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comparison phmmer.xml @ 0:62479bdcc059 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
author iuc
date Tue, 12 May 2015 15:04:26 -0400
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-1:000000000000 0:62479bdcc059
1 <?xml version="1.0"?>
2 <tool id="hmmer_phmmer" name="phmmer" version="@WRAPPER_VERSION@.0">
3 <description>search a protein sequence against a protein database (BLASTP-like)</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[
10 phmmer
11
12 @OFORMAT_WITH_OPTS@
13 @HSSI@
14 @THRESHOLDS@
15 @ACCEL_HEUR@
16 @EVAL_CALIB@
17 @ADV_OPTS@
18
19 @CPU@
20 @SEED@
21
22 $seqfile
23 $seqdb
24 > $output
25 ]]></command>
26 <inputs>
27 <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
28 <!-- todo use Galaxy features like data libraries/data tables/??? -->
29 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
30 <expand macro="oformat_with_opts"/>
31 <expand macro="hssi"/>
32 <expand macro="thresholds_xml"/>
33 <expand macro="accel_heur_xml"/>
34 <expand macro="eval_calib_xml"/>
35 <expand macro="adv_opts"/>
36 <expand macro="seed"/>
37 </inputs>
38 <outputs>
39 <data format="txt" name="output" label="PHMMER search of $seqfile.name in $seqdb.name"/>
40 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name">
41 <filter>'tblout' in str(oformat)</filter>
42 </data>
43 <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
44 <filter>'domtblout' in str(oformat)</filter>
45 </data>
46 <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
47 <filter>'pfamtblout' in str(oformat)</filter>
48 </data>
49 </outputs>
50 <tests>
51 <test>
52 <param name="seqfile" value="globins45.fa"/>
53 <param name="seqdb" value="uniprot_matches.fasta"/>
54 <expand macro="oformat_test" />
55 <expand macro="seed_test" />
56 <output name="output" file="phmmer.out" lines_diff="200"/>
57 <!-- Lines diff is high due to a line of cpu/timing information for EACH sequence -->
58 <output name="domtblout" file="phmmer.domtblout" lines_diff="10"/>
59 <output name="pfamtblout" file="phmmer.pfamtblout" lines_diff="10"/>
60 <output name="tblout" file="phmmer.tblout" lines_diff="10"/>
61 </test>
62 </tests>
63 <help><![CDATA[
64 @HELP_PRE@
65
66 phmmer is used to search one or more query protein sequences against a protein
67 sequence database. For each query sequence in <seqfile>, use that sequence to
68 search the target database of sequences in <seqdb>, and output ranked lists of
69 the sequences with the most significant matches to the query.
70
71
72 @HELP_PRE_OTH@
73
74 @OFORMAT_WITH_OPTS_HELP@
75 @HSSI_HELP@
76 @THRESHOLDS_HELP@
77 @ACCEL_HEUR_HELP@
78 @EVAL_CALIB_HELP@
79 @ADV_OPTS_HELP@
80 @SEED_HELP@
81
82 @ATTRIBUTION@
83 ]]></help>
84 <expand macro="citation"/>
85 </tool>