Mercurial > repos > iuc > tn93_cluster
annotate tn93_cluster.xml @ 2:eb6f0ec5b95e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit e9f254ea1c6712a96512cae4df91bfec8207a492
| author | iuc |
|---|---|
| date | Sat, 28 Sep 2024 16:34:39 +0000 |
| parents | 112d80c9ccca |
| children |
| rev | line source |
|---|---|
|
2
eb6f0ec5b95e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit e9f254ea1c6712a96512cae4df91bfec8207a492
iuc
parents:
1
diff
changeset
|
1 <tool id="tn93_cluster" name="TN93 Cluster" version="@TOOL_VERSION@+galaxy0"> |
|
0
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
2 <description>sequences that lie within a specific distance of each other</description> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
3 <macros> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
4 <import>macros.xml</import> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
5 </macros> |
|
1
112d80c9ccca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents:
0
diff
changeset
|
6 <expand macro="requirements"> |
|
0
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
7 <requirement type="package" version="3.9">python</requirement> |
|
1
112d80c9ccca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents:
0
diff
changeset
|
8 </expand> |
|
0
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
9 <version_command><![CDATA[tn93 --version]]></version_command> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
10 <command detect_errors="exit_code"><![CDATA[ |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
11 python '$__tool_directory__/tn93_cluster.py' --input '$input_fasta' --reference '$reference' --output '$tn93_clusters' |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
12 --threshold $threshold |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
13 --ambigs $ambigs |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
14 --cluster-type $cluster_type |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
15 --overlap $overlap |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
16 --fraction $fraction |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
17 --cluster-count $cluster_count |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
18 #if $compress: |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
19 --compressed '$tn93_compressed_clusters' |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
20 #end if |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
21 ]]></command> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
22 <inputs> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
23 <param name="input_fasta" type="data" format="fasta" label="Input in FASTA format" /> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
24 <param name="reference" type="data" format="fasta" label="Reference in FASTA format" /> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
25 <param argument="--compress" type="boolean" truevalue="--compress" falsevalue="" label="Output additional fasta dataset with compressed clusters" /> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
26 <param argument="--cluster-count" type="integer" value="200" label="Only retain this many clusters" /> |
|
1
112d80c9ccca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents:
0
diff
changeset
|
27 <param argument="--threshold" type="float" value="0.0005" min="0" max="1" label="Distance threshold" help="Sequences which lie within this distance will be clustered" /> |
|
0
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
28 <param argument="--ambigs" type="select" label="Strategy for ambiguous nucleotides"> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
29 <option value="resolve" selected="true">resolve</option> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
30 <option value="average">average</option> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
31 <option value="skip">skip</option> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
32 <option value="gapmm">gapmm</option> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
33 </param> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
34 <param argument="--cluster_type" type="select" label="Clustering rules" help=""All": Each sequence within the cluster must be within the specified distance of every other sequence in the cluster. "Any": Each sequence within the cluster must be within the specified distance of at least one other sequence."> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
35 <option value="all">All</option> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
36 <option value="any">Any</option> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
37 </param> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
38 <param name="overlap" argument="-l" type="integer" value="100" |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
39 label="Only process pairs that overlap by at least N bases" /> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
40 <param name="fraction" argument="-g" type="float" value="1.0" |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
41 label="Maximum tolerated fraction of ambiguous characters" /> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
42 </inputs> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
43 <outputs> |
|
1
112d80c9ccca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents:
0
diff
changeset
|
44 <data format="json" name="tn93_clusters" from_work_dir="clusters.json" /> |
|
112d80c9ccca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents:
0
diff
changeset
|
45 <data format="fasta" name="tn93_compressed_clusters" from_work_dir="clusters.fa"> |
|
0
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
46 <filter>compress</filter> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
47 </data> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
48 </outputs> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
49 <tests> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
50 <test expect_num_outputs="2"> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
51 <param name="input_fasta" value="cluster-in1-1.fa" /> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
52 <param name="reference" value="cluster-in1-2.fa" /> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
53 <param name="threshold" value="0.35" /> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
54 <param name="compress" value="true" /> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
55 <output file="cluster-out1.json" ftype="json" name="tn93_clusters" /> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
56 <output file="cluster-out1.fa" ftype="fasta" name="tn93_compressed_clusters" /> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
57 </test> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
58 </tests> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
59 <help><![CDATA[ |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
60 TN93-Cluster |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
61 ============ |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
62 |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
63 Clusters sequences within a minimum distance of each other using the 1993 |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
64 Tamura-Nei distance calculation. |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
65 |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
66 ]]></help> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
67 <expand macro="citations"> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
68 <citation type="doi">10.1093/oxfordjournals.molbev.a040023</citation> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
69 </expand> |
|
af03f3398f03
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
iuc
parents:
diff
changeset
|
70 </tool> |