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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools commit f57f55a2cb399c5cc8fdd63128970e5f875ca48e
author galaxyp
date Fri, 05 Apr 2019 04:16:26 -0400
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1 <tool id="rawtools" name="Raw Tools" version="@RAWTOOLS_VERSION@.@TOOL_SUBVERSION@" profile="16.04">
2 <description>
3 Perform scan data parsing, quantification and quality control analysis of Thermo Orbitrap raw mass spectrometer files.
4 </description>
5 <macros>
6 <token name="@RAWTOOLS_VERSION@">1.4.2</token>
7 <token name="@TOOL_SUBVERSION@">0</token>
8 <xml name="input_fasta">
9 <param format="fasta" name="input_database" type="data" label="Protein Database"
10 help="Select FASTA database from history"/>
11 </xml>
12 </macros>
13 <requirements>
14 <requirement type="package" version="@RAWTOOLS_VERSION@">rawtools</requirement>
15 </requirements>
16 <command detect_errors="exit_code">
17 <![CDATA[
18 #from datetime import datetime
19 #import json
20 #import os
21 #import re
22 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
23 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
24 #set $temp_stderr = "rawtools_stderr"
25 #set $bin_dir = "bin"
26
27 mkdir output &&
28 cwd=`pwd` &&
29 ## TODO: To remove this patch when dropping support for Galaxy 17_09, adding profile="18.01" to the tool.
30 export HOME=\$cwd &&
31
32 mkdir raws_folder &&
33 #for $input_raw in $input_raws:
34 #set $input_name = re.sub('[^\w\-\.]', '_',$input_raw.element_identifier.split('/')[-1].replace(".raw", "") + ".raw")
35 ln -s -f '${input_raw}' './raws_folder/${input_name}' &&
36 #end for
37
38 #####################
39 ## Raw Tools ##
40 #####################
41 (rawtools.sh
42
43 ## PARSING AND QUANTIFICATION OPTIONS
44
45 ## If any processing option is enabled in parsing & quantification, "parse" command is mandatory
46 #if $pq_options.pq_conditional.matrix_select == "yes" or $pq_options.chromatogram_conditional.chromatogram_select == "yes" or $pq_options.mgf_conditional.mgf_select == "yes" or $pq_options.metrics_boolean == "yes":
47 parse
48 #end if
49 --directory ./raws_folder
50
51 ## Generates Matrix file
52 #if $pq_options.pq_conditional.matrix_select == "yes":
53 --parse
54 #end if
55
56 ## Generates quantification information
57 #if $pq_options.pq_conditional.matrix_select == "yes" and $pq_options.pq_conditional.q_conditional.q_select == "yes" :
58 --quant
59 --labelingreagent ${pq_options.pq_conditional.q_conditional.q_labeling_reagent}
60 #end if
61
62 ## Unlabeled quant
63 #if $pq_options.pq_conditional.matrix_select == "yes" and $pq_options.pq_conditional.unlabeledquant_boolean == "yes":
64 --unlabeledquant
65 #end if
66
67 ## Generates Mgf file
68 #if $pq_options.mgf_conditional.mgf_select == "yes":
69 --writemgf
70 --masscutoff ${pq_options.mgf_conditional.mgf_masscutoff}
71 ## DEPRECATED --intensitycutoff ${pq_options.mgf_conditional.mgf_intensitycutoff}
72 #if $pq_options.mgf_conditional.mgf_refinement == "yes":
73 -R
74 #end if
75 #end if
76
77 ## Generates chromatogram file
78 #if $pq_options.chromatogram_conditional.chromatogram_select == "yes":
79 --chro ${pq_options.chromatogram_conditional.chromatogram_type}${pq_options.chromatogram_conditional.chromatogram_order}
80 #end if
81
82 ## Generates metrics file
83 #if $pq_options.metrics_boolean == "yes":
84 --metrics
85 #end if
86
87 --out \$cwd/output
88
89 2>> $temp_stderr) &&
90
91 cat $temp_stderr 2>&1;
92 ]]>
93 </command>
94 <inputs>
95 <param format="thermo.raw" name="input_raws" type="data" label="Raw file" multiple="true"
96 help="Select the raw file from history"/>
97 <param name="license_agreement" type="boolean" label="Do you agree to the vendor licenses?" help="This tool uses a proprietary vendor library; to run it you must agree to the vendor license. Read it at https://github.com/kevinkovalchik/RawTools/blob/master/RawFileReaderLicense">
