Mercurial > repos > mmonsoor > camera_combinexsannos

annotate macros.xml @ 14:018f73a9e98e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
author lecorguille
date Fri, 31 Mar 2017 11:20:26 -0400
parents ddce949e4b35
children 78d267387462
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
1 <?xml version="1.0"?>
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
2 <macros>
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
3 <xml name="requirements">
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
4 <requirements>
12
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
5 <requirement type="package" version="0.4_1">r-snow</requirement>
4
9a1a72ee9418 planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents: 3
diff changeset
6 <requirement type="package" version="1.26.0">bioconductor-camera</requirement>
9a1a72ee9418 planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents: 3
diff changeset
7 <requirement type="package" version="2.26.0">bioconductor-multtest</requirement>
12
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
8 <requirement type="package" version="1.1_4">r-batch</requirement>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
9 <requirement type="package" version="1.3.23">graphicsmagick</requirement>
2
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
10 </requirements>
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
11 </xml>
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
12 <xml name="stdio">
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
13 <stdio>
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
14 <exit_code range="1" level="fatal" />
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
15 </stdio>
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
16 </xml>
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
17
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
18 <token name="@COMMAND_CAMERA_SCRIPT@">
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
19 LANG=C Rscript $__tool_directory__/CAMERA.r
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
20 </token>
9
972152941964 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 8
diff changeset
21
12
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
22 <!-- raw file load for planemo test -->
9
972152941964 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 8
diff changeset
23 <token name="@COMMAND_FILE_LOAD@">
12
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
24 #if $file_load_section.file_load_conditional.file_load_select == "yes":
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
25 #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"):
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
26 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
27 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
28 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
9
972152941964 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 8
diff changeset
29 #else
12
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
30 zipfile '$file_load_section.file_load_conditional.input'
7
8b9a0e2f35b6 planemo upload commit f8a14a5bfd1843dc3f65b3f713c35dd62bf6996a-dirty
lecorguille
parents: 6
diff changeset
31 #end if
9
972152941964 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 8
diff changeset
32 #end if
6
558f89a7c5dd planemo upload commit 62670148178273a855c42e85438ce731548ada48-dirty
lecorguille
parents: 4
diff changeset
33 </token>
9
972152941964 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 8
diff changeset
34
12
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
35 <xml name="input_file_load">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
36 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
37 <conditional name="file_load_conditional">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
38 <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." >
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
39 <option value="no" >no need</option>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
40 <option value="yes" >yes</option>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
41 </param>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
42 <when value="no">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
43 </when>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
44 <when value="yes">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
45 <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." />
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
46 </when>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
47 </conditional>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
48 </section>
6
558f89a7c5dd planemo upload commit 62670148178273a855c42e85438ce731548ada48-dirty
lecorguille
parents: 4
diff changeset
49 </xml>
9
972152941964 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 8
diff changeset
50
12
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
51 <xml name="test_file_load_zip">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
52 <section name="file_load_section">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
53 <conditional name="file_load_conditional">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
54 <param name="file_load_select" value="yes" />
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
55 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
56 </conditional>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
57 </section>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
58 </xml>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
59
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
60 <xml name="test_file_load_single">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
61 <section name="file_load_section">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
62 <conditional name="file_load_conditional">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
63 <param name="file_load_select" value="yes" />
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
64 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
65 </conditional>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
66 </section>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
67 </xml>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
68
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
69 <!-- peaklist export option management -->
9
972152941964 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 8
diff changeset
70 <token name="@COMMAND_PEAKLIST@">
12
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
71 convertRTMinute $export.convertRTMinute
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
72 numDigitsMZ $export.numDigitsMZ
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
73 numDigitsRT $export.numDigitsRT
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
74 intval $export.intval
9
972152941964 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 8
diff changeset
75 </token>
972152941964 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 8
diff changeset
76
972152941964 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 8
diff changeset
77 <xml name="input_peaklist">
12
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
78 <section name="export" title="Export options">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
79 <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"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
80 <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" />
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
81 <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" />
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
82 <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
83 <option value="into" selected="true">into</option>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
84 <option value="maxo" >maxo</option>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
85 <option value="intb">intb</option>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
86 </param>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
87 </section>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
88 </xml>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
89
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
90 <xml name="test_peaklist">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
91 <section name="export">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
92 <param name="convertRTMinute" value="True"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
93 <param name="numDigitsMZ" value="4" />
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
94 <param name="numDigitsRT" value="1" />
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
95 <param name="intval" value="into"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
96 </section>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
97 </xml>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
98
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
99 <!-- annotate_diffreport <test> commun part -->
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
100 <xml name="test_annotate_diffreport">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
101 <section name="groupfwhm">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
102 <param name="sigma" value="6"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
103 <param name="perfwhm" value="0.6"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
104 </section>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
105 <section name="findisotopes">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
106 <param name="maxcharge" value="3"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
107 <param name="maxiso" value="4"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
108 <param name="minfrac" value="0.5"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
109 </section>
14
018f73a9e98e planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 12
diff changeset
110 <section name="findgeneral">
12
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
111 <param name="ppm" value="5"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
112 <param name="mzabs" value="0.015"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
113 <param name="max_peaks" value="100"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
114 </section>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
115 <section name="diffreport">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
116 <conditional name="options">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
117 <param name="option" value="show"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
118 <param name="eicmax" value="200"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
119 <param name="eicwidth" value="200"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
120 <param name="value" value="into"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
121 <param name="h" value="480"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
122 <param name="w" value="640"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
123 <param name="mzdec" value="2"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
124 <param name="sortpval" value="False"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
125 </conditional>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
126 </section>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
127 <expand macro="test_peaklist"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
128 </xml>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
129
14
018f73a9e98e planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 12
diff changeset
130 <xml name="test_annotate_quick_false">
12
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
131 <param name="quick" value="FALSE"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
132 <section name="groupcorr">
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
133 <param name="cor_eic_th" value="0.75"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
134 <param name="graphMethod" value="hcs"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
135 <param name="pval" value="0.05"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
136 <param name="calcCiS" value="True"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
137 <param name="calcIso" value="False"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
138 <param name="calcCaS" value="False"/>
ddce949e4b35 planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 9
diff changeset
139 </section>
9
972152941964 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 8
diff changeset
140 </xml>
972152941964 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 8
diff changeset
141
14
018f73a9e98e planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 12
diff changeset
142 <xml name="test_annotate_quick_true">
018f73a9e98e planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 12
diff changeset
143 <conditional name="quick_block">
018f73a9e98e planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 12
diff changeset
144 <param name="quick" value="TRUE"/>
018f73a9e98e planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 12
diff changeset
145 </conditional>
018f73a9e98e planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 12
diff changeset
146 </xml>
018f73a9e98e planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 12
diff changeset
147
2
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
148 <token name="@HELP_AUTHORS@">
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
149 .. class:: infomark
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
150
9
972152941964 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 8
diff changeset
151 **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
2
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
152
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
153 .. class:: infomark
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
154
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
155 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
156
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
157 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
158
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
159 ---------------------------------------------------
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
160
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
161 </token>
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
162
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
163
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
164 <xml name="citation">
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
165 <citations>
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
166 <citation type="doi">10.1021/ac202450g</citation>
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
167 <citation type="doi">10.1093/bioinformatics/btu813</citation>
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
168 </citations>
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
169 </xml>
2591056df814 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
170 </macros>