Mercurial > repos > iuc > hmmer_nhmmscan

comparison nhmmscan.xml @ 7:e7d281a290a6 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 20:24:33 +0000
parents e07176c0925d
children fb1305d0d1c6
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6:e07176c0925d 7:e7d281a290a6
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_nhmmscan" name="nhmmscan" version="@TOOL_VERSION@+galaxy0"> 2 <tool id="hmmer_nhmmscan" name="nhmmscan" version="@TOOL_VERSION@+galaxy1">
3 <description>search DNA sequence(s) against a DNA profile database</description> 3 <description>search DNA sequence(s) against a DNA 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 nhmmscan 13 nhmmscan
13 14
14 @OFORMAT_WITH_OPTS@ 15 @OFORMAT_WITH_OPTS@
15 @THRESHOLDS_NODOM@ 16 @THRESHOLDS@
16 @CUT@
17 @ACCEL_HEUR@ 17 @ACCEL_HEUR@
18 --B1 $B1 18 --B1 $B1
19 --B2 $B2 19 --B2 $B2
20 --B3 $B3 20 --B3 $B3
21 21
31 <inputs> 31 <inputs>
32 <expand macro="input_hmm_choice" /> 32 <expand macro="input_hmm_choice" />
33 <!-- todo use Galaxy features like data libraries/data tables/??? --> 33 <!-- todo use Galaxy features like data libraries/data tables/??? -->
34 <param name="seqfile" type="data" format="fasta" label="Sequence file"/> 34 <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
35 <expand macro="oformat_with_opts_dfam_alisc"/> 35 <expand macro="oformat_with_opts_dfam_alisc"/>
36 <expand macro="thresholds_nodom"/> 36 <expand macro="thresholds_cut_xml"/>
37 <expand macro="cut"/>
38 <expand macro="accel_heur_xml"/> 37 <expand macro="accel_heur_xml"/>
39 38
40 <param argument="--B1" type="integer" value="110" label="window length for biased-composition modifier (MSV)" /> 39 <param argument="--B1" type="integer" value="110" label="window length for biased-composition modifier (MSV)" />
41 <param argument="--B2" type="integer" value="240" label="window length for biased-composition modifier (Vit)" /> 40 <param argument="--B2" type="integer" value="240" label="window length for biased-composition modifier (Vit)" />
42 <param argument="--B3" type="integer" value="1000" label="window length for biased-composition modifier (Fwd)" /> 41 <param argument="--B3" type="integer" value="1000" label="window length for biased-composition modifier (Fwd)" />