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comparison QCCalculator.xml @ 14:f6f07c3e99a2 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:34:05 +0000
parents d0607dfea8fa
children
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13:d0607dfea8fa 14:f6f07c3e99a2
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: []-->
4 <tool id="QCCalculator" name="QCCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="QCCalculator" name="QCCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.</description> 4 <description>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">QCCalculator</token> 6 <token name="@EXECUTABLE@">QCCalculator</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 #if $id: 19 #if $id:
21 mkdir id && 20 mkdir id &&
22 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && 21 cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
23 #end if 22 #end if
24 #if $feature: 23 #if $feature:
25 mkdir feature && 24 mkdir feature &&
26 ln -s '$feature' 'feature/${re.sub("[^\w\-_]", "_", $feature.element_identifier)}.$gxy2omsext($feature.ext)' && 25 cp '$feature' 'feature/${re.sub("[^\w\-_]", "_", $feature.element_identifier)}.$gxy2omsext($feature.ext)' &&
27 #end if 26 #end if
28 #if $consensus: 27 #if $consensus:
29 mkdir consensus && 28 mkdir consensus &&
30 ln -s '$consensus' 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)' && 29 cp '$consensus' 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)' &&
31 #end if 30 #end if
32 31
33 ## Main program call 32 ## Main program call
34 33
35 set -o pipefail && 34 set -o pipefail &&
61 <configfiles> 60 <configfiles>
62 <inputs name="args_json" data_style="paths"/> 61 <inputs name="args_json" data_style="paths"/>
63 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 62 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
64 </configfiles> 63 </configfiles>
65 <inputs> 64 <inputs>
66 <param 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)"/> 65 <param argument="-in" type="data" format="mzml" 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)"/>
67 <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help=""> 66 <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
68 <option value="mzQC">mzqc</option> 67 <option value="mzQC">mzqc</option>
69 <option value="qcML">qcml</option> 68 <option value="qcML">qcml</option>
69 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
70 <expand macro="list_string_san" name="out_type"/> 70 <expand macro="list_string_san" name="out_type"/>
71 </param> 71 </param>
72 <param argument="-label" type="text" optional="true" value="label" label="unique name for the run that can be used in a figure label" help=""> 72 <param argument="-label" type="text" value="label" label="unique name for the run that can be used in a figure label" help="">
73 <expand macro="list_string_san" name="label"/> 73 <expand macro="list_string_san" name="label"/>
74 </param> 74 </param>
75 <param argument="-name" type="text" optional="true" value="" label="name of the person creating this mzQC file" help=""> 75 <param argument="-name" type="text" optional="true" value="" label="name of the person creating this mzQC file" help="">
76 <expand macro="list_string_san" name="name"/> 76 <expand macro="list_string_san" name="name"/>
77 </param> 77 </param>
85 <param 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)"/> 85 <param 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)"/>
86 <param 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)"/> 86 <param 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)"/>
87 <param 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=""/> 87 <param 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=""/>
88 <expand macro="adv_opts_macro"> 88 <expand macro="adv_opts_macro">
89 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 89 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
90 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 90 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
91 <expand macro="list_string_san" name="test"/> 91 <expand macro="list_string_san" name="test"/>
92 </param> 92 </param>
93 </expand> 93 </expand>
94 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 94 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
95 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 95 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
103 </data> 103 </data>
104 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 104 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
105 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 105 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
106 </data> 106 </data>
107 </outputs> 107 </outputs>
108 <tests><!-- UTILS_QCCalculator_1 --> 108 <tests>
109 <!-- TOPP_QCCalculator_1 -->
109 <test expect_num_outputs="2"> 110 <test expect_num_outputs="2">
110 <section name="adv_opts"> 111 <section name="adv_opts">
111 <param name="force" value="false"/> 112 <param name="force" value="false"/>
112 <param name="test" value="true"/> 113 <param name="test" value="true"/>
113 </section> 114 </section>
114 <param name="in" value="QCCalculator_input.mzML"/> 115 <param name="in" value="QCCalculator_input.mzML"/>
