Mercurial > repos > galaxyp > openms_maraclusteradapter

comparison MaRaClusterAdapter.xml @ 0:c1f58afbc706 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:17:43 +0000
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children 2be8c63444db
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-1:000000000000 0:c1f58afbc706
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: [ID Processing]-->
4 <tool id="MaRaClusterAdapter" name="MaRaClusterAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Facilitate input to MaRaCluster and reintegrate.</description>
6 <macros>
7 <token name="@EXECUTABLE@">MaRaClusterAdapter</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 &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
21 #if $id_in:
22 mkdir id_in &&
23 ${ ' '.join(["ln -s '%s' 'id_in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _]) }
24 #end if
25 #if "out_FLAG" in str($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
36 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
37 #if $id_in:
38 -id_in
39 ${' '.join(["'id_in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])}
40 #end if
41 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
42 -out
43 'out/output.${gxy2omsext("idxml")}'
44 #end if
45 #if len(str($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.${gxy2omsext("idxml")}' '$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[{"maracluster_executable": "/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
59 </configfiles>
60 <inputs>
61 <param name="in" argument="-in" type="data" format="mgf,mzml" multiple="true" optional="false" label="Input file(s)" help=" select mgf,mzml data sets(s)"/>
62 <param name="id_in" argument="-id_in" type="data" format="idxml" multiple="true" optional="true" label="Optional idXML Input file(s) in the same order as mzML files - for Maracluster Cluster annotation" help=" select idxml data sets(s)"/>
63 <param name="pcut" argument="-pcut" type="float" optional="true" max="0.0" value="-10.0" label="log(p-value) cutoff, has to be &lt; 0.0" help="Default: -10.0"/>
64 <param name="min_cluster_size" argument="-min_cluster_size" type="integer" optional="true" min="1" value="1" label="minimum number of spectra in a cluster for consensus spectra" help=""/>
65 <expand macro="adv_opts_macro">
66 <param name="verbose" argument="-verbose" type="integer" optional="true" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help=""/>
67 <param name="precursor_tolerance" argument="-precursor_tolerance" type="float" optional="true" value="20.0" label="Precursor monoisotopic mass tolerance" help=""/>
68 <param name="precursor_tolerance_units" argument="-precursor_tolerance_units" display="radio" type="select" optional="false" label="tolerance_mass_units 0=ppm, 1=Da" help="">
69 <option value="ppm" selected="true">ppm</option>
70 <option value="Da">Da</option>
71 <expand macro="list_string_san"/>
72 </param>
73 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
74 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
75 <expand macro="list_string_san"/>
76 </param>
77 </expand>
78 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
79 <option value="out_FLAG">out (Enables the test mode (needed for internal use only))</option>
80 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
81 </param>
82 </inputs>
83 <outputs>
84 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">
85 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
86 </data>
87 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
88 <filter>OPTIONAL_OUTPUTS is None</filter>
89 </data>
90 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
91 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
92 </data>
93 </outputs>
94 <tests>
95 <expand macro="autotest_MaRaClusterAdapter"/>
96 <expand macro="manutest_MaRaClusterAdapter"/>
97 </tests>
98 <help><![CDATA[Facilitate input to MaRaCluster and reintegrate.
99
100
101 For more information, visit http://www.openms.de/documentation/TOPP_MaRaClusterAdapter.html]]></help>
102 <expand macro="references"/>
103 </tool>