Mercurial > repos > iuc > hmmer_hmmscan

comparison hmmscan.xml @ 8:347a1f935f4c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 061757dd7b3bfe66b7738fd54bd6c5e135d9afe8
author iuc
date Mon, 06 Nov 2023 20:23:10 +0000
parents be072920a53e
children 4a54e4c9188b
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7:be072920a53e 8:347a1f935f4c
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_hmmscan" name="hmmscan" version="@TOOL_VERSION@+galaxy0"> 2 <tool id="hmmer_hmmscan" name="hmmscan" version="@TOOL_VERSION@+galaxy1">
3 <description>search protein sequence(s) against a protein profile database</description> 3 <description>search protein sequence(s) against a protein profile database</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 8 <expand macro="requirements"/>
8 <expand macro="stdio"/> 9 <expand macro="stdio"/>
9 <command><![CDATA[ 10 <command><![CDATA[
10 @ADDTHREADS@ 11 @ADDTHREADS@
11 @INPUTHMMCHOICE@ 12 @INPUTHMMCHOICE@
12 hmmscan 13 hmmscan
13 14
14 @OFORMAT_WITH_OPTS@ 15 @OFORMAT_WITH_OPTS@
15 @THRESHOLDS@ 16 @THRESHOLDS@
16 @CUT@ 17 @THRESHOLDS_DOM@
17 @ACCEL_HEUR@ 18 @ACCEL_HEUR@
18 @ADV_OPTS@ 19 @ADV_OPTS@
19 @CPU@ 20 @CPU@
20 @SEED@ 21 @SEED@
21 22
26 <inputs> 27 <inputs>
27 <expand macro="input_hmm_choice" /> 28 <expand macro="input_hmm_choice" />
28 <!-- todo use Galaxy features like data libraries/data tables/??? --> 29 <!-- todo use Galaxy features like data libraries/data tables/??? -->
29 <param name="seqfile" type="data" format="fasta" label="Sequence file" help="Please note this file should have a length less than 100K."/> 30 <param name="seqfile" type="data" format="fasta" label="Sequence file" help="Please note this file should have a length less than 100K."/>
30 <expand macro="oformat_with_opts_dom_pfam"/> 31 <expand macro="oformat_with_opts_dom_pfam"/>
31 <expand macro="thresholds_xml"/> 32 <expand macro="thresholds_cut_dom_xml"/>
32 <expand macro="cut"/>
33 <expand macro="accel_heur_xml"/> 33 <expand macro="accel_heur_xml"/>
34 <expand macro="adv_opts"/> 34 <expand macro="adv_opts"/>
35 <expand macro="seed"/> 35 <expand macro="seed"/>
36 </inputs> 36 </inputs>
37 <outputs> 37 <outputs>