98 <validator type="expression" message="You must agree to the vendor license to run RawTools.">True == value</validator>
99 </param>
100 <section name="pq_options" expanded="true" title="Parsing and Quantification">
101 <conditional name="pq_conditional">
102 <param name="matrix_select" type="select"
103 label="Create Matrix file"
104 help="Parses raw file meta and scan data and creates a tab-delimited text file.">
105 <option value="yes" selected="True">Yes</option>
106 <option value="no" >No</option>
107 </param>
108 <when value="yes">
109 <conditional name="q_conditional">
110 <param name="q_select" type="select"
111 label="Quantification"
112 help="Also quantifies reporter ions and write results to output matrix.">
113 <option value="yes" >Yes</option>
114 <option value="no" selected="True">No</option>
115 </param>
116 <when value="yes">
117 <param name="q_labeling_reagent" label="Labeling reagent" type="select"
118 help="Reagents used to label peptides.">
119 <option value="TMT0" selected="True">TMT0</option>
120 <option value="TMT2" >TMT2</option>
121 <option value="TMT6" >TMT6</option>
122 <option value="TMT10" >TMT10</option>
123 <option value="TMT11" >TMT11</option>
124 <option value="iTRAQ4" >iTRAQ4</option>
125 <option value="iTRAQ8" >iTRAQ8</option>
126 </param>
127 </when>
128 <when value="no" />
129 </conditional>
130 <param name="unlabeledquant_boolean" label="Unlabeled quant" type="boolean" truevalue="yes" falsevalue="no"
131 help="Calculate areas of precursor peaks and writes them to the matrix file as ParentPeakArea column."/>
132 </when>
133 <when value="no" />
134 </conditional>
135
136 <conditional name="mgf_conditional">
137 <param name="mgf_select" type="select" label="Creates a mgf file"
138 help="Creates a standard MGF file.">
139 <option value="yes" >Yes</option>
140 <option value="no" selected="True">No</option>
141 </param>
142 <when value="yes">
143 <param name="mgf_masscutoff" label="Mass cutoff" value="0" type="float"
144 help="Specify a mass cutoff to be applied when generating MGF files. May be of use if removal of reporter ions is desired prior to searching of MS2 spectra."/>
145 <!--<param name="mgf_intensitycutoff" label="Intensity cutoff" value="0" type="float"
146 help="Relative intensity cutoff for ions included in a MGF file. The value is relative to the highest intensity ion found in a given scan."/>
147 -->
148 <param name="mgf_refinement" label="Precursor mass and charge refinement" type="boolean" truevalue="yes" falsevalue="no" checked="false"
149 help="Refine precursor charge and monoisotopic mass assignments. Highly recommended if monoisotopic precursor selection was turned off in the instrument method (or peptide match on a QE instrument)."/>
150
151 </when>
152 <when value="no" />
153 </conditional>
154 <conditional name="chromatogram_conditional">
155 <param name="chromatogram_select" type="select"
156 label="Create chromatogram"
157 help="Creates a text file of chromatographic data for investigation or plotting.">
158 <option value="yes" >Yes</option>
159 <option value="no" selected="True">No</option>
160 </param>
161 <when value="yes">
162 <param name="chromatogram_type" label="Chromatogram type" type="select" help="MS Level">
163 <option value="1" selected="True">MS1</option>
164 <option value="2" >MS2</option>
165 <option value="3" >MS3</option>
166 </param>
167 <param name="chromatogram_order" label="Chromatogram order" type="select" help="MS Order">
168 <option value="T" >TIC</option>
169 <option value="B" >Base peak</option>
170 <option value="TB" selected="True">TIC and base peak</option>
171 </param>
172 </when>
173 <when value="no" />
174 </conditional>
175 <param name="metrics_boolean" label="Create metrics" type="boolean" truevalue="yes" falsevalue="no"
176 help="Creates a text file containing general metrics about the Ms run." />
177
178 </section>
179
180 <!-- TODO: QUALITY CONTROL
