root/galaxy-taverna/workflow-to-galaxy/test/Expected_BioAID_ProteinDiscovery_xml @ 85

Revision 85, 3.4 KB (checked in by kostas.karasavvas@…, 3 years ago)

updated test files for new generated output

Line 
1<tool id="BioAID_ProteinDiscovery_id" name="BioAID_ProteinDiscovery">
2  <command interpreter="ruby">
3    BioAID_ProteinDiscovery.rb
4    #if $Query_source.history_or_textfield == "textfield":
5      false "$Query_source.textfield_Query"
6    #else:
7      true  "$Query_source.history_Query"
8    #end if
9    #if $maxHits_parameter_source.history_or_textfield == "textfield":
10      false "$maxHits_parameter_source.textfield_maxHits_parameter"
11    #else:
12      true  "$maxHits_parameter_source.history_maxHits_parameter"
13    #end if
14    $ValidatedProtein $UniProtID
15  </command>
16  <inputs>
17    <conditional name="Query_source">
18      <param name="history_or_textfield" type="select" label="Select source for Query">
19        <option value="history">From history</option>
20        <option value="textfield" selected="true">Type manually</option>
21      </param>
22      <when value="history">
23        <param name="history_Query" type="data" label="Select Query"/>
24      </when>
25      <when value="textfield">
26        <param name="textfield_Query" type="text" area="True" size="2x50" value="&quot;transmembrane proteins&quot; AND amyloid" label="Enter Query"/>
27      </when>
28    </conditional>
29    <conditional name="maxHits_parameter_source">
30      <param name="history_or_textfield" type="select" label="Select source for maxHits_parameter">
31        <option value="history">From history</option>
32        <option value="textfield" selected="true">Type manually</option>
33      </param>
34      <when value="history">
35        <param name="history_maxHits_parameter" type="data" label="Select maxHits_parameter"/>
36      </when>
37      <when value="textfield">
38        <param name="textfield_maxHits_parameter" type="text" area="True" size="2x50" value="100" label="Enter maxHits_parameter"/>
39      </when>
40    </conditional>
41  </inputs>
42  <outputs>
43    <data format="tabular" name="ValidatedProtein" label="ValidatedProtein"/>
44    <data format="tabular" name="UniProtID" label="UniProtID"/>
45  </outputs>
46  <help>
47**What it does**
48
49The workflow extracts protein names from documents retrieved from MedLine based on a user Query (cf Apache Lucene syntax). The protein names are filtered by checking if there exists a valid UniProt ID for the given protein name.
50
51-----
52
53**Inputs**
54
55- **Query** Examples include:
56
57  - "transmembrane proteins" AND amyloid
58
59- **maxHits_parameter** Maximum number of documents to extract proteins from. Use &lt;10 for testing, 100 as default, &gt;100 if you want to live dangerously and can wait (may cause memory problems). Maximum number of documents to extract proteins from. Examples include:
60
61  - 100
62
63
64-----
65
66**Outputs**
67
68- **ValidatedProtein**
69- **UniProtID**
70
71-----
72
73.. class:: warningmark
74
75**Please note that some workflows are not up-to-date or have dependencies** that cannot be met by the specific Taverna server that you specified during generation of this tool. You can make sure that the workflow is valid by running it in the Taverna Workbench first to confirm that it works before running it via Galaxy.
76
77-----
78
79.. class:: warningmark
80
81**Please note that there might be some repetitions in the workflow description** in some of the generated workflows. This is due to a backwards compatibility issue on the myExperiment repository which keeps the old descriptions to make sure that no information is lost.
82
83-----
84
85.. class:: infomark
86
87**For more information on that workflow please visit** http://www.myexperiment.org/workflows/74.
88
89  </help>
90</tool>
Note: See TracBrowser for help on using the browser.