Mercurial > repos > earlhaminst > hcluster_sg
annotate hcluster_sg.xml @ 3:891cc66ea91b draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 588282bf5cbb9909ad9cd8c316ec33158c858727
author | earlhaminst |
---|---|
date | Thu, 18 May 2017 14:10:32 -0400 |
parents | 176639d514ee |
children | 1d2de27d7a9c |
rev | line source |
---|---|
0
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
1 <tool id="hcluster_sg" name="hcluster_sg" version="0.5.1"> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
2 <description>Hierarchically clustering on a sparse graph</description> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
3 <requirements> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
4 <requirement type="package" version="0.5.1">hcluster_sg</requirement> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
5 </requirements> |
3
891cc66ea91b
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents:
2
diff
changeset
|
6 <command detect_errors="exit_code"><![CDATA[ |
0
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
7 hcluster_sg |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
8 -w $w |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
9 -s $s |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
10 -m $m |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
11 $c |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
12 -b $b |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
13 $O.O_selector |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
14 #if $O.O_selector == '-O' |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
15 -r $O.r |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
16 #end if |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
17 #if $C |
2
176639d514ee
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit f5c5f3d6ce676937f5c673ec7fc0631a9f490dc2
earlhaminst
parents:
0
diff
changeset
|
18 -C '$C' |
0
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
19 #end if |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
20 -L $L |
2
176639d514ee
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit f5c5f3d6ce676937f5c673ec7fc0631a9f490dc2
earlhaminst
parents:
0
diff
changeset
|
21 '$inputFile' |
176639d514ee
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit f5c5f3d6ce676937f5c673ec7fc0631a9f490dc2
earlhaminst
parents:
0
diff
changeset
|
22 > '$outputFile' |
3
891cc66ea91b
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents:
2
diff
changeset
|
23 ]]></command> |
0
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
24 <inputs> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
25 <param name="inputFile" type="data" format="tabular" label="Weight file" help="3-columns format: id-1 id-2 integer-weight" /> |
3
891cc66ea91b
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents:
2
diff
changeset
|
26 <param argument="-w" type="integer" min="0" value="20" label="Minimum edge weight" /> |
891cc66ea91b
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents:
2
diff
changeset
|
27 <param argument="-s" type="float" value="0.5" label="Minimum edge density between a join" /> |
891cc66ea91b
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents:
2
diff
changeset
|
28 <param argument="-m" type="integer" value="500" label="Maximum size" /> |
891cc66ea91b
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents:
2
diff
changeset
|
29 <param argument="-c" type="boolean" truevalue="-c" falsevalue="" label="Only find single-linkage clusters" help="Bypass h-cluster" /> |
891cc66ea91b
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents:
2
diff
changeset
|
30 <param argument="-b" type="float" value="0.1" label="Breaking edge density" /> |
0
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
31 <conditional name="O"> |
3
891cc66ea91b
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents:
2
diff
changeset
|
32 <param name="O_selector" argument="-O" type="select" label="Use once-fail-inactive-forever mode"> |
0
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
33 <option value="-O">Yes</option> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
34 <option value="" selected="true">No</option> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
35 </param> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
36 <when value="-O"> |
3
891cc66ea91b
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents:
2
diff
changeset
|
37 <param argument="-r" type="integer" value="5" label="Weight resolution" /> |
0
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
38 </when> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
39 <when value="" /> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
40 </conditional> |
3
891cc66ea91b
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents:
2
diff
changeset
|
41 <param argument="-C" type="data" format="tabular" optional="true" label="Category file" /> |
891cc66ea91b
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents:
2
diff
changeset
|
42 <param argument="-L" type="integer" value="2" label="Stringency level" /> |
0
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
43 </inputs> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
44 <outputs> |
3
891cc66ea91b
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents:
2
diff
changeset
|
45 <data name="outputFile" format="tabular" label="${tool.name} on ${on_string}" /> |
0
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
46 </outputs> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
47 <tests> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
48 <test> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
49 <param name="inputFile" ftype="tabular" value="exam-1.txt" /> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
50 <output name="outputFile" file="hcluster_sg1.txt" /> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
51 </test> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
52 <test> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
53 <param name="inputFile" ftype="tabular" value="exam-1.txt" /> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
54 <param name="c" value="true" /> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
55 <output name="outputFile" file="hcluster_sg2.txt" /> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
56 </test> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
57 </tests> |
3
891cc66ea91b
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents:
2
diff
changeset
|
58 <help><![CDATA[ |
0
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
59 Simple wrapper for `hcluster_sg`_. |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
60 |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
61 .. _hcluster_sg: https://github.com/douglasgscofield/hcluster |
3
891cc66ea91b
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents:
2
diff
changeset
|
62 ]]></help> |
0
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
63 <citations> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
64 </citations> |
4a233271d05a
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
parents:
diff
changeset
|
65 </tool> |