Mercurial > repos > iuc > hmmer_phmmer

comparison phmmer.xml @ 3:ff6e24314c63 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
author iuc
date Sat, 07 Apr 2018 03:48:11 -0400
parents 3c27cd24641d
children c1de05e20868
comparison
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2:3c27cd24641d 3:ff6e24314c63
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_phmmer" name="phmmer" version="@WRAPPER_VERSION@.0"> 2 <tool id="hmmer_phmmer" name="phmmer" version="@TOOL_VERSION@">
3 <description>search a protein sequence against a protein database (BLASTP-like)</description> 3 <description>search a protein sequence against a protein database (BLASTP-like)</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
17 @ADV_OPTS@ 17 @ADV_OPTS@
18 18
19 @CPU@ 19 @CPU@
20 @SEED@ 20 @SEED@
21 21
22 $seqfile 22 '$seqfile'
23 $seqdb 23 '$seqdb'
24 > $output 24 > '$output'
25 ]]></command> 25 ]]></command>
26 <inputs> 26 <inputs>
27 <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/> 27 <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
28 <!-- todo use Galaxy features like data libraries/data tables/??? --> 28 <!-- todo use Galaxy features like data libraries/data tables/??? -->
29 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/> 29 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
30 <expand macro="oformat_with_opts"/> 30 <expand macro="oformat_with_opts"/>
34 <expand macro="eval_calib_xml"/> 34 <expand macro="eval_calib_xml"/>
35 <expand macro="adv_opts"/> 35 <expand macro="adv_opts"/>
36 <expand macro="seed"/> 36 <expand macro="seed"/>
37 </inputs> 37 </inputs>
38 <outputs> 38 <outputs>
39 <data format="txt" name="output" label="PHMMER search of $seqfile.name in $seqdb.name"/> 39 <data name="output" format="txt" 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"> 40 <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name">
41 <filter>oformat and 'tblout' in oformat</filter> 41 <filter>oformat and 'tblout' in oformat</filter>
42 </data> 42 </data>
43 <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name"> 43 <data name="domtblout" format="txt" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
44 <filter>oformat and 'domtblout' in oformat</filter> 44 <filter>oformat and 'domtblout' in oformat</filter>
45 </data> 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"> 46 <data name="pfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
47 <filter>oformat and 'pfamtblout' in oformat</filter> 47 <filter>oformat and 'pfamtblout' in oformat</filter>
48 </data> 48 </data>
49 </outputs> 49 </outputs>
50 <tests> 50 <tests>
51 <test> 51 <test>
78 @EVAL_CALIB_HELP@ 78 @EVAL_CALIB_HELP@
79 @ADV_OPTS_HELP@ 79 @ADV_OPTS_HELP@
80 @SEED_HELP@ 80 @SEED_HELP@
81 81
82 @ATTRIBUTION@ 82 @ATTRIBUTION@
83 ]]></help> 83 ]]></help>
84 <expand macro="citation"/> 84 <expand macro="citation"/>
85 </tool> 85 </tool>