Mercurial > repos > iuc > hmmer_jackhmmer

comparison jackhmmer.xml @ 9:9fdeca68a6b5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 721504306833ba97c91f285e5bfd86efc04875ee
author iuc
date Sun, 25 Feb 2024 18:32:59 +0000
parents 5cbef50c0c63
children
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8:5cbef50c0c63 9:9fdeca68a6b5
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@+galaxy0"> 2 <tool id="hmmer_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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="bio_tools"/> 7 <expand macro="bio_tools"/>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <expand macro="stdio"/> 9 <command detect_errors="aggressive"><![CDATA[
10 <command><![CDATA[
11 @ADDTHREADS@ 10 @ADDTHREADS@
12 jackhmmer 11 jackhmmer
13 -N $N 12 -N $N
14 @OFORMAT_WITH_OPTS@ 13 @OFORMAT_WITH_OPTS@
15 @HSSI@ 14 @HSSI@
29 > '$output' 28 > '$output'
30 ]]></command> 29 ]]></command>
31 <inputs> 30 <inputs>
32 <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"/>
33 <!-- todo use Galaxy features like data libraries/data tables/??? --> 32 <!-- todo use Galaxy features like data libraries/data tables/??? -->
34 <param name="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/> 33 <param argument="-N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/>
35 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/> 34 <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
36 <expand macro="oformat_with_opts_dom"/> 35 <expand macro="oformat_with_opts_dom"/>
37 <expand macro="hssi"/> 36 <expand macro="hssi"/>
38 <expand macro="thresholds_xml"/> 37 <expand macro="thresholds_xml"/>
39 <expand macro="accel_heur_xml"/> 38 <expand macro="accel_heur_xml"/>
54 <expand macro="oformat_test" /> 53 <expand macro="oformat_test" />
55 <expand macro="seed_test" /> 54 <expand macro="seed_test" />
56 <output name="output" file="jackhmmer.out" lines_diff="180"> 55 <output name="output" file="jackhmmer.out" lines_diff="180">
57 <expand macro="assert_out" tool="jackhmmer"/> 56 <expand macro="assert_out" tool="jackhmmer"/>
58 </output> 57 </output>
59 <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10"> 58 <output name="domtblout" file="jackhmmer.domtblout" lines_diff="12">
60 <expand macro="assert_tblout" tool="jackhmmer"/> 59 <expand macro="assert_tblout" tool="jackhmmer"/>
61 </output> 60 </output>
62 <output name="tblout" file="jackhmmer.tblout" lines_diff="10"> 61 <output name="tblout" file="jackhmmer.tblout" lines_diff="12">
63 <expand macro="assert_tblout" tool="jackhmmer"/> 62 <expand macro="assert_tblout" tool="jackhmmer"/>
64 </output> 63 </output>
65 </test> 64 </test>
66 <test expect_num_outputs="1"> 65 <test expect_num_outputs="1">
67 <param name="seqfile" value="uniprot_matches.fasta"/> 66 <param name="seqfile" value="uniprot_matches.fasta"/>