| Previous changeset 8:3bb58751f4ee (2023-11-06) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 721504306833ba97c91f285e5bfd86efc04875ee |
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modified:
hmmsearch.xml macros.xml |
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| diff -r 3bb58751f4ee -r df7a52791be9 hmmsearch.xml --- a/hmmsearch.xml Mon Nov 06 20:22:49 2023 +0000 +++ b/hmmsearch.xml Sun Feb 25 18:31:05 2024 +0000 |
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| @@ -1,13 +1,12 @@ <?xml version="1.0"?> -<tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@+galaxy1"> +<tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>search profile(s) against a sequence database</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@ hmmsearch @@ -42,7 +41,7 @@ <param name="seqdb" value="uniprot_matches.fasta"/> <expand macro="oformat_test" /> <expand macro="seed_test" /> - <output name="output" file="uniprot_globins_match.out" lines_diff="20"> + <output name="output" file="uniprot_globins_match.out" lines_diff="24"> <expand macro="assert_out" tool="hmmsearch"/> </output> <output name="domtblout" file="globins.domtblout" lines_diff="16"> @@ -94,12 +93,10 @@ <expand macro="oformat_test" /> <param name="oformat" value=""/> <expand macro="seed_test" /> - <output name="output" file="cut_ga_test.out" lines_diff="10"> + <output name="output" file="cut_ga_test.out" lines_diff="14"> <expand macro="assert_out" tool="hmmsearch"/> </output> </test> - - </tests> <help><![CDATA[ @HELP_PRE@ |
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| diff -r 3bb58751f4ee -r df7a52791be9 macros.xml --- a/macros.xml Mon Nov 06 20:22:49 2023 +0000 +++ b/macros.xml Sun Feb 25 18:31:05 2024 +0000 |
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| @@ -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@"> |