| Previous changeset 4:b818b23df1e0 (2017-12-09) Next changeset 6:60f888039fb2 (2019-09-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 4364e7d61b72e12afb7ef294955b1c1e57f757b0 |
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modified:
kallisto_quant.xml |
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| diff -r b818b23df1e0 -r 10c98fab6c5a kallisto_quant.xml --- a/kallisto_quant.xml Sat Dec 09 05:33:38 2017 -0500 +++ b/kallisto_quant.xml Fri Nov 30 06:26:27 2018 -0500 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.3"> +<tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.4"> <description>- quantify abundances of RNA-Seq transcripts</description> <macros> <import>macros.xml</import> @@ -15,7 +15,7 @@ #set index_path = $reference_transcriptome.index.fields.path #end if kallisto quant -i '$index_path' - $bias --bootstrap-samples $bootstrap_samples --seed $seed $fusion $pseudobam + $bias --bootstrap-samples $bootstrap_samples --seed $seed $fusion $lib_type $pseudobam #if $pseudobam: -o . #else: @@ -77,6 +77,11 @@ <param name="bootstrap_samples" argument="--bootstrap-samples" type="integer" value="0" label="Number of bootstrap samples" help="default: 0" /> <param argument="--seed" type="integer" value="42" label="Seed for the bootstrap sampling" help="default: 42" /> <param argument="--fusion" type="boolean" truevalue="--fusion" falsevalue="" label="Search for fusions" help="for Pizzly" /> + <param name="lib_type" type="select" label="Library strandness information"> + <option value="">Unstranded</option> + <option value="--fr-stranded">Strand specific reads, first read forward</option> + <option value="--rf-stranded">Strand specific reads, first read reverse</option> + </param> <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" /> </inputs> <outputs> @@ -103,6 +108,20 @@ <param name="reference_transcriptome_source" value="history" /> <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> <param name="single_paired_selector" value="paired" /> + <param name="collection_selector" value="datasets" /> + <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" /> + <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" /> + <param name="lib_type" value="--fr-stranded"/> + <output name="abundance_tab" > + <assert_contents> + <has_text_matching expression="chrM\t16299\t15804.2\t37\t1e\+06" /> + </assert_contents> + </output> + </test> + <test> + <param name="reference_transcriptome_source" value="history" /> + <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> + <param name="single_paired_selector" value="paired" /> <param name="collection_selector" value="collection" /> <param name="reads"> <collection type="paired"> |