Mercurial > repos > mmonsoor > probmetab

comparison macros.xml @ 3:abcfa1648b66 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit c897279aa8cae0a4ad889bb05b143f32d2b6d712
author lecorguille
date Fri, 07 Apr 2017 07:14:12 -0400
parents 3a9914b37f2f
children
comparison
equal deleted inserted replaced
2:3a9914b37f2f 3:abcfa1648b66
14 </xml> 14 </xml>
15 15
16 <token name="@COMMAND_CAMERA_SCRIPT@"> 16 <token name="@COMMAND_CAMERA_SCRIPT@">
17 LANG=C Rscript $__tool_directory__/probmetab.r 17 LANG=C Rscript $__tool_directory__/probmetab.r
18 </token> 18 </token>
19 19
20 <!-- zipfile load for planemo test --> 20 <token name="@COMMAND_LOG_EXIT@">
21 <token name="@COMMAND_ZIPFILE_LOAD@"> 21 ;
22 #if $zipfile_load_conditional.zipfile_load_select == "yes": 22 return=\$?;
23 #if $zipfile_load_conditional.zip_file: 23 cat 'log.txt';
24 zipfile $zipfile_load_conditional.zip_file 24 sh -c "exit \$return"
25 </token>
26
27 <!-- raw file load for planemo test -->
28 <token name="@COMMAND_FILE_LOAD_NEUTRAL@">
29 #if $file_load_section_selected.file_load_conditional.file_load_select == "yes":
30 #if $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("netcdf"):
31 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section_selected.file_load_conditional.input ] )
32 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section_selected.file_load_conditional.input ] )
33 singlefile_galaxyPath$polarity '$singlefile_galaxyPath' singlefile_sampleName$polarity '$singlefile_sampleName'
34 #else
35 zipfile$polarity '$file_load_section_selected.file_load_conditional.input'
25 #end if 36 #end if
26 #end if 37 #end if
27 </token> 38 </token>
28 <xml name="zipfile_load"> 39
29 <conditional name="zipfile_load_conditional"> 40 <token name="@COMMAND_FILE_LOAD_ONE@">
30 <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." > 41 #set file_load_section_selected = $acquisition_options.file_load_section
31 <option value="no" >no need</option> 42 #set polarity=""
32 <option value="yes" selected="peakgroups">yes</option> 43 @COMMAND_FILE_LOAD_NEUTRAL@
33 </param> 44 </token>
34 <when value="no"> 45
35 </when> 46 <token name="@COMMAND_FILE_LOAD_POSITIVE@">
36 <when value="yes"> 47 #set file_load_section_selected = $acquisition_options.file_load_sectionPositive
37 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> 48 #set polarity="Positive"
38 </when> 49 @COMMAND_FILE_LOAD_NEUTRAL@
39 </conditional> 50 </token>
51
52 <token name="@COMMAND_FILE_LOAD_NEGATIVE@">
53 #set file_load_section_selected = $acquisition_options.file_load_sectionNegative
54 #set polarity="Negative"
55 @COMMAND_FILE_LOAD_NEUTRAL@
56 </token>
57
58 <xml name="input_file_load" token_polarity="">
59 <section name="file_load_section@POLARITY@" title="@POLARITY@ Resubmit your raw dataset or your zip file">
60 <conditional name="file_load_conditional">
61 <param name="file_load_select" type="select" label="@POLARITY@ 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." >
62 <option value="no" >no need</option>
63 <option value="yes" >yes</option>
64 </param>
65 <when value="no">
66 </when>
67 <when value="yes">
68 <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." />
69 </when>
70 </conditional>
71 </section>
40 </xml> 72 </xml>
41 73
74 <xml name="test_commun">
75 <section name="getannot">
76 <param name="allowMiss" value="TRUE" />
77 <conditional name="option_toexclude">
78 <param name="option" value="hide" />
79 </conditional>
80 </section>
81 <section name="db">
82 <param name="kegg_db" value="KEGG" />
83 <param name="ppm_tol" value="8" />
84 </section>
85 <section name="export">
86 <param name="prob" value="count" />
87 <param name="html" value="FALSE" />
88 </section>
89 <section name="reac2cor">
90 <param name="opt" value="cor" />
91 <param name="corprob" value="0.8" />
92 <param name="pcorprob" value="0.8" />
93 <param name="corths" value="0.75" />
94 </section>
95 </xml>
96
97 <xml name="test_file_load_zip">
98 <section name="file_load_section">
99 <conditional name="file_load_conditional">
100 <param name="file_load_select" value="yes" />
101 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
102 </conditional>
103 </section>
104 </xml>
105
106 <xml name="test_file_load_single" token_polarity="">>
107 <section name="file_load_section@POLARITY@">
108 <conditional name="file_load_conditional">
109 <param name="file_load_select" value="yes" />
110 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
111 </conditional>
112 </section>
113 </xml>
114
42 <token name="@HELP_AUTHORS@"> 115 <token name="@HELP_AUTHORS@">
43 .. class:: infomark 116 .. class:: infomark
44 117
45 **Authors** Ricardo R. Silva et al. (2013) rsilvabioinfo@usp.br 118 **Authors** Ricardo R. Silva et al. (2013) rsilvabioinfo@usp.br
46 119
47 | If you use this tool, please cite: Silva RR and al.(2010). ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics.. 120 | If you use this tool, please cite: Silva RR and al.(2010). ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics..
48 | For details about this tool, please go to http://labpib.fmrp.usp.br/methods/probmetab/ 121 | For details about this tool, please go to http://labpib.fmrp.usp.br/methods/probmetab/
49 122
50 .. class:: infomark 123 .. class:: infomark
51 124
52 **Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABIMS TEAM, Station biologique de Roscoff. 125 **Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr (and Gildas Le Corguillé) from ABIMS TEAM, Station biologique de Roscoff.
53 126
54 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. 127 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
55 128
56 .. class:: infomark 129 .. class:: infomark
57 130