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comparison createMSP.xml @ 15:70257c77ea04 draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
author tomnl
date Wed, 27 Nov 2019 12:34:20 +0000
parents 5dd61e94d70d
children
comparison
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14:998c58a7abb3 15:70257c77ea04
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 </expand> 7 </expand>
8 <stdio> 8 <command detect_errors="exit_code"><![CDATA[
9 <exit_code range="1:" /> 9 Rscript '$__tool_directory__/createMSP.R'
10 </stdio> 10 --rdata_input '$rdata_input'
11 <command interpreter="Rscript" ><![CDATA[ 11 --method '$method'
12 createMSP.R
13 --rdata_input "$rdata_input"
14 --method "$method"
15 12
16 #if $metadata_cond.metadata_select == "true" 13 #if $metadata_cond.metadata_select == "true"
17 --metadata "$metadata_cond.metadata" 14 --metadata '$metadata_cond.metadata'
18 --metadata_cols "$metadata_cond.metadata_cols" 15 --metadata_cols '$metadata_cond.metadata_cols'
19 --metadata_cols_filter "$metadata_cond.metadata_cols_filter" 16 --metadata_cols_filter '$metadata_cond.metadata_cols_filter'
20 17
21 #end if 18 #end if
22 19
23 #if $xcms_group_cond.xcms_group_select == "true" 20 #if $xcms_group_cond.xcms_group_select == "true"
24 --xcms_groupids "$xcms_group_cond.xcms_groupids" 21 --xcms_groupids '$xcms_group_cond.xcms_groupids'
25 #end if 22 #end if
26 23
27 $filter 24 $filter
28 $adduct_split 25 $adduct_split
29 26
30 --msp_schema "$msp_schema" 27 --msp_schema $msp_schema
31 --intensity_ra "$intensity_ra" 28 --intensity_ra $intensity_ra
32 --include_adducts "$include_adducts" 29 --include_adducts $include_adducts
33 30
34 --out_dir '.' 31 --out_dir '.'
35 ]]></command> 32 ]]></command>
36 <inputs> 33 <inputs>
37 <param name="rdata_input" type="data" format="rdata" label="msPurity purityA dataset" argument="--purity_dataset" 34 <param argument="--rdata_input" type="data" format="rdata" label="msPurity purityA dataset"
38 help="RData file containing the purityA object following frag4feature and/or averageFragmentation"/> 35 help="RData file containing the purityA object following frag4feature and/or averageFragmentation"/>
39 <param name="method" type="select" label="How to choose fragmentation spectra (if precursor was fragmented in >1 scans per XCMS group feature)" 36 <param argument="--method" type="select" label="How to choose fragmentation spectra (if precursor was fragmented in >1 scans per XCMS group feature)"
40 help="'Average all' will use the averaged MS/MS spectra of the XCMS grouped feature, ignoring inter and intra file relationships, 37 help="'Average all' will use the averaged MS/MS spectra of the XCMS grouped feature, ignoring inter and intra file relationships,
41 'Average' (intra)' will use the intra file (within file) averaged MS/MS spectra of the XCMS grouped feature, 38 'Average' (intra)' will use the intra file (within file) averaged MS/MS spectra of the XCMS grouped feature,
42 'Average (inter)' will use the inter file (across file) MS/MS averaged spectra, 39 'Average (inter)' will use the inter file (across file) MS/MS averaged spectra,
43 'All scans' will export all matching MS/MS spectra to XCMS grouped features, 40 'All scans' will export all matching MS/MS spectra to XCMS grouped features,
44 'Max intensity' will choose the most MS/MS spectra with the most intense precursor ion for each XCMS grouped feature" 41 'Max intensity' will choose the most MS/MS spectra with the most intense precursor ion for each XCMS grouped feature"
45 argument="--method"> 42 >
46 <option value="av_all" selected="true">Average (all)</option> 43 <option value="av_all" selected="true">Average (all)</option>
47 <option value="av_intra">Average (intra)</option> 44 <option value="av_intra">Average (intra)</option>
48 <option value="av_inter">Average (inter)</option> 45 <option value="av_inter">Average (inter)</option>
49 <option value="all">All scans</option> 46 <option value="all">All scans</option>
50 <option value="max" >Max intensity</option> 47 <option value="max" >Max intensity</option>
51 </param> 48 </param>
52 49
53 <conditional name="metadata_cond"> 50 <conditional name="metadata_cond">
54 <param name="metadata_select" type="boolean" label="Use additional metadata?" /> 51 <param name="metadata_select" type="boolean" label="Use additional metadata?" />
55 <when value="true"> 52 <when value="true">
56 <param type="data" name="metadata" label="Metadata for each feature" format="tsv,tabular" 53 <param argument="--metadata" type="data" label="Metadata for each feature" format="tsv,tabular"
57 help="Metadata for each grouped XCMS feature, e.g. could be the adduct calculated from CAMERA "/> 54 help="Metadata for each grouped XCMS feature, e.g. could be the adduct calculated from CAMERA "/>
58 55
59 <param name="metadata_cols_filter" type="text" label="Metadata columns to use" value="" 56 <param argument="--metadata_cols_filter" type="text" label="Metadata columns to use" value=""
