Mercurial > repos > iuc > hmmer_jackhmmer
changeset 9:9fdeca68a6b5 draft default tip
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 | |
files | jackhmmer.xml macros.xml |
diffstat | 2 files changed, 11 insertions(+), 26 deletions(-) [+] |
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line diff
--- a/jackhmmer.xml Mon Nov 06 20:26:42 2023 +0000 +++ b/jackhmmer.xml Sun Feb 25 18:32:59 2024 +0000 @@ -1,13 +1,12 @@ <?xml version="1.0"?> -<tool id="hmmer_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@+galaxy0"> +<tool id="hmmer_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>iteratively search a protein sequence against a protein database (PSIBLAST-like)</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools"/> <expand macro="requirements"/> - <expand macro="stdio"/> - <command><![CDATA[ + <command detect_errors="aggressive"><![CDATA[ @ADDTHREADS@ jackhmmer -N $N @@ -31,7 +30,7 @@ <inputs> <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/> <!-- todo use Galaxy features like data libraries/data tables/??? --> - <param name="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/> + <param argument="-N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/> <param name="seqdb" type="data" format="fasta" label="Sequence Database"/> <expand macro="oformat_with_opts_dom"/> <expand macro="hssi"/> @@ -56,10 +55,10 @@ <output name="output" file="jackhmmer.out" lines_diff="180"> <expand macro="assert_out" tool="jackhmmer"/> </output> - <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10"> + <output name="domtblout" file="jackhmmer.domtblout" lines_diff="12"> <expand macro="assert_tblout" tool="jackhmmer"/> </output> - <output name="tblout" file="jackhmmer.tblout" lines_diff="10"> + <output name="tblout" file="jackhmmer.tblout" lines_diff="12"> <expand macro="assert_tblout" tool="jackhmmer"/> </output> </test>
--- a/macros.xml Mon Nov 06 20:26:42 2023 +0000 +++ b/macros.xml Sun Feb 25 18:32:59 2024 +0000 @@ -11,18 +11,8 @@ <xref type="bio.tools">hmmer3</xref> </xrefs> </xml> - <token name="@TOOL_VERSION@">3.3.2</token> - <xml name="stdio"> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:"/> - <exit_code range=":-1"/> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:"/> - <regex match="Exception:"/> - </stdio> - </xml> - + <token name="@TOOL_VERSION@">3.4</token> + <token name="@PROFILE@">22.05</token> <!-- command line for thresholds_* --> <token name="@THRESHOLDS@"> #if $repopt.repopt_sel == "evalue" @@ -363,17 +353,13 @@ <option value="--wnone">don't do any relative weighting; set all to 1 (--wnnoe)</option> <option value="--wgiven">use weights as given in MSA file (--wgiven)</option> </param> - <when value="--wpb"> - </when> - <when value="--wgsc"> - </when> + <when value="--wpb"/> + <when value="--wgsc"/> <when value="--wblosum"> <param argument="--wid" type="float" value="0.62" label="Set identity cutoff" /> </when> - <when value="--wnone"> - </when> - <when value="--wgiven"> - </when> + <when value="--wnone"/> + <when value="--wgiven"/> </conditional> </xml> <token name="@AEEWS@">