| Previous changeset 3:2bad02c1cb0d (2018-02-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup commit 26045b518c15c3f18996f6dc2af7064a9c1941dd |
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modified:
nugen_nudup.xml |
| b |
| diff -r 2bad02c1cb0d -r 0d24a02c555f nugen_nudup.xml --- a/nugen_nudup.xml Mon Feb 05 14:40:52 2018 -0500 +++ b/nugen_nudup.xml Fri Mar 15 12:40:38 2024 +0000 |
| b |
| @@ -2,6 +2,9 @@ <description> mark/remove PCR duplicates based on molecular tags </description> + <xrefs> + <xref type="bio.tools">nudup</xref> + </xrefs> <requirements> <requirement type="package" version="2.3.3">nudup</requirement> </requirements> @@ -38,10 +41,8 @@ format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" help="FASTQ file containing the molecular tag sequence for each read name in the corresponding SAM/BAM file" /> - <param type="boolean" argument="--paired-end" - label="Paired-end deduping" name="paired_end" - truevalue="--paired-end" falsevalue="" - checked="false" + <param type="boolean" argument="--paired-end" label="Paired-end deduping" + truevalue="--paired-end" falsevalue="" checked="false" help="use paired end deduping with template. SAM/BAM alignment must contain paired end reads. Degenerate read pairs (alignments for one read of pair) will be discarded." /> @@ -51,7 +52,7 @@ counts in from the 3' END of the read." /> <param type="integer" argument="--length" label="Tag sequence length" value="6" help="length of molecular tag sequence" /> - <param type="boolean" argument="--rmdup-only" name="rmdup_only" + <param type="boolean" argument="--rmdup-only" label="Only output BAM with duplicates removed" truevalue="--rmdup-only" falsevalue="" checked="false" help="Do not ouput BAM with duplicates marked. Default is to ouput @@ -71,7 +72,7 @@ from_work_dir="prefix_dup_log.txt" /> </outputs> <tests> - <test> + <test expect_num_outputs="3"> <param name="input" value="nudup_test_1.bam" ftype="bam" /> <param name="umi_fastq" value="nudup_umis.fastq" ftype="fastqsanger" /> @@ -81,7 +82,7 @@ <output name="dedup" file="nudup_dedup_1.bam" ftype="bam" /> <output name="log" file="nudup_log_1.txt" ftype="txt" /> </test> - <test> + <test expect_num_outputs="3"> <param name="input" value="nudup_test_1.bam" ftype="bam" /> <param name="umi_fastq" value="nudup_umis.fastq.gz" ftype="fastqsanger.gz" /> |