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comparison macros.xml @ 3:f439ed7a8f03 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author lecorguille
date Tue, 18 Sep 2018 16:09:25 -0400
parents 090cf284d9ff
children
comparison
equal deleted inserted replaced
2:3a5204f14fff 3:f439ed7a8f03
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="0.4_1">r-snow</requirement>
6 <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
7 <requirement type="package" version="1.1_4">r-batch</requirement>
8 </requirements>
9 </xml>
10 <xml name="requirements_light">
11 <requirements>
12 <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
13 </requirements>
14 </xml>
15 <xml name="stdio"> 3 <xml name="stdio">
16 <stdio> 4 <stdio>
17 <exit_code range="1" level="fatal" /> 5 <exit_code range="1" level="fatal" />
18 </stdio> 6 </stdio>
19 </xml> 7 </xml>
20 8
21 <token name="@COMMAND_XCMS_SCRIPT@"> 9 <!-- COMMAND -->
22 LC_ALL=C Rscript $__tool_directory__/xcms.r 10 <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
23 </token>
24 11
25 <token name="@COMMAND_LOG_EXIT@"> 12 <token name="@COMMAND_LOG_EXIT@">
26 ; 13 ;
27 return=\$?; 14 return=\$?;
28 mv log.txt '$log'; 15 cat 'log.txt';
29 cat '$log';
30 sh -c "exit \$return" 16 sh -c "exit \$return"
31 </token> 17 </token>
32 18
33 <!-- zipfile load for planemo test --> 19 <!-- INPUT_VALIDATORS -->
34 20 <xml name="input_validator_range_integer">
35 <token name="@COMMAND_FILE_LOAD@"> 21 <validator type="regex" message="The format is 'min,max'" >[0-9]+ *, *[0-9]+</validator>
36 #if $file_load_section.file_load_conditional.file_load_select == "yes":
37 #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
38 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
39 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
40
41 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
42 #else
43 zipfile '$file_load_section.file_load_conditional.input'
44 #end if
45 #end if
46 </token>
47
48 <xml name="input_file_load">
49 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
50 <conditional name="file_load_conditional">
51 <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
52 <option value="no" >no need</option>
53 <option value="yes" >yes</option>
54 </param>
55 <when value="no">
56 </when>
57 <when value="yes">
58 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
59 </when>
60 </conditional>
61 </section>
62 </xml> 22 </xml>
63 23
64 <xml name="test_file_load_zip"> 24 <xml name="input_validator_range_float">
65 <section name="file_load_section"> 25 <validator type="regex" message="The format is 'min,max'" >[0-9]+\.?[0-9]* *, *[0-9]+\.?[0-9]*</validator>
66 <conditional name="file_load_conditional">
67 <param name="file_load_select" value="yes" />
68 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
69 </conditional>
70 </section>
71 </xml> 26 </xml>
72 27
73 <xml name="test_file_load_single"> 28 <xml name="input_validator_list_integer">
74 <section name="file_load_section"> 29 <validator type="regex" message="The format is '1,2,4,6'" >[0-9, ]+</validator>
75 <conditional name="file_load_conditional">
76 <param name="file_load_select" value="yes" />
77 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
78 </conditional>
79 </section>
80 </xml> 30 </xml>
81 31
82 <token name="@COMMAND_PEAKLIST@">
83 #if $peaklist.peaklistBool
84 variableMetadataOutput '$variableMetadata'
85 dataMatrixOutput '$dataMatrix'
86 convertRTMinute $peaklist.convertRTMinute
87 numDigitsMZ $peaklist.numDigitsMZ
88 numDigitsRT $peaklist.numDigitsRT
89 intval $peaklist.intval
90 #end if
91 </token>
92 32
93 <xml name="input_peaklist"> 33 <token name="@INPUT_IMAGE_LABEL@">RData file</token>
94 <conditional name="peaklist"> 34 <token name="@INPUT_IMAGE_HELP@">It contains a xcms3::XCMSnExp object (named xdata)</token>
95 <param name="peaklistBool" type="boolean" label="Get a Peak List" />
96 <when value="true">
97 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
98 <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
99 <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
100 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
101 <option value="into" selected="true">into</option>
102 <option value="maxo">maxo</option>
103 <option value="intb">intb</option>
104 </param>
105 </when>
106 <when value="false" />
107 </conditional>
108 </xml>
109 35
110 <xml name="output_peaklist" token_function="">
111 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv">
112 <filter>(peaklist['peaklistBool'])</filter>
113 </data>
114 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" >
115 <filter>(peaklist['peaklistBool'])</filter>
116 </data>
117 </xml>
118 36
119 <token name="@HELP_AUTHORS@"> 37 <!-- MISC -->
120 .. class:: infomark 38 <token name="@HELP_AUTHORS_WRAPPERS@">
121
122 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
123 39
124 .. class:: infomark 40 .. class:: infomark
125 41
126 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M] 42 **Galaxy integration** ABiMS TEAM - SU/CNRS - Station biologique de Roscoff and Yann Guitton - LABERCA
43 Part of Workflow4Metabolomics.org [W4M]
127 44
128 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. 45 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
129 46
130 ---------------------------------------------------
131
132 </token> 47 </token>
133 48
134 49 <xml name="citation_w4m">
135 <xml name="citation">
136 <citations>
137 <citation type="doi">10.1021/ac051437y</citation>
138 <citation type="doi">10.1093/bioinformatics/btu813</citation> 50 <citation type="doi">10.1093/bioinformatics/btu813</citation>
139 </citations>
140 </xml> 51 </xml>
141 </macros> 52 </macros>