60 help="Comma separated string of column names where the corresponding values in the metadata will be used"/> 57 help="Comma separated string of column names where the corresponding values in the metadata will be used"/>
61 58
62 <param name="metadata_cols" type="text" label="Metadata columns for MSP spectra name" value="" 59 <param argument="--metadata_cols" type="text" label="Metadata columns for MSP spectra name" value=""
63 help="Comma separated string of column names where the corresponding values in the metadata will be used 60 help="Comma separated string of column names where the corresponding values in the metadata will be used
64 for MSP spectra name"/> 61 for MSP spectra name"/>
65 62
66 </when> 63 </when>
67 <when value="false"> 64 <when value="false">
69 </conditional> 66 </conditional>
70 67
71 <conditional name="xcms_group_cond"> 68 <conditional name="xcms_group_cond">
72 <param name="xcms_group_select" type="boolean" label="Select XCMS groups?" help="if set to no, all XCMS group features will be used" /> 69 <param name="xcms_group_select" type="boolean" label="Select XCMS groups?" help="if set to no, all XCMS group features will be used" />
73 <when value="true"> 70 <when value="true">
74 <param name="xcms_groupids" type="text" label="XCMS peak group ids" value="" 71 <param argument="--xcms_groupids" type="text" label="XCMS peak group ids" value=""
75 help="Comma separated string of XCMS group ids to export MSP spectra for. If blank all XCMS peak groups will be used"/> 72 help="Comma separated string of XCMS group ids to export MSP spectra for. If blank all XCMS peak groups will be used"/>
76 </when> 73 </when>
77 <when value="false"> 74 <when value="false">
78 </when> 75 </when>
79 </conditional> 76 </conditional>
80 77
81 <param name="intensity_ra" type="select" label="Include intensity, relative abundanace or both in the MSP file" 78 <param argument="--intensity_ra" type="select" label="Include intensity, relative abundanace or both in the MSP file">
82 argument="--intensity_ra">
83 <option value="intensity_ra" selected="true">Both intensity and relative abundance</option> 79 <option value="intensity_ra" selected="true">Both intensity and relative abundance</option>
84 <option value="intensity">Intensity only</option> 80 <option value="intensity">Intensity only</option>
85 <option value="ra">Relative abundance only</option> 81 <option value="ra">Relative abundance only</option>
86 </param> 82 </param>
87 83
88 <param name="msp_schema" type="select" label="MSP schema to use for files" 84 <param argument="--msp_schema" type="select" label="MSP schema to use for files">
89 argument="--msp_schema">
90 <option value="massbank" selected="true">MassBank (Europe)</option> 85 <option value="massbank" selected="true">MassBank (Europe)</option>
91 <option value="mona">MoNA</option> 86 <option value="mona">MoNA</option>
92 87
93 </param> 88 </param>
94 89
95 <param name="filter" type="boolean" checked="true" truevalue="--filter" falsevalue="" 90 <param argument="--filter" type="boolean" checked="true" truevalue="--filter" falsevalue=""
96 label="Filter peaks that have been flagged in prior processing steps" help="" /> 91 label="Filter peaks that have been flagged in prior processing steps" help="" />
97 92
98 93
99 <param name="include_adducts" type="select" label="Always include the following adduct descriptions in the MSP file" 94 <param argument="--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" 95 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> 96 <option value="[M+H]+">[M+H]+</option>
103 <option value="[M+Na]+">[M+Na]+</option> 97 <option value="[M+Na]+">[M+Na]+</option>
104 <option value="[M+NH4]+">[M+NH4]+</option> 98 <option value="[M+NH4]+">[M+NH4]+</option>
105 <option value="[M+K]+" >[M+K]+</option> 99 <option value="[M+K]+" >[M+K]+</option>
106 <option value="[M+CH3OH+H]+">[M+CH3OH+H]+</option> 100 <option value="[M+CH3OH+H]+">[M+CH3OH+H]+</option>
110 <option value="[M-H]-">[M-H]-</option> 104 <option value="[M-H]-">[M-H]-</option>
111 <option value="[M+HCOO]-" >[M+HCOO]-</option> 105 <option value="[M+HCOO]-" >[M+HCOO]-</option>
112 <option value="[M+CH3COO]-" >[M+CH3COO]-</option> 106 <option value="[M+CH3COO]-" >[M+CH3COO]-</option>
113 <option value="[M-H+CH3COOH]-" >[M-H+CH3COOH]-</option> 107 <option value="[M-H+CH3COOH]-" >[M-H+CH3COOH]-</option>
114 </param> 108 </param>
115 <param name="adduct_split" type="boolean" checked="true" label="Create MSP spectra for each adduct?" 109 <param argument="--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="" /> 110 help="Useful if the MSP file will be used for further annotation" truevalue="--adduct_split" falsevalue="" />
117 111
118 </inputs> 112 </inputs>
119 <outputs> 113 <outputs>
120 <data name="createMSP_output" format="msp" from_work_dir="lcmsms_spectra.msp" label="${tool.name} on ${on_string}: msp"/> 114 <data name="createMSP_output" format="msp" from_work_dir="lcmsms_spectra.msp" label="${tool.name} on ${on_string}: msp"/>