Mercurial > repos > bebatut > format_cd_hit_output
annotate format_cd_hit_output.xml @ 0:4015e9d6d277 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
author | bebatut |
---|---|
date | Tue, 26 Apr 2016 08:55:33 -0400 |
parents | |
children | 64da677bcee2 |
rev | line source |
---|---|
0
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
1 <tool id="format_cd_hit_output" name="Format cd-hit outputs" version="1.0.0"> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
2 <description>to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file</description> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
3 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
4 <requirements> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
5 </requirements> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
6 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
7 <stdio> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
8 <exit_code range="1:" /> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
9 </stdio> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
10 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
11 <version_command> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
12 </version_command> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
13 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
14 <command><![CDATA[ |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
15 python $__tool_directory__/format_cd_hit_output.py |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
16 --input_cluster_info $input_cluster_info |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
17 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
18 #if $rename_repr_seq.rename_repr_seq_test == "true" |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
19 --input_representative_sequences $rename_repr_seq.input_representative_sequences |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
20 --output_representative_sequences $output_representative_sequences |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
21 #end if |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
22 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
23 #if $extract_cat_distri.extract_cat_distri_test == "true" |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
24 --input_mapping $extract_cat_distri.input_mapping |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
25 --output_category_distribution $output_category_distribution |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
26 $extract_cat_distri.number_sum |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
27 #end if |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
28 ]]> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
29 </command> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
30 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
31 <inputs> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
32 <param type="data" format="txt" name="input_cluster_info" label="Cluster info" help="(--input_cluster_info)"/> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
33 <conditional name="rename_repr_seq"> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
34 <param name='rename_repr_seq_test' type="select" label="Rename representative sequences with the corresponding cluster name?" help=""> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
35 <option value="true" selected="true">Yes</option> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
36 <option value="false">No</option> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
37 </param> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
38 <when value="true"> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
39 <param type="data" format="fasta" |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
40 name="input_representative_sequences" |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
41 label="Representative sequences" help="--input_representative_sequences)"/> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
42 </when> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
43 <when value="false" /> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
44 </conditional> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
45 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
46 <conditional name="extract_cat_distri"> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
47 <param name='extract_cat_distri_test' type="select" label="Extract category distribution of each cluster?" help=""> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
48 <option value="true" selected="true">Yes</option> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
49 <option value="false">No</option> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
50 </param> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
51 <when value="true"> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
52 <param type="data" format="tabular,tsv,csv" name="input_mapping" label="Mapping file" help="The mapping file is a tabular file with 2 columns. First column contains the sequence names and the second one the corresponding category (--input_mapping)"/> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
53 <param name='number_sum' type='boolean' checked="true" truevalue="--number_sum 1" falsevalue="" label="Sum sequence number for each category?" help="The alternative is the sum of size for sequences in each category (if the size information is available in sequence name, --number_sum)"/> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
54 </when> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
55 <when value="false" /> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
56 </conditional> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
57 </inputs> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
58 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
59 <outputs> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
60 <data name="output_representative_sequences" format="fasta" |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
61 label="${tool.name} on ${on_string}: Renamed representative sequences"> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
62 <filter>((rename_repr_seq['rename_repr_seq_test'] == "true"))</filter> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
63 </data> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
64 <data name="output_category_distribution" format="tabular" |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
65 label="${tool.name} on ${on_string}: Category distribution"> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
66 <filter>((extract_cat_distri['extract_cat_distri_test'] == "true"))</filter> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
67 </data> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
68 </outputs> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
69 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
70 <tests> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
71 <test> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
72 <param name="input_cluster_info" value="input_cluster_info.txt"/> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
73 <param name="rename_repr_seq_test" value="true"/> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
74 <param name="input_representative_sequences" value="input_representative_sequences.fasta"/> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
75 <param name="extract_cat_distri_test" value="true"/> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
76 <param name="input_mapping" value="input_mapping.txt"/> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
77 <param name="number_sum" value="true"/> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
78 <output name="output_representative_sequences" file="rename_representative_sequences_output.fasta"/> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
79 <output name="output_category_distribution" file="extract_category_distribution_output.tabular"/> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
80 </test> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
81 </tests> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
82 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
83 <help><![CDATA[ |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
84 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
85 **What it does** |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
86 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
87 This tool format cd-hit outputs (cluster information and cluster representative sequences) to rename representative sequences with cluster name and/or extract category distribution inside clusters given a mapping file. |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
88 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
89 The tool takes as input: |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
90 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
91 - The cd-hit output file with cluster information |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
92 - The cd-hit output file with representative sequences for each cluster (optional) |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
93 - A mapping file in tabular format with first column being the sequence names (corresponding to the ones in cluster information file) and the second column being the corresponding categories (optional) |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
94 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
95 The tool generates different outputs given chosen parameters: |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
96 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
97 - A file with representative sequences of each cluster named with the cluster name |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
98 - A tabular file with lines corresponding to clusters, columns to categories (and one column with sequence number in the cluster), and cases to number of sequences of the given category in the cluster |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
99 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
100 ]]> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
101 </help> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
102 |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
103 <citations></citations> |
4015e9d6d277
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_cd_hit_output/ commit 975a480d80c774a1de58c8fc80b71ea44c5c702b-dirty
bebatut
parents:
diff
changeset
|
104 </tool> |