annotate macros.xml @ 16:a2c49996603e draft

planemo upload commit e440674afa3e58c46100b0ac7c305a6f46ecbbdc
author lecorguille
date Wed, 19 Sep 2018 03:22:21 -0400
parents 6139bfcc95cb
children cb923396e70f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
1 <?xml version="1.0"?>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
2 <macros>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
3 <xml name="requirements">
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
4 <requirements>
15
6139bfcc95cb planemo upload commit 98f8d5d3e1a4356b411f16644ffa4da444ac2bdb
lecorguille
parents: 14
diff changeset
5 <requirement type="package" version="0.4_2">r-snow</requirement>
16
a2c49996603e planemo upload commit e440674afa3e58c46100b0ac7c305a6f46ecbbdc
lecorguille
parents: 15
diff changeset
6 <requirement type="package" version="3.0.0">bioconductor-xcms</requirement>
a2c49996603e planemo upload commit e440674afa3e58c46100b0ac7c305a6f46ecbbdc
lecorguille
parents: 15
diff changeset
7 <requirement type="package" version="1.34.0">bioconductor-camera</requirement>
15
6139bfcc95cb planemo upload commit 98f8d5d3e1a4356b411f16644ffa4da444ac2bdb
lecorguille
parents: 14
diff changeset
8 <requirement type="package" version="2.28.0">bioconductor-multtest</requirement>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
9 <requirement type="package" version="1.1_4">r-batch</requirement>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
10 <requirement type="package" version="1.3.23">graphicsmagick</requirement>
9
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
11 </requirements>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
12 </xml>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
13 <xml name="stdio">
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
14 <stdio>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
15 <exit_code range="1" level="fatal" />
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
16 </stdio>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
17 </xml>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
18
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
19 <token name="@COMMAND_CAMERA_SCRIPT@">
14
225cb8347572 planemo upload commit 239d7043ccba9d1d1861d7d8ac353c77497e0880
lecorguille
parents: 13
diff changeset
20 LC_ALL=C Rscript $__tool_directory__/CAMERA.r
9
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
21 </token>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
22
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
23 <!-- raw file load for planemo test -->
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
24 <token name="@COMMAND_FILE_LOAD@">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
25 #if $file_load_section.file_load_conditional.file_load_select == "yes":
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
26 #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"):
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
27 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
28 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
29 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
30 #else
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
31 zipfile '$file_load_section.file_load_conditional.input'
11
fc1fa0c70378 planemo upload commit f8a14a5bfd1843dc3f65b3f713c35dd62bf6996a-dirty
lecorguille
parents: 10
diff changeset
32 #end if
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
33 #end if
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
34 </token>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
35
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
36 <xml name="input_file_load">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
37 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
38 <conditional name="file_load_conditional">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
39 <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." >
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
40 <option value="no" >no need</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
41 <option value="yes" >yes</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
42 </param>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
43 <when value="no">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
44 </when>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
45 <when value="yes">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
46 <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." />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
47 </when>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
48 </conditional>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
49 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
50 </xml>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
51
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
52 <xml name="test_file_load_zip">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
53 <section name="file_load_section">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
54 <conditional name="file_load_conditional">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
55 <param name="file_load_select" value="yes" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
56 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
57 </conditional>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
58 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
59 </xml>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
60
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
61 <xml name="test_file_load_single">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
62 <section name="file_load_section">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
63 <conditional name="file_load_conditional">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
64 <param name="file_load_select" value="yes" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
65 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
66 </conditional>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
67 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
68 </xml>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
69
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
70 <!-- peaklist export option management -->
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
71 <token name="@COMMAND_PEAKLIST@">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
72 convertRTMinute $export.convertRTMinute
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
73 numDigitsMZ $export.numDigitsMZ
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
74 numDigitsRT $export.numDigitsRT
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
75 intval $export.intval
10
8dd6f0ffa763 planemo upload commit 62670148178273a855c42e85438ce731548ada48-dirty
lecorguille
parents: 9
diff changeset
76 </token>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
77
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
78 <xml name="input_peaklist">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
79 <section name="export" title="Export options">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
80 <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"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
81 <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" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
82 <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" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
83 <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
84 <option value="into" selected="true">into</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
85 <option value="maxo" >maxo</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
86 <option value="intb">intb</option>
10
8dd6f0ffa763 planemo upload commit 62670148178273a855c42e85438ce731548ada48-dirty
lecorguille
parents: 9
diff changeset
87 </param>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
88 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
89 </xml>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
90
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
91 <xml name="test_peaklist">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
92 <section name="export">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
93 <param name="convertRTMinute" value="True"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
94 <param name="numDigitsMZ" value="4" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
95 <param name="numDigitsRT" value="1" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
96 <param name="intval" value="into"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
97 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
98 </xml>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
99
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
100 <!-- annotate_diffreport <test> commun part -->
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
101 <xml name="test_annotate_diffreport">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
102 <section name="groupfwhm">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
103 <param name="sigma" value="6"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
104 <param name="perfwhm" value="0.6"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
105 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
106 <section name="findisotopes">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
107 <param name="maxcharge" value="3"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
108 <param name="maxiso" value="4"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
109 <param name="minfrac" value="0.5"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
110 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
111 <section name="findgeneral">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
112 <param name="ppm" value="5"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
113 <param name="mzabs" value="0.015"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
114 <param name="max_peaks" value="100"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
115 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
116 <section name="diffreport">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
117 <conditional name="options">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
118 <param name="option" value="show"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
119 <param name="eicmax" value="200"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
120 <param name="eicwidth" value="200"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
121 <param name="value" value="into"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
122 <param name="h" value="480"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
123 <param name="w" value="640"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
124 <param name="mzdec" value="2"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
125 <param name="sortpval" value="False"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
126 </conditional>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
127 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
128 <expand macro="test_peaklist"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
129 </xml>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
130
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
131 <xml name="test_annotate_quick_false">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
132 <param name="quick" value="FALSE"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
133 <section name="groupcorr">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
134 <param name="cor_eic_th" value="0.75"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
135 <param name="graphMethod" value="hcs"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
136 <param name="pval" value="0.05"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
137 <param name="calcCiS" value="True"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
138 <param name="calcIso" value="False"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
139 <param name="calcCaS" value="False"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
140 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
141 </xml>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
142
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
143 <xml name="test_annotate_quick_true">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
144 <conditional name="quick_block">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
145 <param name="quick" value="TRUE"/>
10
8dd6f0ffa763 planemo upload commit 62670148178273a855c42e85438ce731548ada48-dirty
lecorguille
parents: 9
diff changeset
146 </conditional>
8dd6f0ffa763 planemo upload commit 62670148178273a855c42e85438ce731548ada48-dirty
lecorguille
parents: 9
diff changeset
147 </xml>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
148
9
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
149 <token name="@HELP_AUTHORS@">
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
150 .. class:: infomark
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
151
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 12
diff changeset
152 **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
9
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
153
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
154 .. class:: infomark
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
155
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
156 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
157
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
158 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
159
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
160 ---------------------------------------------------
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
161
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
162 </token>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
163
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
164
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
165 <xml name="citation">
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
166 <citations>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
167 <citation type="doi">10.1021/ac202450g</citation>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
168 <citation type="doi">10.1093/bioinformatics/btu813</citation>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
169 </citations>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
170 </xml>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
171 </macros>