Mercurial > repos > iuc > hmmer_phmmer

comparison phmmer.xml @ 5:c1de05e20868 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
author iuc
date Tue, 16 Jun 2020 05:34:01 -0400
parents ff6e24314c63
children 8267b6ad0b45
comparison
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4:74fc6d7d40f1 5:c1de05e20868
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_dom_pfam"/>
31 <expand macro="hssi"/> 31 <expand macro="hssi"/>
32 <expand macro="thresholds_xml"/> 32 <expand macro="thresholds_xml"/>
33 <expand macro="accel_heur_xml"/> 33 <expand macro="accel_heur_xml"/>
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 name="output" format="txt" label="PHMMER search of $seqfile.name in $seqdb.name"/> 39 <expand macro="output_dom_pfam" tool="PHMMER"/>
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>
42 </data>
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>
45 </data>
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>
48 </data>
49 </outputs> 40 </outputs>
50 <tests> 41 <tests>
51 <test> 42 <test expect_num_outputs="4">
52 <param name="seqfile" value="globins45.fa"/> 43 <param name="seqfile" value="globins45.fa"/>
53 <param name="seqdb" value="uniprot_matches.fasta"/> 44 <param name="seqdb" value="uniprot_matches.fasta"/>
54 <expand macro="oformat_test" /> 45 <expand macro="oformat_test" />
55 <expand macro="seed_test" /> 46 <expand macro="seed_test" />
56 <output name="output" file="phmmer.out" lines_diff="200"/> 47 <output name="output" file="phmmer.out" lines_diff="200">
48 <expand macro="assert_out" tool="phmmer"/>
49 </output>
57 <!-- Lines diff is high due to a line of cpu/timing information for EACH sequence --> 50 <!-- Lines diff is high due to a line of cpu/timing information for EACH sequence -->
58 <output name="domtblout" file="phmmer.domtblout" lines_diff="10"/> 51 <output name="domtblout" file="phmmer.domtblout" lines_diff="12">
59 <output name="pfamtblout" file="phmmer.pfamtblout" lines_diff="10"/> 52 <expand macro="assert_tblout" tool="phmmer"/>
60 <output name="tblout" file="phmmer.tblout" lines_diff="10"/> 53 </output>
54 <output name="pfamtblout" file="phmmer.pfamtblout" lines_diff="12">
55 <expand macro="assert_tblout" tool="phmmer"/>
56 </output>
57 <output name="tblout" file="phmmer.tblout" lines_diff="12">
58 <expand macro="assert_tblout" tool="phmmer"/>
59 </output>
60 </test>
61 <test expect_num_outputs="1">
62 <param name="seqfile" value="globins45.fa"/>
63 <param name="seqdb" value="uniprot_matches.fasta"/>
64 <expand macro="oformat_test" />
65 <param name="oformat" value=""/>
66 <expand macro="seed_test" />
67 <output name="output" file="phmmer.out" lines_diff="200">
68 <expand macro="assert_out" tool="phmmer"/>
69 </output>
61 </test> 70 </test>
62 </tests> 71 </tests>
63 <help><![CDATA[ 72 <help><![CDATA[
64 @HELP_PRE@ 73 @HELP_PRE@
65 74