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comparison hcluster_sg_parser.xml @ 1:17aa68582a05 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
author earlhaminst
date Fri, 20 Jan 2017 06:13:23 -0500 (2017-01-20)
parents dbc49bd1a3e9
children 0a33fd8ead70
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0:dbc49bd1a3e9 1:17aa68582a05
1 <tool id="hcluster_sg_parser" name="hcluster_sg_parser" version="0.1.1"> 1 <tool id="hcluster_sg_parser" name="hcluster_sg_parser" version="0.2.0">
2 <description>Converts hcluster_sg 3-column output into lists of ids</description> 2 <description>converts hcluster_sg 3-column output into lists of IDs</description>
3 <command> 3 <command>
4 <![CDATA[ 4 <![CDATA[
5 perl $__tool_directory__/hcluster_sg_parser.pl 5 python '$__tool_directory__/hcluster_sg_parser.py' '$inputFile'
6 $inputFile 6 #if str($min_elems)
7 -m $min_elems
8 #end if
9 #if str($max_elems)
10 -M $max_elems
11 #end if
12 '$discarded'
7 ]]> 13 ]]>
8 </command> 14 </command>
9 <inputs> 15 <inputs>
10 <param name="inputFile" type="data" format="tabular" label="hcluster output file in 3-column format" help="3-columns format: cluster_id cluster-size cluster-members" /> 16 <param name="inputFile" type="data" format="tabular" label="hcluster output file in 3-column format" help="3-columns format: cluster_id cluster-size cluster-members" />
17 <param name="min_elems" type="integer" value="" min="0" optional="true" label="Minimum number of cluster elements" />
18 <param name="max_elems" type="integer" value="" min="2" optional="true" label="Maximum number of cluster elements" />
11 </inputs> 19 </inputs>
12 <outputs> 20 <outputs>
13 <collection name="ids_lists" type="list" label="${tool.name} on ${on_string}"> 21 <collection name="ids_lists" type="list" label="${tool.name} on ${on_string}">
14 <discover_datasets pattern="(?P&lt;designation&gt;.+)_output\.txt" ext="txt" /> 22 <discover_datasets pattern="(?P&lt;designation&gt;.+)_output\.txt" ext="txt" />
15 </collection> 23 </collection>
24 <data name="discarded" format="txt" label="${tool.name} on ${on_string}: discarded IDs" />
16 </outputs> 25 </outputs>
17 <tests> 26 <tests>
18 <test> 27 <test>
19 <param name="inputFile" ftype="tabular" value="hcluster_sg.tabular" /> 28 <param name="inputFile" ftype="tabular" value="hcluster_sg.tabular" />
20 <output_collection name="ids_lists" type="list"> 29 <output_collection name="ids_lists" type="list">
21 <element name="0" file="0_output.txt" ftype="txt" /> 30 <element name="0" file="0_output.txt" ftype="txt" />
22 <element name="1" file="1_output.txt" ftype="txt" /> 31 <element name="1" file="1_output.txt" ftype="txt" />
23 <element name="2" file="2_output.txt" ftype="txt" /> 32 <element name="2" file="2_output.txt" ftype="txt" />
24 <element name="3" file="3_output.txt" ftype="txt" /> 33 <element name="3" file="3_output.txt" ftype="txt" />
25 </output_collection> 34 </output_collection>
35 <output name="discarded" file="empty.txt" />
36 </test>
37 <test>
38 <param name="inputFile" ftype="tabular" value="hcluster_sg.tabular" />
39 <param name="min_elems" value="6" />
40 <output_collection name="ids_lists" type="list">
41 <element name="0" file="0_output.txt" ftype="txt" />
42 <element name="1" file="1_output.txt" ftype="txt" />
43 </output_collection>
44 <output name="discarded" file="discarded.txt" />
26 </test> 45 </test>
27 </tests> 46 </tests>
28 <help> 47 <help>
29 <![CDATA[ 48 <![CDATA[
30 Simple wrapper for hcluster_sg output parser. 49 A simple parser to convert the hcluster_sg 3-column output into lists of IDs, one list for each cluster.
50
51 When a minimum and/or maximum number of cluster elements are specified, the IDs contained in the filtered-out clusters are collected in the "discarded IDS" output dataset.
31 ]]> 52 ]]>
32 </help> 53 </help>
33 <citations> 54 <citations>
34 </citations> 55 </citations>
35 </tool> 56 </tool>