Mercurial > repos > iuc > kallisto_quant

comparison kallisto_quant.xml @ 3:2754990eb583 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
author iuc
date Tue, 05 Sep 2017 03:25:35 -0400
parents 7a9158bb6f98
children b818b23df1e0
comparison
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2:552ef00aba90 3:2754990eb583
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.1"> 2 <tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.2">
3 <description>- quantify abundances of RNA-Seq transcripts</description> 3 <description>- quantify abundances of RNA-Seq transcripts</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
96 <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" /> 96 <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" />
97 </inputs> 97 </inputs>
98 <outputs> 98 <outputs>
99 <data format="h5" name="abundance_h5" from_work_dir="abundance.h5" label="${tool.name} on ${on_string}: Abundances (HDF5)" /> 99 <data format="h5" name="abundance_h5" from_work_dir="abundance.h5" label="${tool.name} on ${on_string}: Abundances (HDF5)" />
100 <data format="tabular" name="abundance_tab" from_work_dir="abundance.tsv" label="${tool.name} on ${on_string}: Abundances (tabular)" /> 100 <data format="tabular" name="abundance_tab" from_work_dir="abundance.tsv" label="${tool.name} on ${on_string}: Abundances (tabular)" />
101 <data format="bam" name="pseudobam_output" label="${tool.name} on ${on_string}: Pseudoalignments"> 101 <data format="bam" name="pseudobam_output" from_work_dir="abundance.txt" label="${tool.name} on ${on_string}: Pseudoalignments">
102 <filter>pseudobam</filter> 102 <filter>pseudobam</filter>
103 </data>
104 <data format="tabular" name="fusion_output" from_work_dir="fusion.txt" label="${tool.name} on ${on_string}: Pizzly input (tabular)">
105 <filter>fusion</filter>
103 </data> 106 </data>
104 </outputs> 107 </outputs>
105 <tests> 108 <tests>
106 <test> 109 <test>
107 <param name="reference_genome_source" value="history" /> 110 <param name="reference_genome_source" value="history" />
152 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" /> 155 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />
153 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" /> 156 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" />
154 <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" /> 157 <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" />
155 <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" /> 158 <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" />
156 </test> 159 </test>
160 <test>
161 <param name="reference_genome_source" value="history" />
162 <param name="reference" ftype="fasta" value="hg38_transcripts.fa" />
163 <param name="single_paired_selector" value="paired" />
164 <param name="collection_selector" value="datasets" />
165 <param name="fusion" value="true" />
166 <param name="forward" ftype="fastq" dbkey="hg38" value="hg38_F.fq.gz" />
167 <param name="reverse" ftype="fastq" dbkey="hg38" value="hg38_R.fq.gz" />
168 <output name="fusion_output" file="fusion.txt" ftype="tabular" />
169 </test>
170
157 </tests> 171 </tests>
158 <help> 172 <help>
159 <![CDATA[ 173 <![CDATA[
160 kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks kallisto significantly outperforms existing tools. 174 kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks kallisto significantly outperforms existing tools.
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