annotate thermo_converter.xml @ 8:26c6706bfb07 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a502d3fbf1f1ecfca1c9b115beab9d9c0e358fb5"
author galaxyp
date Sat, 25 Jul 2020 16:26:42 -0400
parents 63769c4217a7
children 92ac8e086317
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1 <tool id="thermo_raw_file_converter" name="Thermo" version="1.2.3+galaxy0">
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2 <description>RAW file converter</description>
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3 <requirements>
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4 <requirement type="package" version="1.2.3">thermorawfileparser</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8 #import re
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10 mkdir ./raws_folder &&
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11 mkdir ./output_folder &&
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12 #for $input_raw in $input_files:
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13 #set $input_name = re.sub('[^\w\-\.]', '_',$input_raw.element_identifier.split('/')[-1].replace(".raw", "") + ".raw")
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14 ln -s -f '${input_raw}' './raws_folder/${input_name}' &&
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15 #end for
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17 ThermoRawFileParser.sh
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18 -d=./raws_folder
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19 -o=./output_folder
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20 -f=$output_format
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21 #if $output_metadata_selector != "off":
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22 --metadata="${output_metadata_selector}"
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23 #end if
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24 $zlib_boolean
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25 $peakpicking_boolean
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26 $ignore_instrument_errors_boolean
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27
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28 ]]>
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29 </command>
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30 <inputs>
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31 <param name="input_files" type="data" format="thermo.raw" label="Thermo RAW file" help="" multiple="true"
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32 optional="False" />
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34 <param name="output_format" type="select" label="Output format">
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35 <option value="0">mgf</option>
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36 <option value="1" selected="True">mzml</option>
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37 <option value="2">Indexed mzml</option>
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38 </param>
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40 <param name="zlib_boolean" type="boolean" truevalue="" falsevalue="-z" checked="true"
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41 label="Use zlib compression for the m/z ratios and intensities" help="" />
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43 <param name="peakpicking_boolean" type="boolean" truevalue="" falsevalue="-p" checked="true"
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44 label="Use the peak picking provided by the native thermo library" help="" />
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46 <param name="ignore_instrument_errors_boolean" type="boolean" truevalue="-e" falsevalue="" checked="true"
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47 label="Ignore missing instrument properties" help="If false, it stops the conversion if instrument properties are missing" />
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49 <param name="output_metadata_selector" type="select" label="Output metadata" >
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50 <option value="off" selected="True">No</option>
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51 <option value="0">json</option>
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52 <option value="1">txt</option>
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53 </param>
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54
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55 </inputs>
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56 <outputs>
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57
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58 <collection name="output_mgf_collection" type="list" label="${tool.name} on ${on_string}: MGF collection">
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59 <filter>output_format == "0"</filter>
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60 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.mgf" directory="output_folder" ext="mgf"/>
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61 </collection>
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62
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63 <collection name="output_mzml_collection" type="list" label="${tool.name} on ${on_string}: mzML collection">
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64 <filter>output_format == "1"</filter>
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65 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.mzML" ext="mzml" directory="output_folder"/>
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66 </collection>
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67
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68 <collection name="output_indexedmzml_collection" type="list" label="${tool.name} on ${on_string}: Indexed mzML collection">
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69 <filter>output_format == "2"</filter>
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70 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.mzML" ext="mzml" directory="output_folder"/>
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71 </collection>
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72
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73 <collection name="output_metadata_collection" type="list" label="${tool.name} on ${on_string}: metadata collection">
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74 <filter>output_metadata_selector != "off"</filter>
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75 <discover_datasets pattern="(?P&lt;designation&gt;.+)-metadata.txt" ext="txt" directory="output_folder"/>
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76 <discover_datasets pattern="(?P&lt;designation&gt;.+)-metadata.json" ext="json" directory="output_folder"/>
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77 </collection>
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78
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79 </outputs>
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81 <tests>
8
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82 <!-- Basic mgf test - 1 file -->
5
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83 <test expect_num_outputs="1">
8
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84 <param name="input_files" value="really_small.raw" ftype="thermo.raw"/>
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85 <param name="output_format" value="0"/>
