| Previous changeset 8:2ec5e1ad1da7 (2023-11-06) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 721504306833ba97c91f285e5bfd86efc04875ee |
|
modified:
macros.xml nhmmer.xml |
| b |
| diff -r 2ec5e1ad1da7 -r 54b92ae4f75b macros.xml --- a/macros.xml Mon Nov 06 20:23:30 2023 +0000 +++ b/macros.xml Sun Feb 25 18:34:55 2024 +0000 |
| b |
| @@ -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@"> |
| b |
| diff -r 2ec5e1ad1da7 -r 54b92ae4f75b nhmmer.xml --- a/nhmmer.xml Mon Nov 06 20:23:30 2023 +0000 +++ b/nhmmer.xml Sun Feb 25 18:34:55 2024 +0000 |
| [ |
| @@ -1,13 +1,12 @@ <?xml version="1.0"?> -<tool id="hmmer_nhmmer" name="nhmmer" version="@TOOL_VERSION@+galaxy1"> +<tool id="hmmer_nhmmer" name="nhmmer" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>search a DNA model or alignment against a DNA database (BLASTN-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@ nhmmer @@ -48,7 +47,7 @@ <expand macro="oformat_test" /> <param name="oformat" value="tblout,dfamtblout,aliscoresout"/> <expand macro="seed_test" /> - <output name="output" file="nhmmer.out" lines_diff="16"> + <output name="output" file="nhmmer.out" lines_diff="18"> <expand macro="assert_out" tool="nhmmer"/> </output> <output name="tblout" file="nhmmer.out.tblout" lines_diff="12"> |