sites.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">PhosphoScoring</token> 7 <token name="@EXECUTABLE@">PhosphoScoring</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[PhosphoScoring 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_id: 21 mkdir id &&
19 -id $param_id 22 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
20 #end if 23 mkdir out &&
21 #if $param_out: 24
22 -out $param_out 25 ## Main program call
23 #end if 26
24 #if $param_fragment_mass_tolerance: 27 set -o pipefail &&
25 -fragment_mass_tolerance $param_fragment_mass_tolerance 28 @EXECUTABLE@ -write_ctd ./ &&
26 #end if 29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
27 #if $param_fragment_mass_unit: 30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
28 -fragment_mass_unit 31 -in
29 #if " " in str($param_fragment_mass_unit): 32 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
30 "$param_fragment_mass_unit" 33 -id
31 #else 34 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
32 $param_fragment_mass_unit 35 -out
33 #end if 36 'out/output.${gxy2omsext("idxml")}'
34 #end if 37
35 #if $param_max_peptide_length: 38 ## Postprocessing
36 -max_peptide_length $param_max_peptide_length 39 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
37 #end if 40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
38 #if $param_max_num_perm: 41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
39 -max_num_perm $param_max_num_perm 42 #end if]]></command>
40 #end if 43 <configfiles>
41 #if $adv_opts.adv_opts_selector=='advanced': 44 <inputs name="args_json" data_style="paths"/>
42 #if $adv_opts.param_force: 45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
43 -force 46 </configfiles>
44 #end if
45 #end if
46 ]]></command>
47 <inputs> 47 <inputs>
48 <param name="param_in" type="data" format="mzml" optional="False" label="Input file with MS/MS spectra" help="(-in) "/> 48 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file with MS/MS spectra" help=" select mzml data sets(s)"/>
49 <param name="param_id" type="data" format="idxml" optional="False" label="Identification input file which contains a search against a concatenated sequence database" help="(-id) "/> 49 <param name="id" 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)"/>
50 <param name="param_fragment_mass_tolerance" type="float" value="0.05" label="Fragment mass erro" help="(-fragment_mass_tolerance) "/> 50 <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0" value="0.05" label="Fragment mass tolerance for spectrum comparisons" help=""/>
51 <param name="param_fragment_mass_unit" display="radio" type="select" optional="False" value="Da" label="Unit of fragment mass erro" help="(-fragment_mass_unit) "> 51 <param name="fragment_mass_unit" argument="-fragment_mass_unit" display="radio" type="select" optional="false" label="Unit of fragment mass tolerance" help="">
52 <option value="Da" selected="true">Da</option> 52 <option value="Da" selected="true">Da</option>
53 <option value="ppm">ppm</option> 53 <option value="ppm">ppm</option>
54 <expand macro="list_string_san"/>
54 </param> 55 </param>
55 <param name="param_max_peptide_length" type="integer" min="1" optional="True" value="40" label="Restrict scoring to peptides with a length shorter than this value" help="(-max_peptide_length) "/> 56 <expand macro="adv_opts_macro">
56 <param name="param_max_num_perm" type="integer" min="1" optional="True" value="16384" label="Maximum number of permutations a sequence can have" help="(-max_num_perm) "/> 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 <expand macro="advanced_options"> 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="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 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=""/>
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"/>
63 </param>
59 </expand> 64 </expand>
65 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
66 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
67 </param>
60 </inputs> 68 </inputs>
61 <outputs> 69 <outputs>
62 <data name="param_out" format="idxml"/> 70 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
71 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
72 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
73 </data>
63 </outputs> 74 </outputs>
64 <help>Scores potential phosphorylation sites in order to localize the most probable sites. 75 <tests>
76 <expand macro="autotest_PhosphoScoring"/>
77 <expand macro="manutest_PhosphoScoring"/>
78 </tests>
79 <help><![CDATA[Scores potential phosphorylation sites in order to localize the most probable sites.
65 80
66 81
67 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PhosphoScoring.html</help> 82 For more information, visit http://www.openms.de/documentation/TOPP_PhosphoScoring.html]]></help>
83 <expand macro="references"/>
68 </tool> 84 </tool>