Mercurial > repos > computational-metabolomics > mspurity_createmsp

comparison createMSP.xml @ 3:2e8e367c4937 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
author computational-metabolomics
date Thu, 09 Apr 2020 14:18:48 -0400
parents 35898942bfbb
children
comparison
equal deleted inserted replaced
2:54593159627d 3:2e8e367c4937
25 $adduct_split 25 $adduct_split
26 26
27 --msp_schema $msp_schema 27 --msp_schema $msp_schema
28 --intensity_ra $intensity_ra 28 --intensity_ra $intensity_ra
29 --include_adducts $include_adducts 29 --include_adducts $include_adducts
30 #if $include_adducts_custom
31 --include_adducts_custom "$include_adducts_custom"
32 #end if
30 33
31 --out_dir '.' 34 --out_dir '.'
32 ]]></command> 35 ]]></command>
33 <inputs> 36 <inputs>
34 <param argument="--rdata_input" type="data" format="rdata" label="msPurity purityA dataset" 37 <param argument="--rdata_input" type="data" format="rdata" label="msPurity purityA dataset"
104 <option value="[M-H]-">[M-H]-</option> 107 <option value="[M-H]-">[M-H]-</option>
105 <option value="[M+HCOO]-" >[M+HCOO]-</option> 108 <option value="[M+HCOO]-" >[M+HCOO]-</option>
106 <option value="[M+CH3COO]-" >[M+CH3COO]-</option> 109 <option value="[M+CH3COO]-" >[M+CH3COO]-</option>
107 <option value="[M-H+CH3COOH]-" >[M-H+CH3COOH]-</option> 110 <option value="[M-H+CH3COOH]-" >[M-H+CH3COOH]-</option>
108 </param> 111 </param>
112 <param argument="--include_adducts_custom" type="text" label="Always include the following custom adducts"
113 help="Additional custom adducts to include, should be comma separated" optional="true">
114 <expand macro="text-adduct-regex-validator"/>
115 </param>
116
109 <param argument="--adduct_split" type="boolean" checked="true" label="Create MSP spectra for each adduct?" 117 <param argument="--adduct_split" type="boolean" checked="true" label="Create MSP spectra for each adduct?"
110 help="Useful if the MSP file will be used for further annotation" truevalue="--adduct_split" falsevalue="" /> 118 help="Useful if the MSP file will be used for further annotation" truevalue="--adduct_split" falsevalue=""/>
111 119
112 </inputs> 120 </inputs>
113 <outputs> 121 <outputs>
114 <data name="createMSP_output" format="msp" from_work_dir="lcmsms_spectra.msp" label="${tool.name} on ${on_string}: msp"/> 122 <data name="createMSP_output" format="msp" from_work_dir="lcmsms_spectra.msp" label="${tool.name} on ${on_string}: msp"/>
115 </outputs> 123 </outputs>
116 <tests> 124 <tests>
117 125
118 <test> 126 <test>
119 <!-- 3) Test all average with metadata --> 127 <!-- Test all average with metadata -->
120 <param name="method" value="av_all"/> 128 <param name="method" value="av_all"/>
121 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/> 129 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
122 <param name="metadata_cond|metadata_select" value="true"/> 130 <param name="metadata_cond|metadata_select" value="true"/>
123 <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/> 131 <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/>
124 <param name="xcms_group_cond|xcms_group_select" value="true"/> 132 <param name="xcms_group_cond|xcms_group_select" value="true"/>
125 <param name="xcms_group_cond|xcms_groupids" value="8,12"/> 133 <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
126 <param name="metadata_cond|adduct_split" value="true"/> 134 <param name="metadata_cond|adduct_split" value="true"/>
127 <output name="createMSP_output" file="createMSP_output_av_all_metadata.msp"/> 135 <output name="createMSP_output" file="createMSP_output_av_all_metadata.msp"/>
128 </test> 136 </test>
137
138 <test>
139 <!-- Test custom adducts average with metadata -->
140 <param name="method" value="av_all"/>
141 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
142 <param name="metadata_cond|metadata_select" value="true"/>
143 <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/>
144 <param name="xcms_group_cond|xcms_group_select" value="true"/>
145 <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
146 <param name="metadata_cond|adduct_split" value="true"/>
147 <param name="include_adducts_custom" value="[M+]+,[M-H]-,[M+TEST SPACE+]+"/>
148 <output name="createMSP_output" file="createMSP_output_av_all_metadata_custom_adducts.msp"/>
149 </test>
150
151
129 152
130 </tests> 153 </tests>
131 <help><![CDATA[ 154 <help><![CDATA[
132 ------------------------------ 155 ------------------------------
133 Create MSP Files from msPurity 156 Create MSP Files from msPurity