Mercurial > repos > galaxyp > openms_mapstatistics

comparison MapStatistics.xml @ 9:05215884f6d0 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 20:11:20 +0000
parents d44dc4282101
children 9e25560d4ded
comparison
equal deleted inserted replaced
8:93144434098d 9:05215884f6d0
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: [File Handling]--> 3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="MapStatistics" name="MapStatistics" version="2.3.0"> 4 <tool id="MapStatistics" name="MapStatistics" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Extract extended statistics on the features of a map for quality control.</description> 5 <description>Extract extended statistics on the features of a map for quality control.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MapStatistics</token> 7 <token name="@EXECUTABLE@">MapStatistics</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[MapStatistics 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_out: 21 mkdir out &&
19 -out $param_out 22
20 #end if 23 ## Main program call
21 #if $param_n: 24
22 -n $param_n 25 set -o pipefail &&
23 #end if 26 @EXECUTABLE@ -write_ctd ./ &&
24 #if $param_m: 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 -m 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 #end if 29 -in
27 #if $param_p: 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 -p 31 -out
29 #end if 32 'out/output.${gxy2omsext("txt")}'
30 #if $param_s: 33
31 -s 34 ## Postprocessing
32 #end if 35 && mv 'out/output.${gxy2omsext("txt")}' '$out'
33 #if $adv_opts.adv_opts_selector=='advanced': 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 #if $adv_opts.param_force: 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
35 -force 38 #end if]]></command>
36 #end if 39 <configfiles>
37 #end if 40 <inputs name="args_json" data_style="paths"/>
38 ]]></command> 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles>
39 <inputs> 43 <inputs>
40 <param name="param_in" type="data" format="featurexml,consensusxml" optional="False" label="Input file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="Input file" help=" select consensusxml,featurexml data sets(s)"/>
41 <param name="param_n" type="integer" min="1" max="100" optional="True" value="4" label="Report separate statistics for each of n RT slices of the map" help="(-n) "/> 45 <param name="n" argument="-n" type="integer" optional="true" min="1" max="100" value="4" label="Report separate statistics for each of n RT slices of the map" help=""/>
42 <param name="param_m" display="radio" type="boolean" truevalue="-m" falsevalue="" checked="false" optional="True" label="Show meta information about the whole experiment" help="(-m) "/> 46 <param name="m" argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/>
43 <param name="param_p" display="radio" type="boolean" truevalue="-p" falsevalue="" checked="false" optional="True" label="Shows data processing information" help="(-p) "/> 47 <param name="p" argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/>
44 <param name="param_s" display="radio" type="boolean" truevalue="-s" falsevalue="" checked="false" optional="True" label="Computes a summary statistics of intensities, qualities, and widths" help="(-s) "/> 48 <param name="s" argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a summary statistics of intensities, qualities, and widths" help=""/>
45 <expand macro="advanced_options"> 49 <expand macro="adv_opts_macro">
46 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 50 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
51 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
52 <expand macro="list_string_san"/>
53 </param>
47 </expand> 54 </expand>
55 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
56 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
57 </param>
48 </inputs> 58 </inputs>
49 <outputs> 59 <outputs>
50 <data name="param_out" format="txt"/> 60 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
61 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
62 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
63 </data>
51 </outputs> 64 </outputs>
52 <help>Extract extended statistics on the features of a map for quality control. 65 <tests>
66 <expand macro="autotest_MapStatistics"/>
67 <expand macro="manutest_MapStatistics"/>
68 </tests>
69 <help><![CDATA[Extract extended statistics on the features of a map for quality control.
53 70
54 71
55 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MapStatistics.html</help> 72 For more information, visit http://www.openms.de/documentation/TOPP_MapStatistics.html]]></help>
73 <expand macro="references"/>
56 </tool> 74 </tool>