Mercurial > repos > tomnl > mspurity_createmsp

comparison createMSP.xml @ 12:5dd61e94d70d draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
author tomnl
date Fri, 13 Sep 2019 11:53:46 -0400
parents 4b3b0f5a55d9
children 70257c77ea04
comparison
equal deleted inserted replaced
11:4b3b0f5a55d9 12:5dd61e94d70d
14 --method "$method" 14 --method "$method"
15 15
16 #if $metadata_cond.metadata_select == "true" 16 #if $metadata_cond.metadata_select == "true"
17 --metadata "$metadata_cond.metadata" 17 --metadata "$metadata_cond.metadata"
18 --metadata_cols "$metadata_cond.metadata_cols" 18 --metadata_cols "$metadata_cond.metadata_cols"
19 --adduct_split "$metadata_cond.adduct_split" 19 --metadata_cols_filter "$metadata_cond.metadata_cols_filter"
20
20 #end if 21 #end if
21 22
22 #if $xcms_group_cond.xcms_group_select == "true" 23 #if $xcms_group_cond.xcms_group_select == "true"
23 --xcms_groupids "$xcms_group_cond.xcms_groupids" 24 --xcms_groupids "$xcms_group_cond.xcms_groupids"
24 #end if 25 #end if
25 26
26 $filter 27 $filter
28 $adduct_split
27 29
28 --msp_schema "$msp_schema" 30 --msp_schema "$msp_schema"
29 --intensity_ra "$intensity_ra" 31 --intensity_ra "$intensity_ra"
32 --include_adducts "$include_adducts"
30 33
31 --out_dir '.' 34 --out_dir '.'
32 ]]></command> 35 ]]></command>
33 <inputs> 36 <inputs>
34 <param name="rdata_input" type="data" format="rdata" label="msPurity purityA dataset" argument="--purity_dataset" 37 <param name="rdata_input" type="data" format="rdata" label="msPurity purityA dataset" argument="--purity_dataset"
49 52
50 <conditional name="metadata_cond"> 53 <conditional name="metadata_cond">
51 <param name="metadata_select" type="boolean" label="Use additional metadata?" /> 54 <param name="metadata_select" type="boolean" label="Use additional metadata?" />
52 <when value="true"> 55 <when value="true">
53 <param type="data" name="metadata" label="Metadata for each feature" format="tsv,tabular" 56 <param type="data" name="metadata" label="Metadata for each feature" format="tsv,tabular"
54 help="Metadata for each grouped XCMS feature, the data will be added to the MSP metadata. 57 help="Metadata for each grouped XCMS feature, e.g. could be the adduct calculated from CAMERA "/>
55 Using the MassBank format e.g. https://github.com/MassBank/MassBank-data/blob/master/MetaboLights/ML003001.txt "/>
56 58
57 <param name="metadata_cols" type="text" label="Metadata columns for name" value="CH$NAME, MS$FOCUSED_ION: PRECURSOR_TYPE" help="Comma separated string of column names where the corresponding values in the metadata will be used for the MSP spectra name"/> 59 <param name="metadata_cols_filter" type="text" label="Metadata columns to use" value=""
58 <param name="adduct_split" type="boolean" checked="true" label="Create MSP spectra for each adduct?" help="If either 'adduct' or 'MS$FOCUSED_ION: PRECURSOR_TYPE' 60 help="Comma separated string of column names where the corresponding values in the metadata will be used"/>
59 column is in metadata then each adduct will have it's own MSP spectra. 61
60 (Useful, if the MSP file will be used for further annotation)" /> 62 <param name="metadata_cols" type="text" label="Metadata columns for MSP spectra name" value=""
61 </when> 63 help="Comma separated string of column names where the corresponding values in the metadata will be used
64 for MSP spectra name"/>
65
66 </when>
62 <when value="false"> 67 <when value="false">
63 </when> 68 </when>
64 </conditional> 69 </conditional>
65 70
66 <conditional name="xcms_group_cond"> 71 <conditional name="xcms_group_cond">
85 <option value="massbank" selected="true">MassBank (Europe)</option> 90 <option value="massbank" selected="true">MassBank (Europe)</option>
86 <option value="mona">MoNA</option> 91 <option value="mona">MoNA</option>
87 92
88 </param> 93 </param>
89 94
90 <param name="filter" type="boolean" checked="true" truevalue="--filter" falsevalue="" label="Filter peaks that have been flagged in prior processing steps" help="" /> 95 <param name="filter" type="boolean" checked="true" truevalue="--filter" falsevalue=""
96 label="Filter peaks that have been flagged in prior processing steps" help="" />
97
98
99 <param name="include_adducts" type="select" label="Always include the following adduct descriptions in the MSP file"
100 help="Additional adducts to include, can be useful for downstream processing" multiple="true"
101 argument="--include_adducts">
102 <option value="[M+H]+">[M+H]+</option>
103 <option value="[M+Na]+">[M+Na]+</option>
104 <option value="[M+NH4]+">[M+NH4]+</option>
105 <option value="[M+K]+" >[M+K]+</option>
106 <option value="[M+CH3OH+H]+">[M+CH3OH+H]+</option>
107 <option value="[M+ACN+H]+">[M+ACN+H]+</option>
108 <option value="[M+ACN+Na]+">[M+ACN+Na]+</option>
109 <option value="[M+2ACN+H]+">[M+2ACN+H]+</option>
110 <option value="[M-H]-">[M-H]-</option>
111 <option value="[M+HCOO]-" >[M+HCOO]-</option>
112 <option value="[M+CH3COO]-" >[M+CH3COO]-</option>
113 <option value="[M-H+CH3COOH]-" >[M-H+CH3COOH]-</option>
114 </param>
115 <param name="adduct_split" type="boolean" checked="true" label="Create MSP spectra for each adduct?"