115 <output name="out" file="QCCalculator_1.qcML" compare="sim_size" delta_frac="0.7" ftype="qcml"/> 116 <output name="out" value="QCCalculator_1_output.qcML" compare="sim_size" delta_frac="0.7" ftype="qcml"/>
116 <param name="out_type" value="qcML"/> 117 <param name="out_type" value="qcML"/>
117 <param name="label" value="label"/> 118 <param name="label" value="label"/>
118 <param name="name" value=""/> 119 <param name="name" value=""/>
119 <param name="address" value=""/> 120 <param name="address" value=""/>
120 <param name="description" value=""/> 121 <param name="description" value=""/>
123 <output name="ctd_out" ftype="xml"> 124 <output name="ctd_out" ftype="xml">
124 <assert_contents> 125 <assert_contents>
125 <is_valid_xml/> 126 <is_valid_xml/>
126 </assert_contents> 127 </assert_contents>
127 </output> 128 </output>
129 <assert_stdout>
130 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
131 </assert_stdout>
128 </test> 132 </test>
129 <!-- UTILS_QCCalculator_2 --> 133 <!-- TOPP_QCCalculator_2 -->
130 <test expect_num_outputs="2"> 134 <test expect_num_outputs="2">
131 <section name="adv_opts"> 135 <section name="adv_opts">
132 <param name="force" value="false"/> 136 <param name="force" value="false"/>
133 <param name="test" value="true"/> 137 <param name="test" value="true"/>
134 </section> 138 </section>
135 <param name="in" value="QCCalculator_input.mzML"/> 139 <param name="in" value="QCCalculator_input.mzML"/>
136 <output name="out" file="QCCalculator_2.mzQC" compare="sim_size" delta_frac="0.7" ftype="mzqc"/> 140 <output name="out" value="QCCalculator_2_output.mzQC" compare="sim_size" delta_frac="0.7" ftype="mzqc"/>
137 <param name="out_type" value="mzQC"/> 141 <param name="out_type" value="mzQC"/>
138 <param name="label" value="label"/> 142 <param name="label" value="label"/>
139 <param name="name" value="name"/> 143 <param name="name" value="name"/>
140 <param name="address" value="address"/> 144 <param name="address" value="address"/>
141 <param name="description" value="description"/> 145 <param name="description" value="description"/>
146 <output name="ctd_out" ftype="xml"> 150 <output name="ctd_out" ftype="xml">
147 <assert_contents> 151 <assert_contents>
148 <is_valid_xml/> 152 <is_valid_xml/>
149 </assert_contents> 153 </assert_contents>
150 </output> 154 </output>
155 <assert_stdout>
156 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
157 </assert_stdout>
151 </test> 158 </test>
152 <test expect_num_outputs="1"><!-- took test data from another test w mzML input --> 159 <test expect_num_outputs="1">
153 <param name="adv_opts|test" value="true"/> 160 <!-- took test data from another test w mzML input -->
154 <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/> 161 <param name="adv_opts|test" value="true"/>
155 <param name="out_type" value="qcML"/> 162 <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
156 <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/> 163 <param name="out_type" value="qcML"/>
157 </test> 164 <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/>
158 <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,consensusXML input --> 165 </test>
159 <param name="adv_opts|test" value="true"/> 166 <test expect_num_outputs="1">
160 <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/> 167 <!-- took test data from another test w mzML,idXML,consensusXML input -->
161 <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/> 168 <param name="adv_opts|test" value="true"/>
162 <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/> 169 <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
163 <param name="out_type" value="qcML"/> 170 <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/>
164 <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/> 171 <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/>
165 </test> 172 <param name="out_type" value="qcML"/>
166 <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,featureXML input --> 173 <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/>
167 <param name="adv_opts|test" value="true"/> 174 </test>
168 <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/> 175 <test expect_num_outputs="1">
169 <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/> 176 <!-- took test data from another test w mzML,idXML,featureXML input -->
170 <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/> 177 <param name="adv_opts|test" value="true"/>
171 <param name="out_type" value="qcML"/> 178 <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/>
172 <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/> 179 <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/>
173 </test> 180 <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/>
174 </tests> 181 <param name="out_type" value="qcML"/>
182 <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/>
183 </test>
184 </tests>
175 <help><![CDATA[Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection. 185 <help><![CDATA[Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.
176 186
177 187
178 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCCalculator.html]]></help> 188 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCCalculator.html]]></help>
179 <expand macro="references"/> 189 <expand macro="references"/>
180 </tool> 190 </tool>