Mercurial > repos > iuc > hmmer_hmmscan

annotate hmmscan.xml @ 7:d02bc72e520b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
author iuc
date Tue, 16 Jun 2020 09:23:51 +0000
parents 8e797aaf03fb
children 63f1dd395c05
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
5
8e797aaf03fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents: 3
diff changeset
2 <tool id="hmmer_hmmscan" name="hmmscan" version="@TOOL_VERSION@">
8e797aaf03fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents: 3
diff changeset
3 <description>search protein sequence(s) against a protein profile database</description>
0
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
4 <macros>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
5 <import>macros.xml</import>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
6 </macros>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
8 <expand macro="stdio"/>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
9 <command><![CDATA[
5
8e797aaf03fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents: 3
diff changeset
10 @INPUTHMMCHOICE@
0
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
11 hmmscan
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
12
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
13 @OFORMAT_WITH_OPTS@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
14 @THRESHOLDS@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
15 @CUT@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
16 @ACCEL_HEUR@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
17 @ADV_OPTS@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
18 @CPU@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
19 @SEED@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
20
5
8e797aaf03fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents: 3
diff changeset
21 '$input_hmm_filename'
3
4a09810b41ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents: 2
diff changeset
22 '$seqfile'
4a09810b41ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents: 2
diff changeset
23 > '$output'
5
8e797aaf03fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents: 3
diff changeset
24 ]]></command>
0
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
25 <inputs>
3
4a09810b41ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents: 2
diff changeset
26 <expand macro="input_hmm_choice" />
0
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
27 <!-- todo use Galaxy features like data libraries/data tables/??? -->
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
28 <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
7
d02bc72e520b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 5
diff changeset
29 <expand macro="oformat_with_opts_dom_pfam"/>
0
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
30 <expand macro="thresholds_xml"/>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
31 <expand macro="cut"/>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
32 <expand macro="accel_heur_xml"/>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
33 <expand macro="adv_opts"/>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
34 <expand macro="seed"/>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
35 </inputs>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
36 <outputs>
7
d02bc72e520b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 5
diff changeset
37 <expand macro="output_dom_pfam" tool="HMMSCAN"/>
0
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
38 </outputs>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
39 <tests>
7
d02bc72e520b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 5
diff changeset
40 <test expect_num_outputs="4">
3
4a09810b41ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents: 2
diff changeset
41 <param name="input_hmm_conditional|input_hmm_source" value="history"/>
4a09810b41ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
iuc
parents: 2
diff changeset
42 <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/>
0
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
43 <param name="seqfile" value="dna_target.fa"/>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
44 <expand macro="oformat_test" />
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
45 <expand macro="seed_test" />
7
d02bc72e520b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 5
diff changeset
46 <output name="output" file="MADE1.out" lines_diff="24">
d02bc72e520b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 5
diff changeset
47 <expand macro="assert_out" tool="hmmscan"/>
d02bc72e520b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 5
diff changeset
48 </output>
d02bc72e520b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 5
diff changeset
49 <output name="tblout" file="MADE1.out.tblout" lines_diff="14">
d02bc72e520b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 5
diff changeset
50 <expand macro="assert_tblout" tool="hmmscan"/>
d02bc72e520b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 5
diff changeset
51 </output>
d02bc72e520b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 5
diff changeset
52 <output name="domtblout" file="MADE1.out.domtblout" lines_diff="10">
d02bc72e520b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 5
diff changeset
53 <expand macro="assert_tblout" tool="hmmscan"/>
d02bc72e520b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 5
diff changeset
54 </output>
d02bc72e520b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 5
diff changeset
55 <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="10">
d02bc72e520b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 5
diff changeset
56 <expand macro="assert_tblout" tool="hmmscan"/>
d02bc72e520b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
iuc
parents: 5
diff changeset
57 </output>
0
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
58 </test>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
59 </tests>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
60 <help><![CDATA[
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
61 @HELP_PRE@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
62
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
63 hmmscan is used to search protein sequences against collections of protein
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
64 profiles. For each sequence in <seqfile>, use that query sequence to search the
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
65 target database of profiles in <hmmfile>, and output ranked lists of the profiles
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
66 with the most significant matches to the sequence.
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
67
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
68 @HELP_PRE_OTH@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
69
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
70 @OFORMAT_WITH_OPTS_HELP@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
71 @THRESHOLDS_HELP@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
72 @CUT_HELP@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
73 @ACCEL_HEUR_HELP@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
74 @ADV_OPTS_HELP@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
75 @SEED_HELP@
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
76
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
77 @ATTRIBUTION@
5
8e797aaf03fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
iuc
parents: 3
diff changeset
78 ]]></help>
0
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
79 <expand macro="citation"/>
c5952e194e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 86a44bf15f8184b690ee1af98aa1d5f86ad2fb3d-dirty
iuc
parents:
diff changeset
80 </tool>