Mercurial > repos > davidvanzessen > change_o
comparison parsedb.xml @ 0:183edf446dcf draft default tip
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| author | davidvanzessen |
|---|---|
| date | Mon, 17 Jul 2017 07:44:27 -0400 |
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| children |
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| -1:000000000000 | 0:183edf446dcf |
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| 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> |