Mercurial > repos > iuc > hmmer_jackhmmer

comparison jackhmmer.xml @ 3:036df14999e8 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 03:48:57 -0400
parents d4fda6672a64
children 793967b6ae8a
comparison
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2:d4fda6672a64 3:036df14999e8
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_jackhmmer" name="jackhmmer" version="@WRAPPER_VERSION@.0"> 2 <tool id="hmmer_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@">
3 <description>iteratively search a protein sequence against a protein database (PSIBLAST-like)</description> 3 <description>iteratively search a protein sequence against a protein database (PSIBLAST-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"/>
21 @EVAL_CALIB@ 21 @EVAL_CALIB@
22 @ADV_OPTS@ 22 @ADV_OPTS@
23 @CPU@ 23 @CPU@
24 @SEED@ 24 @SEED@
25 25
26 $seqfile 26 '$seqfile'
27 $seqdb 27 '$seqdb'
28 > $output 28 > '$output'
29 ]]></command> 29 ]]></command>
30 <inputs> 30 <inputs>
31 <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/> 31 <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
32 <!-- todo use Galaxy features like data libraries/data tables/??? --> 32 <!-- todo use Galaxy features like data libraries/data tables/??? -->
33 <param name="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/> 33 <param name="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/>
34 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/> 34 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
43 <expand macro="eval_calib_xml"/> 43 <expand macro="eval_calib_xml"/>
44 <expand macro="adv_opts"/> 44 <expand macro="adv_opts"/>
45 <expand macro="seed"/> 45 <expand macro="seed"/>
46 </inputs> 46 </inputs>
47 <outputs> 47 <outputs>
48 <data format="txt" name="output" label="PHMMER search of $seqfile.name in $seqdb.name"/> 48 <data name="output" format="txt" label="PHMMER search of $seqfile.name in $seqdb.name"/>
49 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name"> 49 <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name">
50 <filter>oformat and 'tblout' in oformat</filter> 50 <filter>oformat and 'tblout' in oformat</filter>
51 </data> 51 </data>
52 <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name"> 52 <data name="domtblout" format="txt" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
53 <filter>oformat and 'domtblout' in oformat</filter> 53 <filter>oformat and 'domtblout' in oformat</filter>
54 </data> 54 </data>
55 </outputs> 55 </outputs>
56 <tests> 56 <tests>
57 <test> 57 <test>
89 @EVAL_CALIB_HELP@ 89 @EVAL_CALIB_HELP@
90 @ADV_OPTS_HELP@ 90 @ADV_OPTS_HELP@
91 @SEED_HELP@ 91 @SEED_HELP@
92 92
93 @ATTRIBUTION@ 93 @ATTRIBUTION@
94 ]]></help> 94 ]]></help>
95 <expand macro="citation"/> 95 <expand macro="citation"/>
96 </tool> 96 </tool>