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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq commit 7e54991bc641a1f70855b686c987f3f331142db1"
author galaxyp
date Tue, 21 Jan 2020 15:21:38 -0500
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1 <tool id="quantwiz_iq" name="QuantWiz-IQ" version="2.0">
2 <description>Isobaric Quantitation using QuantWiz-IQ</description>
3 <requirements>
4 <requirement type="package" version="2.0">quantwiz-iq</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 cp '$input_file' '$input_file.name'
8 &&
9 cat '$new_param_file' > '$iq_params'
10 #if $input_purity_file.input_purity_file_option == "history":
11 && cp '$input_purity_file.purity_type' '$input_purity_file.purity_type.name'
12 && echo "Purity_corrections_values=$input_purity_file.purity_type.name" >> '$iq_params'
13 #else:
14 && PROG_PATH=`which QuantWiz_IQ`
15 && cp \${PROG_PATH%/*}/Purity_correction/$input_purity_file.purity_type .
16 && echo "Purity_corrections_values=$input_purity_file.purity_type" >> '$iq_params'
17 #end if
18
19 &&
20 QuantWiz_IQ '$iq_params'
21 && cp '${input_file.name.rsplit('.',1)[0]}_${area_method}_${min_tol}.tsv' '$quant'
22 && cp '${input_file.name.rsplit('.',1)[0]}_${area_method}_${min_tol}_noquant.tsv' '$noquant'
23 ]]>
24 </command>
25 <configfiles>
26 <configfile name="new_param_file"><![CDATA[#slurp
27 Spectra_Folder=.
28 #if $input_file.ext == "mgf":
29 Input_file_extension=mgf
30 #else if $input_file.ext == "mzml":
31 Input_file_extension=mzML
32 #end if
33 Label_type=$input_label.label_type
34 Plex=$input_label.num_plex
35 min_reporters=$min_reporters
36 Spectrum_area=$area_method
37 Base_reporter=$input_label.base_reporter
38 Normalization=$normalization
39 Peak_intensity_threshold=$peak_intensity_threshold
40 Tol_unit=$tol_unit
41 Tol_min=$min_tol
42 Tol_max=$max_tol
43 #slurp
44 ]]></configfile>
45 </configfiles>
46
47 <inputs>
48 <param type="data" name="input_file" format="mgf,mzml" label="MGF/mzML file"/>
49
50 <conditional name="input_label">
51 <param name="label_type" type="select" label="Isobaric reporter labeling type (MS2 level): iTRAQ or TMT">
52 <option value="iTRAQ" selected="true">iTRAQ</option>
53 <option value="TMT">TMT</option>
54 </param>
55 <when value="iTRAQ">
56 <param name="num_plex" type="select" display="radio" label="You are using iTRAQ: 4Plex or 8Plex">
57 <option value="4plex" selected="true">4Plex</option>
58 <option value="8plex">8Plex</option>
59 </param>
60 <param name="base_reporter" type="select" label="Denominator reporter tag for ratio calculation (mention only base reporter integer value)">
61 <option value="113" selected="true">113</option>
62 <option value="114">114</option>
63 <option value="115">115</option>
64 <option value="116">116</option>
65 <option value="117">117</option>
66 <option value="118">118</option>
67 <option value="119">119</option>
68 <option value="121">121</option>
69 </param>
70 </when>
71 <when value="TMT">
72 <param name="num_plex" type="select" display="radio" label="You are using TMT: 2Plex, 6Plex or 10Plex">
73 <option value="2plex">2Plex</option>
74 <option value="6plex">6Plex</option>
75 <option value="10plex" selected="true">10Plex</option>
76 </param>
77 <param name="base_reporter" type="select" label="Denominator reporter tag for ratio calculation (mention only base reporter integer value)">
78 <option value="126" selected="true">126</option>
79 <option value="127">127</option>
80 <option value="128">128</option>
81 <option value="129">129</option>
82 <option value="130">130</option>
83 <option value="131">131</option>
84 </param>
85 </when>
86 </conditional>
87
88 <param name="min_reporters" type="integer" value="2" min="0" label="Minimum number of reporter types required to consider a spectrum for quantitation. Default is 2" />
89
90 <param name="area_method" type="select" label="Spectrum area calculation method">
91 <option value="T">Trapezoid</option>
92 <option value="S" selected="true">Sum intensity</option>
93 <option value="B">Baseline corrected sum intensity</option>
94 </param>
95
96 <param name="normalization" type="select" display="radio" label="Perform normalization">
