Mercurial > repos > galaxyp > openms_gnpsexport

comparison GNPSExport.xml @ 0:22885d201eb8 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 13:01:50 +0000
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children 2dabae2814df
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-1:000000000000 0:22885d201eb8
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: []-->
4 <tool id="GNPSExport" name="GNPSExport" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Tool to export consensus features into MGF format</description>
6 <macros>
7 <token name="@EXECUTABLE@">GNPSExport</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_cm &&
20 ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
21 mkdir in_mzml &&
22 ${ ' '.join(["ln -s '%s' 'in_mzml/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_mzml if _]) }
23 mkdir out &&
24
25 ## Main program call
26
27 set -o pipefail &&
28 @EXECUTABLE@ -write_ctd ./ &&
29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
31 -in_cm
32 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)'
33 -in_mzml
34 ${' '.join(["'in_mzml/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_mzml if _])}
35 -out
36 'out/output.${gxy2omsext("mgf")}'
37
38 ## Postprocessing
39 && mv 'out/output.${gxy2omsext("mgf")}' '$out'
40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
42 #end if]]></command>
43 <configfiles>
44 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles>
47 <inputs>
48 <param name="in_cm" argument="-in_cm" type="data" format="consensusxml" optional="false" label="input file containing consensus elements with 'peptide' annotations" help=" select consensusxml data sets(s)"/>
49 <param name="in_mzml" argument="-in_mzml" type="data" format="mzml" multiple="true" optional="false" label="original mzml files containing ms/ms spectrum information" help=" select mzml data sets(s)"/>
50 <param name="output_type" argument="-output_type" display="radio" type="select" optional="false" label="specificity of mgf output information" help="">
51 <option value="full_spectra" selected="true">full_spectra</option>
52 <option value="merged_spectra">merged_spectra</option>
53 <expand macro="list_string_san"/>
54 </param>
55 <param name="precursor_mz_tolerance" argument="-precursor_mz_tolerance" type="float" optional="true" value="0.0001" label="Tolerance mz window for precursor selection" help=""/>
56 <param name="precursor_rt_tolerance" argument="-precursor_rt_tolerance" type="float" optional="true" value="5.0" label="Tolerance rt window for precursor selection" help=""/>
57 <section name="merged_spectra" title="Options for exporting mgf file with merged spectra per feature" help="" expanded="false">
58 <param name="cos_similarity" argument="-merged_spectra:cos_similarity" type="float" optional="true" value="0.95" label="Cosine similarity threshold for merged_spectra output" help=""/>
59 </section>
60 <expand macro="adv_opts_macro">
61 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
62 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
63 <expand macro="list_string_san"/>
64 </param>
65 </expand>
66 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
67 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
68 </param>
69 </inputs>
70 <outputs>
71 <data name="out" label="${tool.name} on ${on_string}: out" format="mgf"/>
72 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
73 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
74 </data>
75 </outputs>
76 <tests>
77 <expand macro="autotest_GNPSExport"/>
78 <expand macro="manutest_GNPSExport"/>
79 </tests>
80 <help><![CDATA[Tool to export consensus features into MGF format
81
82 ]]></help>
83 <expand macro="references"/>
84 </tool>