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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:41:43 +0000
parents fb0ebc6f97f3
children
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0:fb0ebc6f97f3 1:f9675543622a
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: [Utilities]--> 2 <!--Proposed Tool Section: [File Converter]-->
4 <tool id="TriqlerConverter" name="TriqlerConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="TriqlerConverter" name="TriqlerConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Converter to input for Triqler</description> 4 <description>Converter to input for Triqler</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">TriqlerConverter</token> 6 <token name="@EXECUTABLE@">TriqlerConverter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
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($in.ext)' &&
19 mkdir in_design && 18 mkdir in_design &&
20 ln -s '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' && 19 cp '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' &&
21 mkdir out && 20 mkdir out &&
21 ## advanced options
22 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames: 22 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
23 mkdir adv_opts.reannotate_filenames_cond.reannotate_filenames && 23 mkdir adv_opts.reannotate_filenames_cond.reannotate_filenames &&
24 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no" 24 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
25 mkdir ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s'" % (i) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} && 25 mkdir ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s'" % (i) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} &&
26 ${' '.join(["ln -s '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} 26 ${' '.join(["cp '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
27 #else 27 #else
28 ln -s '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' && 28 cp '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' &&
29 #end if 29 #end if
30 #end if 30 #end if
31
31 32
32 ## Main program call 33 ## Main program call
33 34
34 set -o pipefail && 35 set -o pipefail &&
35 @EXECUTABLE@ -write_ctd ./ && 36 @EXECUTABLE@ -write_ctd ./ &&
39 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' 40 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
40 -in_design 41 -in_design
41 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' 42 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)'
42 -out 43 -out
43 'out/output.${gxy2omsext("csv")}' 44 'out/output.${gxy2omsext("csv")}'
45 ## advanced options
44 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames: 46 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
45 -reannotate_filenames 47 -reannotate_filenames
46 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no" 48 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
47 ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} 49 ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
48 #else 50 #else
49 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' 51 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)'
50 #end if 52 #end if
51 #end if 53 #end if
54
52 55
53 ## Postprocessing 56 ## Postprocessing
54 && mv 'out/output.${gxy2omsext("csv")}' '$out' 57 && mv 'out/output.${gxy2omsext("csv")}' '$out'
55 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 58 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
56 && mv '@EXECUTABLE@.ctd' '$ctd_out' 59 && mv '@EXECUTABLE@.ctd' '$ctd_out'
58 <configfiles> 61 <configfiles>
59 <inputs name="args_json" data_style="paths"/> 62 <inputs name="args_json" data_style="paths"/>
60 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 63 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
61 </configfiles> 64 </configfiles>
62 <inputs> 65 <inputs>
63 <param argument="-in" type="data" format="consensusxml" optional="false" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/> 66 <param argument="-in" type="data" format="consensusxml" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
64 <param argument="-in_design" type="data" format="tabular" optional="false" label="Experimental Design file" help=" select tabular data sets(s)"/> 67 <param argument="-in_design" type="data" format="tabular" label="Experimental Design file" help=" select tabular data sets(s)"/>
65 <param argument="-Triqler_condition" type="text" optional="true" value="Triqler_Condition" label="Which column in the condition table should be used for Triqler 'Condition'" help=""> 68 <param argument="-Triqler_condition" type="text" value="Triqler_Condition" label="Which column in the condition table should be used for Triqler 'Condition'" help="">
66 <expand macro="list_string_san" name="Triqler_condition"/> 69 <expand macro="list_string_san" name="Triqler_condition"/>
67 </param> 70 </param>
68 <expand macro="adv_opts_macro"> 71 <expand macro="adv_opts_macro">
69 <conditional name="reannotate_filenames_cond"> 72 <conditional name="reannotate_filenames_cond">
70 <param name="reannotate_filenames_select" type="select" label="Run tool in batch mode for -reannotate_filenames"> 73 <param name="reannotate_filenames_select" type="select" label="Run tool in batch mode for -reannotate_filenames">
73 </param> 76 </param>
74 <when value="no"> 77 <when value="no">
75 <param argument="-reannotate_filenames" type="data" format="mzml" multiple="true" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/> 78 <param argument="-reannotate_filenames" type="data" format="mzml" multiple="true" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
76 </when> 79 </when>
77 <when value="yes"> 80 <when value="yes">
78 <param argument="-reannotate_filenames" type="data" format="mzml" multiple="false" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/> 81 <param argument="-reannotate_filenames" type="data" format="mzml" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
79 </when> 82 </when>
80 </conditional> 83 </conditional>
81 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 84 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
82 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 85 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
83 <expand macro="list_string_san" name="test"/> 86 <expand macro="list_string_san" name="test"/>
84 </param> 87 </param>
85 </expand> 88 </expand>
86 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 89 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
87 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 90 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
95 </outputs> 98 </outputs>
96 <tests/> 99 <tests/>
97 <help><![CDATA[Converter to input for Triqler 100 <help><![CDATA[Converter to input for Triqler
98 101
99 102
100 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TriqlerConverter.html]]></help> 103 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TriqlerConverter.html]]></help>
101 <expand macro="references"/> 104 <expand macro="references"/>
102 </tool> 105 </tool>