Mercurial > repos > galaxyp > thermo_raw_file_converter

comparison thermo_converter.xml @ 6:2d80c8b2dfc2 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 51cb9a683762b514de76c1654e5e5cac3ff443f8"
author galaxyp
date Mon, 06 Apr 2020 19:00:54 -0400
parents 77a18a61aeed
children 63769c4217a7
comparison
equal deleted inserted replaced
5:77a18a61aeed 6:2d80c8b2dfc2
1 <tool id="thermo_raw_file_converter" name="Thermo" version="1.1.10"> 1 <tool id="thermo_raw_file_converter" name="Thermo" version="1.1.10">
2 <description>RAW file converter</description> 2 <description>RAW file converter</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.10">ThermoRawFileParser</requirement> 4 <requirement type="package" version="1.1.10">thermorawfileparser</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 <![CDATA[ 7 <![CDATA[
8 #import re 8 #import re
9
10 #set $temp_stderr = "thermo_converter_stderr"
11
12 echo "" > $temp_stderr &&
13 9
14 mkdir ./raws_folder && 10 mkdir ./raws_folder &&
15 mkdir ./output_folder && 11 mkdir ./output_folder &&
16 #for $input_raw in $input: 12 #for $input_raw in $input:
17 #if len($input) > 1 13 #if len($input) > 1
20 #else: 16 #else:
21 ln -s -f '${input_raw}' './raws_folder/input.raw' && 17 ln -s -f '${input_raw}' './raws_folder/input.raw' &&
22 #end if 18 #end if
23 #end for 19 #end for
24 20
25 (ThermoRawFileParser.sh 21 ThermoRawFileParser.sh
26 -d=./raws_folder 22 -d=./raws_folder
27 -o=./output_folder 23 -o=./output_folder
28 -f=$output_format 24 -f=$output_format
29 #if $output_metadata_selector != "off": 25 #if $output_metadata_selector != "off":
30 --metadata="${output_metadata_selector}" 26 --metadata="${output_metadata_selector}"
31 #end if 27 #end if
32 $zlib_boolean 28 $zlib_boolean
33 $peakpicking_boolean 29 $peakpicking_boolean
34 $ignore_instrument_errors_boolean 30 $ignore_instrument_errors_boolean
35 31
36 2>> $temp_stderr)
37
38 &&
39
40 #if len($input) == 1: 32 #if len($input) == 1:
41 #if $output_format == "0": 33 #if $output_format == "0":
42 mv ./output_folder/input.mgf ./output_file.out && 34 && mv ./output_folder/input.mgf ./output_file.out
43 #else if $output_format == "1": 35 #else if $output_format == "1":
44 mv ./output_folder/input.mzML ./output_file.out && 36 && mv ./output_folder/input.mzML ./output_file.out
45 #else if $output_format == "2": 37 #else if $output_format == "2":
46 mv ./output_folder/input.mzML ./output_file.out && 38 && mv ./output_folder/input.mzML ./output_file.out
47 #end if 39 #end if
48 40
49 #if $output_metadata_selector != "off": 41 #if $output_metadata_selector != "off":
50 #if $output_metadata_selector == "0": 42 #if $output_metadata_selector == "0":
51 mv ./output_folder/input-metadata.json ./input-metadata.txt && 43 && mv ./output_folder/input-metadata.json ./input-metadata.txt
52 #else if $output_metadata_selector == "1": 44 #else if $output_metadata_selector == "1":
53 mv ./output_folder/input-metadata.txt ./input-metadata.txt && 45 && mv ./output_folder/input-metadata.txt ./input-metadata.txt
54 #end if 46 #end if
55 #end if 47 #end if
56 #end if 48 #end if
57
58 cat $temp_stderr 2>&1;
59 ]]> 49 ]]>
60 </command> 50 </command>
61 <inputs> 51 <inputs>
62 <param name="input" type="data" format="thermo.raw" label="Thermo RAW file" help="" multiple="true" 52 <param name="input" type="data" format="thermo.raw" label="Thermo RAW file" help="" multiple="true"
63 optional="False" /> 53 optional="False" />
134 </outputs> 124 </outputs>
135 125
136 <tests> 126 <tests>
137 <!-- Basic test --> 127 <!-- Basic test -->
138 <test expect_num_outputs="1"> 128 <test expect_num_outputs="1">
139 <param name="input" value="really_small.raw"/> 129 <param name="input" value="really_small.raw" ftype="thermo.raw"/>
140 <param name="output_format" value="1"/> 130 <param name="output_format" value="1"/>
141 <output name="output" file="really_small.mzml" ftype="mzml" compare="sim_size" delta="3000" /> 131 <output name="output" file="really_small.mzml" ftype="mzml" compare="sim_size" delta="3000" />
142 </test> 132 </test>
143 133
144 <!-- Testing contents of converted mgf file with txt metadata --> 134 <!-- Testing contents of converted mgf file with txt metadata -->
145 <test expect_num_outputs="2"> 135 <test expect_num_outputs="2">
146 <param name="input" value="really_small.raw"/> 136 <param name="input" value="really_small.raw" ftype="thermo.raw"/>
147 <param name="output_format" value="0"/> 137 <param name="output_format" value="0"/>
148 <param name="output_metadata_selector" value="1"/> 138 <param name="output_metadata_selector" value="1"/>
149 <output name="output"> 139 <output name="output" ftype="mgf">
150 <assert_contents> 140 <assert_contents>
151 <has_text text="SCANS=36"/> 141 <has_text text="SCANS=36"/>
152 <has_text text="RTINSECONDS=73.863181104"/> 142 <has_text text="RTINSECONDS=73.863181104"/>
153 <has_text text="PEPMASS=675.248779296875"/> 143 <has_text text="PEPMASS=675.248779296875"/>
154 <has_text text="CHARGE=2+"/> 144 <has_text text="CHARGE=2+"/>
174 164
175 </test> 165 </test>
176 166
177 <!-- Basic mzml collection test --> 167 <!-- Basic mzml collection test -->
178 <test expect_num_outputs="1"> 168 <test expect_num_outputs="1">
179 <param name="input" value="really_small.raw,really_small_2.raw"/> 169 <param name="input" value="really_small.raw,really_small_2.raw" ftype="thermo.raw"/>
180 <param name="output_format" value="1"/> 170 <param name="output_format" value="1"/>
181 <output_collection name="output_mzml_collection" type="list" count="2"/> 171 <output_collection name="output_mzml_collection" type="list" count="2"/>
182 </test> 172 </test>
183 173
184 <!-- mgf collection test with metadata --> 174 <!-- mgf collection test with metadata -->