Mercurial > repos > bebatut > cdhit

annotate cd_hit_est.xml @ 1:2f0a6f227f87 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
author bebatut
date Tue, 12 Apr 2016 02:54:39 -0400
parents 617a5f3baf7f
children aa923171e225
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
1 <tool id="cd_hit_est" name="CD-HIT-EST" version="1.2">
1
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
2 <description>Cluster a nucleotide dataset into representative sequences</description>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
3
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
4 <macros>
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
5 <import>cdhit_macros.xml</import>
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
6 </macros>
1
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
7
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
8 <requirements>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
9 <requirement type="package" version="4.6.1">cd-hit</requirement>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
10 </requirements>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
11
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
12 <command><![CDATA[
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
13 cd-hit-est
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
14 -i "$fasta_in"
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
15 -o rep_seq
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
16 -c $similarity
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
17 -n $wordsize $strand
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
18
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
19 #include source=$common_cdhit_options#
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
20 #include source=$runtime_tuning#
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
21 ]]></command>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
22
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
23 <inputs>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
24 <param name="fasta_in" type="data" format="fasta" label="EST Sequences to cluster"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
25 <param name="similarity" type="float" value="0.9" label="similarity threshold: .75 - 1.0, default is .9">
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
26 <validator type="in_range" message="sequence similarity threshold should be .75 - 1.0" min=".75" max="1.0"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
27 </param>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
28 <param name="wordsize" type="integer" value="8" label="word size">
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
29 <help> Suggested word size:
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
30 8,9,10 for thresholds 0.90 ~ 1.0
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
31 7 for thresholds 0.88 ~ 0.9
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
32 6 for thresholds 0.85 ~ 0.88
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
33 5 for thresholds 0.80 ~ 0.85
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
34 4 for thresholds 0.75 ~ 0.8
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
35 </help>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
36 <validator type="in_range" message="word size should be between 4 and 10" min="4" max="10"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
37 </param>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
38 <param name="strand" type="boolean" truevalue="-r 1" falsevalue="" checked="false" label="Compare both strands"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
39 <expand macro="common_cdhit_options" />
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
40 <expand macro="runtime_tuning" />
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
41 </inputs>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
42
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
43 <outputs>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
44 <data format="txt" name="clusters_out" label="${tool.name} on ${on_string}: clusters" from_work_dir="rep_seq.clstr"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
45 <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: representatives.fasta" from_work_dir="rep_seq"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
46 </outputs>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
47
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
48 <tests>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
49 <test>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
50 <!-- Expect 3 clusters: 0,1,2 -->
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
51 <param name="fasta_in" value="cd_hit_est_in.fa" />
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
52 <param name="similarity" value="0.9"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
53 <param name="wordsize" value="8"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
54 <param name="strand" value="true"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
55 <!-- conditionals in macros -->
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
56 <param name="settings" value="no"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
57 <param name="tuning" value="default"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
58 <output name="clusters_out">
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
59 <assert_contents>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
60 <has_text text=">Cluster 0" />
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
61 <!-- There should not be a Cluster 3 -->
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
62 <not_has_text text="Cluster 3" />
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
63 <has_text_matching expression="F12Fcsw_481739" />
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
64 </assert_contents>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
65 </output>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
66 <output name="fasta_out">
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
67 <assert_contents>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
68 <has_text_matching expression="^>[MF]\d\dFcsw_\d*" />
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
69 </assert_contents>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
70 </output>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
71 </test>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
72 <test>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
73 <!-- tighter constraints should yield more clusters -->
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
74 <param name="fasta_in" value="cd_hit_est_in.fa" />
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
75 <param name="similarity" value="0.95"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
76 <param name="wordsize" value="9"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
77 <param name="strand" value="true"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
78 <!-- conditionals in macros -->
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
79 <param name="settings" value="no"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
80 <param name="tuning" value="default"/>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
81 <output name="clusters_out">
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
82 <assert_contents>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
83 <has_text text=">Cluster 4" />
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
84 <has_text_matching expression=">F12Fcsw_481739" />
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
85 </assert_contents>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
86 </output>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
87 <output name="fasta_out">
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
88 <assert_contents>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
89 <has_text_matching expression="^>[MF]\d\dFcsw_\d*" />
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
90 </assert_contents>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
91 </output>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
92 </test>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
93 </tests>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
94
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
95 <help><![CDATA[
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
96 **What it does**
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
97
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
98 CD-HIT_ stands for Cluster Database at High Identity with Tolerance. The program (cd-hit) takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr) representative sequences as output. In addition cd-hit outputs a cluster file, documenting the sequence 'groupies' for each nr sequence representative. The idea is to reduce the overall size of the database without removing any sequence information by only removing 'redundant' (or highly similar) sequences. This is why the resulting database is called non-redundant (nr). Essentially, cd-hit produces a set of closely related protein families from a given fasta sequence database.
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
99
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
100 .. _CD-HIT: http://www.bioinformatics.org/cd-hit/
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
101
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
102 ------
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
103
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
104 **Inputs**
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
105
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
106 cd-hit-est requires a fasta dataset as input.
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
107
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
108 ------
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
109
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
110 **Outputs**
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
111
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
112 A fasta datasets containing representative sequences.
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
113
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
114 A text file listing the mapping of sequences to the representative sequences::
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
115
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
116 >Cluster 0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
117 0 2799aa, >PF04998.6|RPOC2_CHLRE/275-3073... *
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
118 >Cluster 1
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
119 0 2214aa, >PF06317.1|Q6Y625_9VIRU/1-2214... at 80%
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
120 1 2215aa, >PF06317.1|O09705_9VIRU/1-2215... at 84%
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
121 2 2217aa, >PF06317.1|Q6Y630_9VIRU/1-2217... *
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
122 3 2216aa, >PF06317.1|Q6GWS6_9VIRU/1-2216... at 84%
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
123 4 527aa, >PF06317.1|Q67E14_9VIRU/6-532... at 63%
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
124 >Cluster 2
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
125 0 2202aa, >PF06317.1|Q6UY61_9VIRU/8-2209... at 60%
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
126 1 2208aa, >PF06317.1|Q6IVU4_JUNIN/1-2208... *
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
127 2 2207aa, >PF06317.1|Q6IVU0_MACHU/1-2207... at 73%
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
128 3 2208aa, >PF06317.1|RRPO_TACV/1-2208... at 69%
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
129
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
130
1
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
131 ]]></help>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
132
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
133 <citations>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
134 <citation type="doi">10.1093/bioinformatics/btl158</citation>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
135 <citation type="doi">10.1093/bioinformatics/bts565</citation>
2f0a6f227f87 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
bebatut
parents: 0
diff changeset
136 </citations>
0
617a5f3baf7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit 822c081d971c1fa6eef307936fb07dcf9d5db1c5-dirty
bebatut
parents:
diff changeset
137 </tool>