181 <section name="quality_control_options" expanded="false" title="Quality control">
182
183 </section>
184 -->
185
186 </inputs>
187 <outputs>
188 <!-- Matrix -->
189
190 <collection name="output_matrix" type="list" label="${tool.name} - ${on_string}: Matrix">
191 <filter>pq_options['pq_conditional']['matrix_select'] == "yes"</filter>
192 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.raw_Matrix.txt" ext="txt" directory="output"/>
193 </collection>
194
195 <!-- MGF file -->
196
197 <collection name="output_mgf" type="list" label="${tool.name} - ${on_string}: MGF">
198 <filter>pq_options['mgf_conditional']['mgf_select'] == "yes"</filter>
199 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.mgf" ext="mgf" directory="output"/>
200 </collection>
201
202 <!-- Chromatogram file -->
203
204 <collection name="output_chromatogram" type="list" label="${tool.name} - ${on_string}: Chromatogram" >
205 <filter>pq_options['chromatogram_conditional']['chromatogram_select'] == "yes"</filter>
206 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.raw_Ms_BP_chromatogram.txt" ext="txt" directory="output"/>
207 </collection>
208
209 <!-- Metrics file -->
210
211 <collection name="output_metrics" type="list" label="${tool.name} - ${on_string}: Metrics" >
212 <filter>pq_options['metrics_boolean'] is True</filter>
213 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.raw_Metrics.txt" ext="txt" directory="output"/>
214 </collection>
215 </outputs>
216 <tests>
217
218 <!-- Test Matrix -->
219 <test>
220 <param name="input_raws" value="really_small.raw" ftype="thermo.raw"/>
221 <param name="license_agreement" value="true" />
222 <param name="pq_conditional|matrix_select" value="yes"/>
223 <output_collection name="output_matrix" type="list">
224 <element name="really_small" file="really_small.raw_Matrix.txt" ftype="txt" compare="sim_size" delta="3000"/>
225 </output_collection>
226 </test>
227
228 <!-- Test mgf conversion -->
229 <test>
230 <param name="input_raws" value="really_small.raw" ftype="thermo.raw"/>
231 <param name="license_agreement" value="true" />
232 <param name="pq_conditional|matrix_select" value="no"/>
233 <param name="mgf_conditional|mgf_select" value="yes"/>
234 <param name="mgf_conditional|mgf_refinement" value="yes"/>
235 <output_collection name="output_mgf" type="list">
236 <element name="really_small.raw" ftype="mgf">
237 <assert_contents>
238 <has_text text="PEPMASS=675.248779296875"/>
239 <has_text text="RTINSECONDS=73.863181104"/>
240 <has_text text="SCANS=36"/>
241 <has_text text="121.31165 920.2368"/>
242 </assert_contents>
243 </element>
244 </output_collection>
245 </test>
246 <!-- Test chromatogram -->
247 <test>
248 <param name="input_raws" value="really_small.raw" ftype="thermo.raw"/>
249 <param name="license_agreement" value="true" />
250 <param name="pq_conditional|matrix_select" value="no"/>
251 <param name="chromatogram_conditional|chromatogram_select" value="yes"/>
252 <output_collection name="output_chromatogram" type="list" >
253 <element name="really_small" file="really_small.raw_Ms_BP_chromatogram.txt" ftype="txt" compare="sim_size" delta="3000"/>
254 </output_collection>
255 </test>
256
257
258 </tests>
259 <help>
260 **What it does**
261
262 RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis (to be developed in further versions) of Thermo Orbitrap raw mass spectrometer files.
263
264 RawTools is written in C# and uses the Thermo RawFileReader library. RawTools is the replacement for RawQuant Python package.
265
266 https://github.com/kevinkovalchik/RawTools
267
268 **License**
269
270 Raw Tools is a free open-source project, following an Apache License 2.0.
271
272 RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
273 Using this software implies the acceptance of RawFileReader license terms.
274
275 </help>
276 <citations>
277 <citation type="doi">doi:10.1021/acs.jproteome.8b00721</citation>
278 </citations>
279 </tool>