Mercurial > repos > galaxyp > openms_clustermasstraces

comparison ClusterMassTraces.xml @ 0:8fad84d1a74d 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 20:04:20 +0000
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children 6d513a5aaa36
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-1:000000000000 0:8fad84d1a74d
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="ClusterMassTraces" name="ClusterMassTraces" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Creates pseudo spectra.</description>
6 <macros>
7 <token name="@EXECUTABLE@">ClusterMassTraces</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 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir out &&
22
23 ## Main program call
24
25 set -o pipefail &&
26 @EXECUTABLE@ -write_ctd ./ &&
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
29 -in
30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
31 -out
32 'out/output.${gxy2omsext("mzml")}'
33
34 ## Postprocessing
35 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
38 #end if]]></command>
39 <configfiles>
40 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles>
43 <inputs>
44 <param name="in" argument="-in" type="data" format="consensusxml" optional="false" label="Mass traces" help=" select consensusxml data sets(s)"/>
45 <param name="min_pearson_correlation" argument="-min_pearson_correlation" type="float" optional="true" value="0.7" label="Minimal pearson correlation score" help=""/>
46 <param name="min_peak_nr" argument="-min_peak_nr" type="integer" optional="true" value="1" label="Minimal peak nr to output pseudo spectra" help=""/>
47 <param name="max_lag" argument="-max_lag" type="integer" optional="true" value="1" label="Maximal lag" help=""/>
48 <param name="max_rt_apex_difference" argument="-max_rt_apex_difference" type="float" optional="true" value="5.0" label="Maximal difference of the apex in retention time" help=""/>
49 <param name="max_intensity_cutoff" argument="-max_intensity_cutoff" type="float" optional="true" value="0.0" label="Maximal intensity to be added to a spectrum" help=""/>
50 <param name="add_precursor" argument="-add_precursor" type="float" optional="true" value="0.0" label="Add a precursor mass" help=""/>
51 <expand macro="adv_opts_macro">
52 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
53 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
54 <expand macro="list_string_san"/>
55 </param>
56 </expand>
57 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
58 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
59 </param>
60 </inputs>
61 <outputs>
62 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
63 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
64 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
65 </data>
66 </outputs>
67 <tests>
68 <expand macro="autotest_ClusterMassTraces"/>
69 <expand macro="manutest_ClusterMassTraces"/>
70 </tests>
71 <help><![CDATA[Creates pseudo spectra.
72 ]]></help>
73 <expand macro="references"/>
74 </tool>