| Previous changeset 10:d58c27d2c5a7 (2024-11-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit b3c4dcad33ad59a50c953f409896dc2279e776ab |
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modified:
bbduk.xml macros.xml |
| b |
| diff -r d58c27d2c5a7 -r 55e500606bbe bbduk.xml --- a/bbduk.xml Tue Nov 19 14:48:01 2024 +0000 +++ b/bbduk.xml Thu Feb 13 12:08:29 2025 +0000 |
| [ |
| @@ -142,6 +142,9 @@ enthist='${output_enthist}' #end if #end if +#if $log_file + 2> >(tee '$log_output' >&2) +#end if t=\${GALAXY_SLOTS:-4} ]]></command> <inputs> @@ -226,6 +229,7 @@ </param> </when> </conditional> + <param name="log_file" type="boolean" label="Generate a log file" help="Generates a log file, which can be used as MultiQC input"/> </inputs> <outputs> <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)"> @@ -283,15 +287,32 @@ <data name="output_enthist" format="tabular" label="${tool.name} on ${on_string} (Read entropy)"> <filter>output_hists_cond['output_hists'] == 'yes' and 'enthist' in output_hists_cond['output_hists_select']</filter> </data> + <data name="log_output" format="txt" label="${tool.name} on ${on_string} (Log file)"> + <filter>log_file</filter> + </data> </outputs> <tests> <!-- Single read --> - <test expect_num_outputs="1"> + <test expect_num_outputs="2"> <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/> <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/> <param name="reference_type" value="files"/> <param name="outputs_select" value="outu"/> + <param name="log_file" value="true"/> <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/> + <output name="log_output" ftype="txt"> + <assert_contents> + <has_text text="Executing jgi.BBDuk"/> + <has_text text="Input"/> + <has_text text="Contaminants"/> + <has_text text="Total Removed"/> + <has_text text="Result"/> + <has_text text="10000 bases"/> + <has_text text="100 reads"/> + <has_text text="0 reads"/> + <has_text text="0 bases"/> + </assert_contents> + </output> </test> <!-- Paired reads in separate datasets --> <test expect_num_outputs="4"> @@ -349,4 +370,4 @@ * **Single** - Singleton reads whose mate was trimmed shorter than the value of **Minimum read length**. </help> <expand macro="citations"/> -</tool> +</tool> \ No newline at end of file |
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| diff -r d58c27d2c5a7 -r 55e500606bbe macros.xml --- a/macros.xml Tue Nov 19 14:48:01 2024 +0000 +++ b/macros.xml Thu Feb 13 12:08:29 2025 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">39.08</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">22.01</token> <xml name="edam_ontology"> <edam_topics> |