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86 <output_collection name="output_mgf_collection" type="list" count="1"/>
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87
26c6706bfb07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a502d3fbf1f1ecfca1c9b115beab9d9c0e358fb5"
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88 <!--<output name="output" file="really_small.mzml" ftype="mzml" compare="sim_size" delta="3000" />-->
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89 </test>
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90
26c6706bfb07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a502d3fbf1f1ecfca1c9b115beab9d9c0e358fb5"
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91
26c6706bfb07 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a502d3fbf1f1ecfca1c9b115beab9d9c0e358fb5"
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92 <!-- Basic mzml test - 2 files -->
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93 <test expect_num_outputs="1">
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94 <param name="input_files" value="really_small.raw,really_small_2.raw" ftype="thermo.raw"/>
5
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95 <param name="output_format" value="1"/>
8
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96 <output_collection name="output_mzml_collection" type="list" count="2"/>
0
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97 </test>
5
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98
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99 <!-- Testing contents of converted mgf file with txt metadata -->
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100 <test expect_num_outputs="2">
8
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101 <param name="input_files" value="really_small.raw" ftype="thermo.raw"/>
1
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102 <param name="output_format" value="0"/>
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103 <param name="output_metadata_selector" value="1"/>
8
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104 <output_collection name="output_mgf_collection" type="list" count="1">
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105 <element name="really_small" ftype="mgf">
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106 <assert_contents>
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107 <has_text text="SCANS=36"/>
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108 <has_text text="RTINSECONDS=73.863181104"/>
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109 <has_text text="PEPMASS=675.248779296875"/>
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110 <has_text text="CHARGE=2+"/>
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111 <has_text text="121.3116455 920.2367553711"/>
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112 <has_text text="229.2241211 1137.6958007813"/>
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113 <has_text text="1577.8967285 1487.9519042969"/>
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114 </assert_contents>
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115 </element>
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116 </output_collection>
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117 <output_collection name="output_metadata_collection" type="list">
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118 <element name="really_small" ftype="txt">
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119 <assert_contents>
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120 <has_text text="Instrument model=[MS, MS:1000494, Thermo Scientific instrument model, Orbitrap Fusion]"/>
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121 <has_text text="Instrument name=Orbitrap Fusion"/>
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122 <has_text text="Instrument serial number=[MS, MS:1000529, instrument serial number, FSN10188]"/>
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123 <has_text text="Software version=[NCIT, NCIT:C111093, Software Version, 3.1.2412.17]"/>
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124 <has_text text="Mass resolution=[MS, MS:1000011, mass resolution, 0.500]"/>
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125 <has_text text="Number of scans=101"/>
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126 <has_text text="Scan range=1;101"/>
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127 <has_text text="Scan start time=[MS, MS:1000016, scan start time, 0.89]"/>
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128 <has_text text="Time range=0.89;1.59"/>
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129 <has_text text="Mass range=120.0000;2000.0000"/>
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130 </assert_contents>
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131 </element>
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132 </output_collection>
5
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133 </test>
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134
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135 <!-- mgf collection test with metadata -->
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136 <test expect_num_outputs="2">
8
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137 <param name="input_files" value="really_small.raw,really_small_2.raw,really_small_3.raw"/>
5
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138 <param name="output_format" value="0"/>
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139 <param name="output_metadata_selector" value="0"/>
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140 <output_collection name="output_mgf_collection" type="list" count="3"/>
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141 <output_collection name="output_metadata_collection" type="list" count="3"/>
1
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142 </test>
0
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143 </tests>
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144 <help>
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145 <![CDATA[
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146
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147 Thermo RAW file converter based on the great `ThermoRawFileParser <https://github.com/compomics/ThermoRawFileParser>`_ project.
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148
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149 ]]>
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150 </help>
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151 <citations>
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152 <citation type="bibtex">@misc{Galaxy Proteomics Tools,
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153 author = {Niels Hulstaert, et al.},
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154 title = {Galaxy Proteomics Tools},
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155 publisher = {GitHub},
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156 journal = {GitHub repository},
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157 year = {2017}, url = {https://github.com/compomics/ThermoRawFileParser}}
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158 </citation>
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159 </citations>
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160 </tool>