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comparison MaRaClusterAdapter.xml @ 4:f7195ee7e18d draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:14:16 +0000
parents 2be8c63444db
children
comparison
equal deleted inserted replaced
3:56d5a3b741f6 4:f7195ee7e18d
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="MaRaClusterAdapter" name="MaRaClusterAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="MaRaClusterAdapter" name="MaRaClusterAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Facilitate input to MaRaCluster and reintegrate.</description> 5 <description>Facilitate input to MaRaCluster and reintegrate.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MaRaClusterAdapter</token> 7 <token name="@EXECUTABLE@">MaRaClusterAdapter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
16 #import re 14 #import re
17 15
18 ## Preprocessing 16 ## Preprocessing
19 mkdir in && 17 mkdir in_cond.in &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } 18 #if $in_cond.in_select == "no"
21 #if $id_in: 19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
22 mkdir id_in && 20 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
23 ${ ' '.join(["ln -s '%s' 'id_in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _]) } 21 #else
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
23 #end if
24 #if $id_in_cond.id_in:
25 mkdir id_in_cond.id_in &&
26 #if $id_in_cond.id_in_select == "no"
27 mkdir ${' '.join(["'id_in_cond.id_in/%s'" % (i) for i, f in enumerate($id_in_cond.id_in) if f])} &&
28 ${' '.join(["ln -s '%s' 'id_in_cond.id_in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
29 #else
30 ln -s '$id_in_cond.id_in' 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)' &&
31 #end if
24 #end if 32 #end if
25 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 33 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
26 mkdir out && 34 mkdir out &&
27 #end if 35 #end if
28 36
31 set -o pipefail && 39 set -o pipefail &&
32 @EXECUTABLE@ -write_ctd ./ && 40 @EXECUTABLE@ -write_ctd ./ &&
33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 41 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 42 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
35 -in 43 -in
36 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 44 #if $in_cond.in_select == "no"
37 #if $id_in: 45 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
46 #else
47 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
48 #end if
49 #if $id_in_cond.id_in:
38 -id_in 50 -id_in
39 ${' '.join(["'id_in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])} 51 #if $id_in_cond.id_in_select == "no"
52 ${' '.join(["'id_in_cond.id_in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
53 #else
54 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)'
55 #end if
40 #end if 56 #end if
41 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 57 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
42 -out 58 -out
43 'out/output.${gxy2omsext("idxml")}' 59 'out/output.${gxy2omsext("idxml")}'
44 #end if 60 #end if
56 <configfiles> 72 <configfiles>
57 <inputs name="args_json" data_style="paths"/> 73 <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> 74 <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> 75 </configfiles>
60 <inputs> 76 <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)"/> 77 <conditional name="in_cond">
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)"/> 78 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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"/> 79 <option value="no">No: process all datasets jointly</option>
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=""/> 80 <option value="yes">Yes: process each dataset in an independent job</option>
81 </param>
82 <when value="no">
83 <param argument="-in" type="data" format="mgf,mzml" multiple="true" optional="false" label="Input file(s)" help=" select mgf,mzml data sets(s)"/>
84 </when>
85 <when value="yes">
86 <param argument="-in" type="data" format="mgf,mzml" multiple="false" optional="false" label="Input file(s)" help=" select mgf,mzml data sets(s)"/>
87 </when>
88 </conditional>
89 <conditional name="id_in_cond">
90 <param name="id_in_select" type="select" label="Run tool in batch mode for -id_in">
91 <option value="no">No: process all datasets jointly</option>
92 <option value="yes">Yes: process each dataset in an independent job</option>
93 </param>
94 <when value="no">
95 <param 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)"/>
96 </when>
97 <when value="yes">
98 <param argument="-id_in" type="data" format="idxml" multiple="false" 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)"/>
99 </when>
100 </conditional>
101 <param 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"/>
102 <param 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"> 103 <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=""/> 104 <param 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=""/> 105 <param 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=""> 106 <param argument="-precursor_tolerance_units" type="select" optional="true" label="tolerance_mass_units 0=ppm, 1=Da" help="">
69 <option value="ppm" selected="true">ppm</option> 107 <option value="ppm" selected="true">ppm</option>
70 <option value="Da">Da</option> 108 <option value="Da">Da</option>
71 <expand macro="list_string_san"/> 109 <expand macro="list_string_san" name="precursor_tolerance_units"/>
72 </param> 110 </param>
73 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 111 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides 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=""> 112 <param 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"/> 113 <expand macro="list_string_san" name="test"/>
76 </param> 114 </param>
77 </expand> 115 </expand>
78 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 116 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
79 <option value="out_FLAG">out (Output file in idXML format)</option> 117 <option value="out_FLAG">out (Output file in idXML format)</option>
80 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 118 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
89 </data> 127 </data>
90 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 128 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
91 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 129 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
92 </data> 130 </data>
93 </outputs> 131 </outputs>
94 <tests> 132 <tests><!-- TOPP_MaRaClusterAdapter_2 -->
95 <expand macro="autotest_MaRaClusterAdapter"/>
96 <expand macro="manutest_MaRaClusterAdapter"/>
97 </tests> 133 </tests>
98 <help><![CDATA[Facilitate input to MaRaCluster and reintegrate. 134 <help><![CDATA[Facilitate input to MaRaCluster and reintegrate.
99 135
100 136
101 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MaRaClusterAdapter.html]]></help> 137 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MaRaClusterAdapter.html]]></help>
102 <expand macro="references"/> 138 <expand macro="references"/>
103 </tool> 139 </tool>