| Previous changeset 0:04d05400d3a6 (2022-05-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit faa8c4bf004428988500537078264968ae05fa67 |
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modified:
adapter_removal.xml macros.xml |
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| diff -r 04d05400d3a6 -r 40874f772ea1 adapter_removal.xml --- a/adapter_removal.xml Wed May 04 13:45:52 2022 +0000 +++ b/adapter_removal.xml Mon Aug 26 13:47:54 2024 +0000 |
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| @@ -50,6 +50,8 @@ --qualitybase '33' --qualitybase-output '33' --qualitymax $fastq_options.qualitymax +$fastq_options.convert_uracils +$fastq_options.mask_degenerate_bases ###### FASTQ Trimming Options --adapter1 '$fastq_trimming_options.adapter1' @@ -143,6 +145,8 @@ <!-- FASTQ Options --> <section name="fastq_options" title="FASTQ Options" expanded="false"> <param argument="--qualitymax" type="integer" value="41" min="0" max="93" label="Maximum Phred score expected in input files and used when writing output files" help="Possible values are 0 to 93 for Phred+33 encoded files"/> + <param argument="--mask-degenerate-bases" type="boolean" truevalue="--mask-degenerate-bases" falsevalue="" checked="false" label="Mask degenerate/ambiguous bases (B/D/H/K/M/N/R/S/V/W/Y)" help="This option will replace 'N's; if this option is not used, AdapterRemoval will abort upon encountering degenerate bases."/> + <param argument="--convert-uracils" type="boolean" truevalue="--convert-uracils" falsevalue="" checked="false" label="Convert uracils (U) to thymine (T) " help="If this option is not used, AdapterRemoval will abort upon encountering uracils."/> </section> <!-- FASTQ Trimming Options --> <section name="fastq_trimming_options" title="FASTQ Trimming Options" expanded="false"> @@ -265,6 +269,10 @@ <param name="input_type" value="pair"/> <param name="read1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/> <param name="read2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/> + <section name="fastq_options"> + <param name="convert_uracils" value="false"/> + <param name="mask_degenerate_bases" value="true"/> + </section> <output name="output_settings" ftype="txt"> <assert_contents> <has_size value="2594" delta="10"/> |
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| diff -r 04d05400d3a6 -r 40874f772ea1 macros.xml --- a/macros.xml Wed May 04 13:45:52 2022 +0000 +++ b/macros.xml Mon Aug 26 13:47:54 2024 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">2.3.3</token> + <token name="@TOOL_VERSION@">2.3.4</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">20.09</token> <token name="@DATATYPES@">fastqsanger.gz,fastqsanger</token> |