Mercurial > repos > iuc > hmmer_hmmbuild

comparison phmmer.xml.orig @ 10:51970d0e7bd7 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:40:07 +0000
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9:5c83ba4417e6 10:51970d0e7bd7
1 <?xml version="1.0"?>
2 <<<<<<< HEAD
3 <tool id="hmmer_phmmer" name="phmmer" version="@TOOL_VERSION@+galaxy1">
4 <description>search a protein sequence against a protein database (BLASTP-like)</description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements"/>
9 <expand macro="stdio"/>
10 <command><![CDATA[
11 @ADDTHREADS@
12 =======
13 <tool id="hmmer_phmmer" name="phmmer" version="@TOOL_VERSION@">
14 <description>search a protein sequence against a protein database (BLASTP-like)</description>
15 <expand macro="bio_tools"/>
16 <macros>
17 <import>macros.xml</import>
18 </macros>
19 <expand macro="requirements"/>
20 <expand macro="stdio"/>
21 <command><![CDATA[
22 >>>>>>> c37d72558 (add more bio.tool IDs)
23 phmmer
24
25 @OFORMAT_WITH_OPTS@
26 @HSSI@
27 @THRESHOLDS@
28 @ACCEL_HEUR@
29 @EVAL_CALIB@
30 @ADV_OPTS@
31
32 @CPU@
33 @SEED@
34
35 '$seqfile'
36 '$seqdb'
37 > '$output'
38 ]]></command>
39 <inputs>
40 <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
41 <!-- todo use Galaxy features like data libraries/data tables/??? -->
42 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
43 <expand macro="oformat_with_opts_dom_pfam"/>
44 <expand macro="hssi"/>
45 <expand macro="thresholds_xml"/>
46 <expand macro="accel_heur_xml"/>
47 <expand macro="eval_calib_xml"/>
48 <expand macro="adv_opts"/>
49 <expand macro="seed"/>
50 </inputs>
51 <outputs>
52 <expand macro="output_dom_pfam" tool="PHMMER"/>
53 </outputs>
54 <tests>
55 <test expect_num_outputs="4">
56 <param name="seqfile" value="globins45.fa"/>
57 <param name="seqdb" value="uniprot_matches.fasta"/>
58 <expand macro="oformat_test" />
59 <expand macro="seed_test" />
60 <output name="output" file="phmmer.out" lines_diff="200">
61 <expand macro="assert_out" tool="phmmer"/>
62 </output>
63 <!-- Lines diff is high due to a line of cpu/timing information for EACH sequence -->
64 <output name="domtblout" file="phmmer.domtblout" lines_diff="12">
65 <expand macro="assert_tblout" tool="phmmer"/>
66 </output>
67 <output name="pfamtblout" file="phmmer.pfamtblout" lines_diff="12">
68 <expand macro="assert_tblout" tool="phmmer"/>
69 </output>
70 <output name="tblout" file="phmmer.tblout" lines_diff="12">
71 <expand macro="assert_tblout" tool="phmmer"/>
72 </output>
73 </test>
74 <test expect_num_outputs="1">
75 <param name="seqfile" value="globins45.fa"/>
76 <param name="seqdb" value="uniprot_matches.fasta"/>
77 <expand macro="oformat_test" />
78 <param name="oformat" value=""/>
79 <expand macro="seed_test" />
80 <output name="output" file="phmmer.out" lines_diff="200">
81 <expand macro="assert_out" tool="phmmer"/>
82 </output>
83 </test>
84 </tests>
85 <help><![CDATA[
86 @HELP_PRE@
87
88 phmmer is used to search one or more query protein sequences against a protein
89 sequence database. For each query sequence in <seqfile>, use that sequence to
90 search the target database of sequences in <seqdb>, and output ranked lists of
91 the sequences with the most significant matches to the query.
92
93
94 @HELP_PRE_OTH@
95
96 @OFORMAT_WITH_OPTS_HELP@
97 @HSSI_HELP@
98 @THRESHOLDS_HELP@
99 @ACCEL_HEUR_HELP@
100 @EVAL_CALIB_HELP@
101 @ADV_OPTS_HELP@
102 @SEED_HELP@
103
104 @ATTRIBUTION@
105 ]]></help>
106 <expand macro="citation"/>
107 </tool>