97 <option value="yes">Yes</option>
98 <option value="no" selected="true">No</option>
99 </param>
100
101 <param name="peak_intensity_threshold" type="float" value="0.0" min="0.0" label="Reporter label maximum peak intensity threshold" help="Reporter label maximum peak intensity threshold to consider the tag for quantitation. Default is 0. It depends on signal to noise ratio (S/N)" />
102
103 <param name="tol_unit" type="select" display="radio" label="MS/MS (MS2) tolerance unit">
104 <option value="Da" selected="true">Dalton (Da)</option>
105 <option value="ppm">Parts per million (ppm)</option>
106 </param>
107
108 <param name="min_tol" type="float" value="0.05" min="0.0" label="Minimum MS/MS (MS2) tolerance range" />
109 <param name="max_tol" type="float" value="0.05" min="0.0" label="Maximum MS/MS (MS2) tolerance range" />
110
111 <conditional name="input_purity_file">
112 <param name="input_purity_file_option" type="select" display="radio" label="Use default or from the history">
113 <option value="default" selected="true">Use Default</option>
114 <option value="history">Use file from the history</option>
115 </param>
116 <when value="default">
117 <param name="purity_type" type="select" label="Select default purity correction type">
118 <option value="iTRAQ4plex.tsv">iTRAQ 4plex</option>
119 <option value="iTRAQ8plex.tsv" selected="true">iTRAQ 8plex</option>
120 <option value="TMT6plex.tsv">TMT 6plex</option>
121 <option value="TMT10plex.tsv">TMT 10plex</option>
122 </param>
123 </when>
124 <when value="history">
125 <param type="data" name="purity_type" format="txt" label="Select purity correction file from the history"/>
126 </when>
127 </conditional>
128 </inputs>
129
130 <outputs>
131 <data name="quant" format="tabular" label="${tool.name}_Quant.tabular" from_work_dir="${input_file.name.rsplit('.',1)[0]}_${area_method}_${min_tol}.tsv"/>
132 <data name="noquant" format="tabular" label="${tool.name}_No_Quant.tabular" from_work_dir="${input_file.name.rsplit('.',1)[0]}_${area_method}_${min_tol}_noquant.tsv"/>
133 <data name="iq_params" format="txt" label="${tool.name}_QuantWiz_IQ_parameters"/>
134 </outputs>
135
136 <tests>
137 <test>
138 <param name="input_file" value="Test_Orbi_iTRAQ_8plex.mgf" ftype="mgf"/>
139 <param name="label_type" value="iTRAQ"/>
140 <param name="num_plex" value="8plex"/>
141 <param name="min_reporters" value="1"/>
142 <param name="area_method" value="S"/>
143 <param name="base_reporter" value="113"/>
144 <param name="normalization" value="no"/>
145 <param name="peak_intensity_threshold" value="0.0"/>
146 <param name="tol_unit" value="Da"/>
147 <param name="min_tol" value="0.05"/>
148 <param name="max_tol" value="0.05"/>
149 <param name="input_purity_file_option" value="default"/>
150 <param name="purity_type" value="iTRAQ8plex.tsv"/>
151 <output name="quant" file="Test_Orbi_iTRAQ_8plex_S_0.05.tsv">
152 <assert_contents>
153 <has_text text="Retention_time"/>
154 </assert_contents>
155 </output>
156 <output name="noquant" file="Test_Orbi_iTRAQ_8plex_S_0.05_noquant.tsv">
157 <assert_contents>
158 <has_text text="Base_Intensity"/>
159 </assert_contents>
160 </output>
161 </test>
162 </tests>
163
164 <help><![CDATA[
165
166 **QuantWiz-IQ** for Isobaric Quantitation
167
168 IQ stands for Isobaric Quantitator, a tool for quantitation based on of Isobaric tags (iTRAQ and TMT) that takes
169 MGF as well as the HUPO-PSI standard mzML as input. It supports 4-plex and 8-plex quantitation for iTRAQ;
170 and 2-plex, 6-plex and 10-plex quantitation for TMT.
171
172 **Outputs**:
173
174 Outputs parameters file along with two tabular files. One tabular file contains spectra that shows quantitation,
175 and the other tabular file with spectra that didn't show any qualified quantitation.
176
177 ]]></help>
178
179 <citations>
180 <citation type="bibtex">
181 @misc{quantwiz_iq,
182 author={Aggarwal, Suruchi and Yadav, Amit Kumar and Kumar, Praveen},
183 year={2020},
184 title={QuantWiz-IQ Galaxy Wrapper}
185 }
186 </citation>
187 <citation type="doi">10.1007/978-1-4939-3106-4_18</citation>
188 </citations>
189 </tool>