116 help="Useful if the MSP file will be used for further annotation" truevalue="--adduct_split" falsevalue="" />
91 117
92 </inputs> 118 </inputs>
93 <outputs> 119 <outputs>
94 <data name="createMSP_output" format="msp" from_work_dir="lcmsms_spectra.msp" label="${tool.name} on ${on_string}: msp"/> 120 <data name="createMSP_output" format="msp" from_work_dir="lcmsms_spectra.msp" label="${tool.name} on ${on_string}: msp"/>
95 </outputs> 121 </outputs>
96 <tests> 122 <tests>
123
97 <test> 124 <test>
98 <param name="method" value="all"/> 125 <!-- 3) Test all average with metadata -->
99 <param name="rdata_input" value="frag4feature_output.RData"/>
100 <output name="createMSP_output" file="createMSP_output_scans_all.msp"/>
101 </test>
102 <test>
103 <param name="method" value="av_all"/>
104 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
105 <output name="createMSP_output" file="createMSP_output_av_all.msp"/>
106 </test>
107 <test>
108 <param name="method" value="av_all"/> 126 <param name="method" value="av_all"/>
109 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/> 127 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
110 <param name="metadata_cond|metadata_select" value="true"/> 128 <param name="metadata_cond|metadata_select" value="true"/>
111 <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/> 129 <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/>
112 <param name="metadata_cond|metadata_cols" value="AC$CHROMATOGRAPHY: COLUMN_NAME, AC$MASS_SPECTROMETRY: ION_MODE, AC$MASS_SPECTROMETRY: MS_TYPE, CH$LINK: INCHIKEY, CH$LINK: PUBCHEM CH$NAME
113 "/>
114 <param name="xcms_group_cond|xcms_group_select" value="true"/> 130 <param name="xcms_group_cond|xcms_group_select" value="true"/>
115 <param name="xcms_group_cond|xcms_groupids" value="8,12"/> 131 <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
116 <param name="metadata_cond|adduct_split" value="true"/> 132 <param name="metadata_cond|adduct_split" value="true"/>
117 <output name="createMSP_output" file="createMSP_output_av_all_metadata.msp"/> 133 <output name="createMSP_output" file="createMSP_output_av_all_metadata.msp"/>
118 </test> 134 </test>
119 <test> 135
120 <param name="method" value="av_all"/>
121 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
122 <param name="xcms_group_cond|xcms_group_select" value="true"/>
123 <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
124 <output name="createMSP_output" file="createMSP_output_av_all_and_all_xcms.msp"/>
125 </test>
126 <test>
127 <param name="method" value="av_intra"/>
128 <param name="rdata_input" value="averageFragSpectra_output_intra.RData"/>
129 <output name="createMSP_output" file="createMSP_output_av_intra.msp"/>
130 </test>
131 <test>
132 <param name="method" value="av_inter"/>
133 <param name="rdata_input" value="averageFragSpectra_output_inter.RData"/>
134 <output name="createMSP_output" file="createMSP_output_av_inter.msp"/>
135 </test>
136 <test>
137 <param name="method" value="max"/>
138 <param name="rdata_input" value="frag4feature_output.RData"/>
139 <output name="createMSP_output" file="createMSP_output_max.msp"/>
140 </test>
141 </tests> 136 </tests>
142 <help><![CDATA[ 137 <help><![CDATA[
143 ------------------------------ 138 ------------------------------
144 Create MSP Files from msPurity 139 Create MSP Files from msPurity
145 ------------------------------ 140 ------------------------------