annotate dbAnnot.xml @ 2:f29b264120f9 draft default tip

Uploaded
author cheanney
date Thu, 16 Jul 2015 11:03:16 -0400
parents 5af6f6e0a0da
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
1 <tool id="dbAnnot" name="dbAnnot" version="1.0">
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
2 <description>Database Annotation (dbAnnot) allows for easy annotations of biological identifiers. </description>
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
3 <command interpreter="/usr/bin/php">
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
4 dbAnnotRestClient.php inputValues='$inputValues' annotations='$annotations' taxonId='$taxon' fileType='$filetype' > $result
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
5 </command>
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
6 <inputs>
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
7 <param name="annotations" type="text" size="30" label="Enter annotation ID name(s)" />
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
8 <param name="inputValues" type="text" area="true" size="4x40" label="Paste input ID value(s)" /> <param name="taxon" size="30" type="text" label="Enter a taxon id (optional)" />
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
9 <param name="filetype" type="select" label="fileType options">
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
10 <option value="table">table</option>
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
11 <option value="xml">xml</option>
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
12 <option value="json">json</option>
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
13 </param>
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
14 </inputs>
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
15
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
16 <outputs>
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
17 <data format="html" name="result" label="dbAnnot.results">
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
18 <change_format>
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
19 <when input="filetype" value="xml" format="xml" />
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
20 </change_format>
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
21 </data>
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
22 </outputs>
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
23
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
24
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
25 <help>
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
26
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
27 .. class:: infomark
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
28
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
29 **What it does**
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
30
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
31 Add instructions here.
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
32
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
33 -----
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
34
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
35
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
36 **Usage**
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
37 dbAnnot.php inputValues='SP140' annotations='Genes,Pathways' fileType='table' TaxonId='9606' (optional)
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
38 </help>
5af6f6e0a0da Uploaded
cheanney
parents:
diff changeset
39 </tool>