Mercurial > repos > earlhaminst > hcluster_sg_parser

comparison hcluster_sg_parser.xml @ 4:02d73e6ca869 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
author earlhaminst
date Fri, 19 Jul 2019 11:44:07 -0400
parents f9e418125021
children
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3:f9e418125021 4:02d73e6ca869
1 <tool id="hcluster_sg_parser" name="hcluster_sg parser" version="0.2.0"> 1 <tool id="hcluster_sg_parser" name="hcluster_sg parser" version="0.2.1">
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 detect_errors="exit_code"> 3 <command detect_errors="exit_code">
4 <![CDATA[ 4 <![CDATA[
5 python '$__tool_directory__/hcluster_sg_parser.py' '$inputFile' 5 python '$__tool_directory__/hcluster_sg_parser.py' '$inputFile'
6 #if str($min_elems) 6 #if str($min_elems)
7 -m $min_elems 7 -m $min_elems
8 #end if 8 #end if
9 #if str($max_elems) 9 #if str($max_elems)
10 -M $max_elems 10 -M $max_elems
11 #end if 11 #end if
12 '$discarded' 12 '$discarded_min'
13 '$discarded_max'
13 ]]> 14 ]]>
14 </command> 15 </command>
15 <inputs> 16 <inputs>
16 <param name="inputFile" type="data" format="tabular" label="hcluster output file" help="Tab-separated format: cluster_id [other optional columns] cluster-size cluster-members" /> 17 <param name="inputFile" type="data" format="tabular" label="hcluster output file" help="Tab-separated format: cluster_id [other optional columns] 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="min_elems" type="integer" value="" min="0" optional="true" label="Minimum number of cluster elements" />
19 </inputs> 20 </inputs>
20 <outputs> 21 <outputs>
21 <collection name="ids_lists" type="list" label="${tool.name} on ${on_string}"> 22 <collection name="ids_lists" type="list" label="${tool.name} on ${on_string}">
22 <discover_datasets pattern="(?P&lt;designation&gt;.+)_output\.txt" ext="txt" /> 23 <discover_datasets pattern="(?P&lt;designation&gt;.+)_output\.txt" ext="txt" />
23 </collection> 24 </collection>
24 <data name="discarded" format="txt" label="${tool.name} on ${on_string}: discarded IDs" /> 25 <data name="discarded_min" format="txt" label="${tool.name} on ${on_string}: discarded IDs less than specified" />
26 <data name="discarded_max" format="txt" label="${tool.name} on ${on_string}: discarded IDs more than specified" />
25 </outputs> 27 </outputs>
26 <tests> 28 <tests>
27 <test> 29 <test>
28 <param name="inputFile" ftype="tabular" value="hcluster_sg.tabular" /> 30 <param name="inputFile" ftype="tabular" value="hcluster_sg.tabular" />
29 <output_collection name="ids_lists" type="list"> 31 <output_collection name="ids_lists" type="list">
30 <element name="0" file="0_output.txt" ftype="txt" /> 32 <element name="0" file="0_output.txt" ftype="txt" />
31 <element name="1" file="1_output.txt" ftype="txt" /> 33 <element name="1" file="1_output.txt" ftype="txt" />
32 <element name="2" file="2_output.txt" ftype="txt" /> 34 <element name="2" file="2_output.txt" ftype="txt" />
33 <element name="3" file="3_output.txt" ftype="txt" /> 35 <element name="3" file="3_output.txt" ftype="txt" />
34 </output_collection> 36 </output_collection>
35 <output name="discarded" file="empty.txt" /> 37 <output name="discarded_min" file="empty.txt" />
38 <output name="discarded_max" file="empty.txt" />
36 </test> 39 </test>
37 <test> 40 <test>
38 <param name="inputFile" ftype="tabular" value="hcluster_sg.tabular" /> 41 <param name="inputFile" ftype="tabular" value="hcluster_sg.tabular" />
39 <param name="min_elems" value="6" /> 42 <param name="min_elems" value="6" />
40 <output_collection name="ids_lists" type="list"> 43 <output_collection name="ids_lists" type="list">
41 <element name="0" file="0_output.txt" ftype="txt" /> 44 <element name="0" file="0_output.txt" ftype="txt" />
42 <element name="1" file="1_output.txt" ftype="txt" /> 45 <element name="1" file="1_output.txt" ftype="txt" />
43 </output_collection> 46 </output_collection>
44 <output name="discarded" file="discarded.txt" /> 47 <output name="discarded_min" file="discarded.txt" />
48 <output name="discarded_max" file="empty.txt" />
45 </test> 49 </test>
46 <test> 50 <test>
47 <param name="inputFile" ftype="tabular" value="hcluster_sg1.txt" /> 51 <param name="inputFile" ftype="tabular" value="hcluster_sg1.tabular" />
48 <output_collection name="ids_lists" type="list"> 52 <output_collection name="ids_lists" type="list">
49 <element name="0" file="hcluster_sg1_0_output.txt" ftype="txt" /> 53 <element name="0" file="hcluster_sg1_0_output.txt" ftype="txt" />
50 <element name="1" file="hcluster_sg1_1_output.txt" ftype="txt" /> 54 <element name="1" file="hcluster_sg1_1_output.txt" ftype="txt" />
51 <element name="2" file="hcluster_sg1_2_output.txt" ftype="txt" /> 55 <element name="2" file="hcluster_sg1_2_output.txt" ftype="txt" />
52 <element name="3" file="hcluster_sg1_3_output.txt" ftype="txt" /> 56 <element name="3" file="hcluster_sg1_3_output.txt" ftype="txt" />
54 <element name="5" file="hcluster_sg1_5_output.txt" ftype="txt" /> 58 <element name="5" file="hcluster_sg1_5_output.txt" ftype="txt" />
55 <element name="6" file="hcluster_sg1_6_output.txt" ftype="txt" /> 59 <element name="6" file="hcluster_sg1_6_output.txt" ftype="txt" />
56 <element name="7" file="hcluster_sg1_7_output.txt" ftype="txt" /> 60 <element name="7" file="hcluster_sg1_7_output.txt" ftype="txt" />
57 <element name="8" file="hcluster_sg1_8_output.txt" ftype="txt" /> 61 <element name="8" file="hcluster_sg1_8_output.txt" ftype="txt" />
58 </output_collection> 62 </output_collection>
59 <output name="discarded" file="empty.txt" /> 63 <output name="discarded_min" file="empty.txt" />
64 <output name="discarded_max" file="empty.txt" />
60 </test> 65 </test>
61 </tests> 66 </tests>
62 <help> 67 <help>
63 <![CDATA[ 68 <![CDATA[
64 A simple parser to convert the hcluster_sg output into lists of IDs, one list for each cluster. 69 A simple parser to convert the hcluster_sg output into lists of IDs, one list for each cluster.