Mercurial > repos > galaxyp > openms_triqlerconverter

comparison TriqlerConverter.xml @ 0:fb0ebc6f97f3 draft

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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 19:22:27 +0000
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children f9675543622a
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-1:000000000000 0:fb0ebc6f97f3
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: [Utilities]-->
4 <tool id="TriqlerConverter" name="TriqlerConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Converter to input for Triqler</description>
6 <macros>
7 <token name="@EXECUTABLE@">TriqlerConverter</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="requirements"/>
11 <expand macro="stdio"/>
12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 @EXT_FOO@
14 #import re
15
16 ## Preprocessing
17 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir in_design &&
20 ln -s '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' &&
21 mkdir out &&
22 #if $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"
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])}
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($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' &&
29 #end if
30 #end if
31
32 ## Main program call
33
34 set -o pipefail &&
35 @EXECUTABLE@ -write_ctd ./ &&
36 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
37 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
38 -in
39 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
40 -in_design
41 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)'
42 -out
43 'out/output.${gxy2omsext("csv")}'
44 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
45 -reannotate_filenames
46 #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])}
48 #else
49 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)'
50 #end if
51 #end if
52
53 ## Postprocessing
54 && mv 'out/output.${gxy2omsext("csv")}' '$out'
55 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
56 && mv '@EXECUTABLE@.ctd' '$ctd_out'
57 #end if]]></command>
58 <configfiles>
59 <inputs name="args_json" data_style="paths"/>
60 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
61 </configfiles>
62 <inputs>
63 <param argument="-in" type="data" format="consensusxml" optional="false" 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)"/>
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="">
66 <expand macro="list_string_san" name="Triqler_condition"/>
67 </param>
68 <expand macro="adv_opts_macro">
69 <conditional name="reannotate_filenames_cond">
70 <param name="reannotate_filenames_select" type="select" label="Run tool in batch mode for -reannotate_filenames">
71 <option value="no">No: process all datasets jointly</option>
72 <option value="yes">Yes: process each dataset in an independent job</option>
73 </param>
74 <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)"/>
76 </when>
77 <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)"/>
79 </when>
80 </conditional>
81 <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="">
83 <expand macro="list_string_san" name="test"/>
84 </param>
85 </expand>
86 <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>
88 </param>
89 </inputs>
90 <outputs>
91 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
92 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
93 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
94 </data>
95 </outputs>
96 <tests/>
97 <help><![CDATA[Converter to input for Triqler
98
99
100 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TriqlerConverter.html]]></help>
101 <expand macro="references"/>
102 </tool>