Mercurial > repos > galaxyp > openms_qccalculator

comparison QCCalculator.xml @ 9:8bcc0d2ad96e 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 12:49:14 +0000
parents 1fc9e74f040c
children 044adca691a7
comparison
equal deleted inserted replaced
8:5f8715a13da8 9:8bcc0d2ad96e
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="QCCalculator" name="QCCalculator" version="2.3.0"> 4 <tool id="QCCalculator" name="QCCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.</description> 5 <description>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">QCCalculator</token> 7 <token name="@EXECUTABLE@">QCCalculator</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[QCCalculator 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir out &&
22 #if $id:
23 mkdir id &&
24 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
17 #end if 25 #end if
18 #if $param_out: 26 #if $feature:
19 -out $param_out 27 mkdir feature &&
28 ln -s '$feature' 'feature/${re.sub("[^\w\-_]", "_", $feature.element_identifier)}.$gxy2omsext($feature.ext)' &&
20 #end if 29 #end if
21 #if $param_id: 30 #if $consensus:
22 -id $param_id 31 mkdir consensus &&
32 ln -s '$consensus' 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)' &&
23 #end if 33 #end if
24 #if $param_feature: 34
25 -feature $param_feature 35 ## Main program call
36
37 set -o pipefail &&
38 @EXECUTABLE@ -write_ctd ./ &&
39 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
40 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
41 -in
42 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
43 -out
44 'out/output.${gxy2omsext("qcml")}'
45 #if $id:
46 -id
47 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
26 #end if 48 #end if
27 #if $param_consensus: 49 #if $feature:
28 -consensus $param_consensus 50 -feature
51 'feature/${re.sub("[^\w\-_]", "_", $feature.element_identifier)}.$gxy2omsext($feature.ext)'
29 #end if 52 #end if
30 #if $param_remove_duplicate_features: 53 #if $consensus:
31 -remove_duplicate_features 54 -consensus
55 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)'
32 #end if 56 #end if
33 #if $adv_opts.adv_opts_selector=='advanced': 57
34 #if $adv_opts.param_force: 58 ## Postprocessing
35 -force 59 && mv 'out/output.${gxy2omsext("qcml")}' '$out'
36 #end if 60 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
37 #end if 61 && mv '@EXECUTABLE@.ctd' '$ctd_out'
38 ]]></command> 62 #end if]]></command>
63 <configfiles>
64 <inputs name="args_json" data_style="paths"/>
65 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
66 </configfiles>
39 <inputs> 67 <inputs>
40 <param name="param_in" type="data" format="mzml" optional="False" label="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" help="(-in) "/> 68 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" help=" select mzml data sets(s)"/>
41 <param name="param_id" type="data" format="idxml" optional="True" label="Input idXML file containing the identifications" help="(-id) Your identifications will be exported in an easy-to-read format"/> 69 <param name="id" argument="-id" type="data" format="idxml" optional="true" label="Input idXML file containing the identifications" help="Your identifications will be exported in an easy-to-read format select idxml data sets(s)"/>
42 <param name="param_feature" type="data" format="featurexml" optional="True" label="feature input file (this is relevant for most QC issues)" help="(-feature) "/> 70 <param name="feature" argument="-feature" type="data" format="featurexml" optional="true" label="feature input file (this is relevant for most QC issues)" help=" select featurexml data sets(s)"/>
43 <param name="param_consensus" type="data" format="consensusxml" optional="True" label="consensus input file (this is only used for charge state deconvoluted output" help="(-consensus) Use the consensusXML output form the DeCharger)"/> 71 <param name="consensus" argument="-consensus" type="data" format="consensusxml" optional="true" label="consensus input file (this is only used for charge state deconvoluted output" help="Use the consensusXML output form the DeCharger) select consensusxml data sets(s)"/>
44 <param name="param_remove_duplicate_features" display="radio" type="boolean" truevalue="-remove_duplicate_features" falsevalue="" checked="false" optional="True" label="This flag should be set, if you work with a set of merged features" help="(-remove_duplicate_features) "/> 72 <param name="remove_duplicate_features" argument="-remove_duplicate_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="This flag should be set, if you work with a set of merged features" help=""/>
45 <expand macro="advanced_options"> 73 <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) "/> 74 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
75 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
76 <expand macro="list_string_san"/>
77 </param>
47 </expand> 78 </expand>
79 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
80 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
81 </param>
48 </inputs> 82 </inputs>
49 <outputs> 83 <outputs>
50 <data name="param_out" format="qcml"/> 84 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/>
85 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
86 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
87 </data>
51 </outputs> 88 </outputs>
52 <help>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection. 89 <tests>
90 <expand macro="autotest_QCCalculator"/>
91 <expand macro="manutest_QCCalculator"/>
92 </tests>
93 <help><![CDATA[Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.
53 94
54 95
55 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_QCCalculator.html</help> 96 For more information, visit http://www.openms.de/documentation/UTILS_QCCalculator.html]]></help>
97 <expand macro="references"/>
56 </tool> 98 </tool>