Mercurial > repos > tomnl > create_sqlite_db

comparison create_sqlite_db.xml @ 11:c59965822dc8 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
author tomnl
date Mon, 07 May 2018 12:09:36 -0400
parents 9ab472c5714c
children 4acad02faf32
comparison
equal deleted inserted replaced
10:cf82f99f3638 11:c59965822dc8
1 <tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.4"> 1 <tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.6">
2 <description> 2 <description>
3 Create SQLite database of an XCMS-CAMERA dataset 3 Create SQLite database of an XCMS-CAMERA dataset
4 </description> 4 </description>
5 5
6 6
34 $i.name, 34 $i.name,
35 #end for 35 #end for
36 ' 36 '
37 #end if 37 #end if
38 38
39
40 #if $metfrag_conditional.metfrag_select=="yes"
41 --metfrag_result=$metfrag_result
42 #end if
43
44 #if $sirius_csifingerid_conditional.sirius_csifingerid_select=="yes"
45 --sirius_csifingerid_result=$sirius_csifingerid_result
46 #end if
47
48 #if $probmetab_conditional.probmetab_select=="yes"
49 --probmetab_result=$probmetab_result
50 #end if
51
39 #if $eic 52 #if $eic
40 --eic 53 --eic
41 #end if 54 #end if
42 #if $raw_rt_columns 55 #if $raw_rt_columns
43 --raw_rt_columns 56 --raw_rt_columns
69 82
70 <expand macro="grp_peaklist" /> 83 <expand macro="grp_peaklist" />
71 84
72 85
73 <expand macro="fileload" /> 86 <expand macro="fileload" />
87 <conditional name="metfrag_conditional">
88 <param name="metfrag_select" type="select" label="Include MetFrag results?">
89 <option value="no" >no</option>
90 <option value="yes" >yes</option>
91 </param>
92 <when value="no">
93 </when>
94 <when value="yes">
95 <param type="data" name="metfrag_result" label="MetFrag result" format="tsv,tabular"
96 help="MetFrag result from corresponding dataset"/>
97 </when>
98 </conditional>
74 99
100 <conditional name="sirius_csifingerid_conditional">
101 <param name="sirius_csifingerid_select" type="select" label="Include Sirius CSI-FingerID results?">
102 <option value="no" >no</option>
103 <option value="yes" >yes</option>
104 </param>
105 <when value="no">
106 </when>
107 <when value="yes">
108 <param type="data" name="sirius_csifingerid_result" label="Sirius CSI-FingerID result" format="tsv,tabular"
109 help="Sirius CSI-FingerID result from corresponding dataset"/>
110 </when>
111 </conditional>
112
113
114 <conditional name="probmetab_conditional">
115 <param name="probmetab_select" type="select" label="Include ProbMetab results?">
116 <option value="no" >no</option>
117 <option value="yes" >yes</option>
118 </param>
119 <when value="no">
120 </when>
121 <when value="yes">
122 <param type="data" name="probmetab_result" label="ProbMetab result" format="tsv,tabular"
123 help="ProbMetab result from corresponding dataset"/>
124 </when>
125 </conditional>
126
75 </inputs> 127 </inputs>
76 <outputs> 128 <outputs>
77 <data name="lcms_data_sqlite" format="sqlite" label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db" 129 <data name="lcms_data_sqlite" format="sqlite" label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db"
78 from_work_dir="lcms_data.sqlite" /> 130 from_work_dir="lcms_data.sqlite" />
79 <data name="cpeakgroup_msms" format="tsv" label="${tool.name} on ${on_string}: c-peak-group-msms" 131 <data name="cpeakgroup_msms" format="tsv" label="${tool.name} on ${on_string}: c-peak-group-msms"