Mercurial > repos > earlhaminst > hcluster_sg_parser

annotate hcluster_sg_parser.xml @ 4:02d73e6ca869 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
diff changeset
1 <tool id="hcluster_sg_parser" name="hcluster_sg parser" version="0.2.1">
1
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
2 <description>converts hcluster_sg 3-column output into lists of IDs</description>
2
0a33fd8ead70 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit f5c5f3d6ce676937f5c673ec7fc0631a9f490dc2
earlhaminst
parents: 1
diff changeset
3 <command detect_errors="exit_code">
0
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
4 <![CDATA[
1
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
5 python '$__tool_directory__/hcluster_sg_parser.py' '$inputFile'
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
6 #if str($min_elems)
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
7 -m $min_elems
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
8 #end if
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
9 #if str($max_elems)
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
10 -M $max_elems
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
11 #end if
4
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
diff changeset
12 '$discarded_min'
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
diff changeset
13 '$discarded_max'
0
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
14 ]]>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
15 </command>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
16 <inputs>
3
f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 2
diff changeset
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" />
1
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
18 <param name="min_elems" type="integer" value="" min="0" optional="true" label="Minimum number of cluster elements" />
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
19 <param name="max_elems" type="integer" value="" min="2" optional="true" label="Maximum number of cluster elements" />
0
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
20 </inputs>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
21 <outputs>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
22 <collection name="ids_lists" type="list" label="${tool.name} on ${on_string}">
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
23 <discover_datasets pattern="(?P&lt;designation&gt;.+)_output\.txt" ext="txt" />
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
24 </collection>
4
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
diff changeset
25 <data name="discarded_min" format="txt" label="${tool.name} on ${on_string}: discarded IDs less than specified" />
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
diff changeset
26 <data name="discarded_max" format="txt" label="${tool.name} on ${on_string}: discarded IDs more than specified" />
0
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
27 </outputs>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
28 <tests>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
29 <test>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
30 <param name="inputFile" ftype="tabular" value="hcluster_sg.tabular" />
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
31 <output_collection name="ids_lists" type="list">
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
32 <element name="0" file="0_output.txt" ftype="txt" />
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
33 <element name="1" file="1_output.txt" ftype="txt" />
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
34 <element name="2" file="2_output.txt" ftype="txt" />
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
35 <element name="3" file="3_output.txt" ftype="txt" />
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
36 </output_collection>
4
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
diff changeset
37 <output name="discarded_min" file="empty.txt" />
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
diff changeset
38 <output name="discarded_max" file="empty.txt" />
1
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
39 </test>
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
40 <test>
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
41 <param name="inputFile" ftype="tabular" value="hcluster_sg.tabular" />
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
42 <param name="min_elems" value="6" />
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
43 <output_collection name="ids_lists" type="list">
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
44 <element name="0" file="0_output.txt" ftype="txt" />
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
45 <element name="1" file="1_output.txt" ftype="txt" />
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
46 </output_collection>
4
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
diff changeset
47 <output name="discarded_min" file="discarded.txt" />
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
diff changeset
48 <output name="discarded_max" file="empty.txt" />
0
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
49 </test>
3
f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 2
diff changeset
50 <test>
4
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
diff changeset
51 <param name="inputFile" ftype="tabular" value="hcluster_sg1.tabular" />
3
f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 2
diff changeset
52 <output_collection name="ids_lists" type="list">
f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 2
diff changeset
53 <element name="0" file="hcluster_sg1_0_output.txt" ftype="txt" />
f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 2
diff changeset
54 <element name="1" file="hcluster_sg1_1_output.txt" ftype="txt" />
f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 2
diff changeset
55 <element name="2" file="hcluster_sg1_2_output.txt" ftype="txt" />
f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 2
diff changeset
56 <element name="3" file="hcluster_sg1_3_output.txt" ftype="txt" />
f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 2
diff changeset
57 <element name="4" file="hcluster_sg1_4_output.txt" ftype="txt" />
f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 2
diff changeset
58 <element name="5" file="hcluster_sg1_5_output.txt" ftype="txt" />
f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 2
diff changeset
59 <element name="6" file="hcluster_sg1_6_output.txt" ftype="txt" />
f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 2
diff changeset
60 <element name="7" file="hcluster_sg1_7_output.txt" ftype="txt" />
f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 2
diff changeset
61 <element name="8" file="hcluster_sg1_8_output.txt" ftype="txt" />
f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 2
diff changeset
62 </output_collection>
4
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
diff changeset
63 <output name="discarded_min" file="empty.txt" />
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
diff changeset
64 <output name="discarded_max" file="empty.txt" />
3
f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 2
diff changeset
65 </test>
0
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
66 </tests>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
67 <help>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
68 <![CDATA[
3
f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 2
diff changeset
69 A simple parser to convert the hcluster_sg output into lists of IDs, one list for each cluster.
1
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
70
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents: 0
diff changeset
71 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.
0
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
72 ]]>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
73 </help>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
74 <citations>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
75 </citations>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
76 </tool>