|
0
|
1 <tool id="change_o_parsedb_galaxy" name="ParseDB" version="1.0">
|
|
|
2 <description>Change-O</description>
|
|
|
3 <command interpreter="bash">
|
|
|
4 #if $action.action_select=="fasta"
|
|
|
5 parsedb.sh fasta $input $out_file
|
|
|
6 #elif $action.action_select=="clip"
|
|
|
7 parsedb.sh clip $input $out_file
|
|
|
8 #elif $action.action_select=="split"
|
|
|
9 parsedb.sh split $input $out_file $action.column '$input.name'
|
|
|
10 #elif $action.action_select=="add"
|
|
|
11 parsedb.sh add $input $out_file $action.column $action.value
|
|
|
12 #elif $action.action_select=="delete"
|
|
|
13 parsedb.sh delete $input $out_file $action.column $action.value $action.regex
|
|
|
14 #elif $action.action_select=="drop"
|
|
|
15 parsedb.sh drop $input $out_file $action.column
|
|
|
16 #elif $action.action_select=="index"
|
|
|
17 parsedb.sh index $input $out_file $action.column
|
|
|
18 #elif $action.action_select=="rename"
|
|
|
19 parsedb.sh rename $input $out_file $action.column $action.newname
|
|
|
20 #elif $action.action_select=="select"
|
|
|
21 parsedb.sh select $input $out_file $action.column $action.value $action.regex
|
|
|
22 #elif $action.action_select=="sort"
|
|
|
23 parsedb.sh sort $input $out_file $action.column $action.num $action.desc
|
|
|
24 #elif $action.action_select=="update"
|
|
|
25 parsedb.sh update $input $out_file $action.column $action.value $action.update $action.regex
|
|
|
26 #end if
|
|
|
27 </command>
|
|
|
28 <inputs>
|
|
|
29 <param name="input" type="data" format="tabular" label="Change-o DB file" />
|
|
|
30 <conditional name="action">
|
|
|
31 <param name="action_select" type="select" label="Action">
|
|
|
32 <option value="fasta">Create a fasta file from database records</option>
|
|
|
33 <option value="clip">Create a clip-fasta file from database records</option>
|
|
|
34 <option value="split">Split database files by field values</option>
|
|
|
35 <option value="add">Add field and value pairs</option>
|
|
|
36 <option value="delete">Delete specific records</option>
|
|
|
37 <option value="drop">Delete entire fields</option>
|
|
|
38 <option value="index">Add a numeric index field</option>
|
|
|
39 <option value="rename">Renames fields</option>
|
|
|
40 <option value="select">Select specific records</option>
|
|
|
41 <option value="sort">Sort records by field values</option>
|
|
|
42 <option value="update">Update field and value pairs</option>
|
|
|
43 </param>
|
|
|
44 <when value="fasta">
|
|
|
45
|
|
|
46 </when>
|
|
|
47 <when value="clip">
|
|
|
48
|
|
|
49 </when>
|
|
|
50 <when value="split">
|
|
|
51 <param name="column" label="Select the column to split on" type="data_column" data_ref="input" numerical="False" use_header_names="True" force_select="True" />
|
|
|
52 </when>l
|
|
|
53 <when value="add">
|
|
|
54 <param name="column" type="text" size="20" label="The new column name." />
|
|
|
55 <param name="value" type="text" size="20" label="The value that will be put in the new column" />
|
|
|
56 </when>
|
|
|
57 <when value="delete">
|
|
|
58 <param name="column" label="Select the column to search on." type="data_column" data_ref="input" numerical="False" use_header_names="True" force_select="True" />
|
|
|
59 <param name="value" type="text" size="20" label="The value that will be used" />
|
|
|
60 <param name="regex" type="select" label="Regex" help="Treat values as regular expressions and allow partial string matches.">
|
|
|
61 <option value="text" selected="true">False</option>
|
|
|
62 <option value="regex">True</option>
|
|
|
63 </param>
|
|
|
64 </when>
|
|
|
65 <when value="drop">
|
|
|
66 <param name="column" label="Select the column to remove" type="data_column" data_ref="input" numerical="False" use_header_names="True" force_select="True" />
|
|
|
67 </when>
|
|
|
68 <when value="index">
|
|
|
69 <param name="column" type="text" size="20" value="INDEX" label="The index column name" />
|
|
|
70 </when>
|
|
|
71 <when value="rename">
|
|
|
72 <param name="column" label="Select the column to delete on" type="data_column" data_ref="input" numerical="False" use_header_names="True" force_select="True" />
|
|
|
73 <param name="newname" type="text" size="20" value="newname" label="The new column name" />
|
|
|
74 </when>
|
|
|
75 <when value="select">
|
|
|
76 <param name="column" label="Select the column to search on" type="data_column" data_ref="input" numerical="False" use_header_names="True" force_select="True" />
|
|
|
77 <param name="value" type="text" size="20" label="The value that will be used" />
|
|
|
78 <param name="regex" type="select" label="Regex" help="Treat values as regular expressions and allow partial string matches">
|
|
|
79 <option value="text" selected="true">False</option>
|
|
|
80 <option value="regex">True</option>
|
|
|
81 </param>
|
|
|
82 </when>
|
|
|
83 <when value="sort">
|
|
|
84 <param name="column" label="Select the column to sort on" type="data_column" data_ref="input" numerical="False" use_header_names="True" force_select="True" />
|
|
|
85 <param name="num" type="select" label="Numerical" help="Define the sort column as numeric rather than textual.">
|
|
|
86 <option value="false" selected="true">False</option>
|
|
|
87 <option value="true">True</option>
|
|
|
88 </param>
|
|
|
89 <param name="desc" type="select" label="Descending" help="Sort records in descending">
|
|
|
90 <option value="false" selected="true">False</option>
|
|
|
91 <option value="true">True</option>
|
|
|
92 </param>
|
|
|
93 </when>
|
|
|
94 <when value="update">
|
|
|
95 <param name="column" label="Select the column to search on" type="data_column" data_ref="input" numerical="False" use_header_names="True" force_select="True" />
|
|
|
96 <param name="value" type="text" size="20" label="The value that will be replaced" />
|
|
|
97 <param name="update" type="text" size="20" label="The value that will replace the original" />
|
|
|
98 <param name="regex" type="select" label="Regex" help="Treat values as regular expressions and allow partial string matches">
|
|
|
99 <option value="text" selected="true">False</option>
|
|
|
100 <option value="regex">True</option>
|
|
|
101 </param>
|
|
|
102 </when>
|
|
|
103 </conditional>
|
|
|
104 </inputs>
|
|
|
105 <outputs>
|
|
|
106 <data format="tabular" name="out_file" label = "Change-o DB ${input.name}">
|
|
|
107 <filter>action['action_select'] != "split"</filter>
|
|
|
108 </data>
|
|
|
109 <data format="txt" name="split">
|
|
|
110 <discover_datasets pattern="(?P<designation>.+)\.tab" ext="tabular" directory="split" visible="true" />
|
|
|
111 <filter>action['action_select'] == "split"</filter>
|
|
|
112 </data>
|
|
|
113 </outputs>
|
|
|
114 <citations>
|
|
|
115 <citation type="doi">10.1093/bioinformatics/btv359</citation>
|
|
|
116 </citations>
|
|
|
117 <help>
|
|
|
118
|
|
|
119 </help>
|
|
|
120 </tool>
|
