Mercurial > repos > iuc > kallisto_pseudo
diff kallisto_pseudo.xml @ 0:2953303df011 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit fc0426e784d0eb5ca37484d2d0c088da289996dd
| author | iuc |
|---|---|
| date | Tue, 22 Aug 2017 04:16:08 -0400 |
| parents | |
| children | 1c75aa5de15e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kallisto_pseudo.xml Tue Aug 22 04:16:08 2017 -0400 @@ -0,0 +1,224 @@ +<?xml version="1.0"?> +<tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.0"> + <description>- run pseudoalignment on RNA-Seq transcripts</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"> + <![CDATA[ + #if $reference_genome.reference_genome_source == "history": + ln -s '$reference_genome.reference' reference.fa && + kallisto index reference.fa -i reference.kallisto && + #set index_path = 'reference.kallisto' + #else: + #set index_path = $reference_genome.index.fields.path + #end if + kallisto pseudo -i '$index_path' + #if $pseudobam: + $pseudobam -o . + #else: + --threads \${GALAXY_SLOTS:-1} + -o . + #end if + + + #if str($single_paired.single_paired_selector) == 'single': + --single --fragment-length $single_paired.fragment_length + --sd $single_paired.sd '$single_paired.reads' + #else: + #if str($single_paired.collection.collection_selector) == 'collection': + '$single_paired.collection.reads.forward' + '$single_paired.collection.reads.reverse' + #else: + #if str($single_paired.collection.fastq_umi.umi) == 'yes': + --batch '$batch' --umi + #else: + '$single_paired.collection.fastq_umi.forward' + '$single_paired.collection.fastq_umi.reverse' + #end if + #end if + #end if + #if $pseudobam: + | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o '$pseudobam_output' - + #end if + && if [ -f run_info.json ] ; then cat run_info.json ; fi && + mkdir outputs && + if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && + if [ -f matrix.tsv ] ; then mv matrix.tsv outputs/Matrix.tabular ; fi && + if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && + if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && + if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi + ]]> + </command> + <configfiles> + <configfile name="batch"> +<![CDATA[ +#if str($single_paired.single_paired_selector) == 'single': +cell1 $single_paired.reads +#else: +#if str($single_paired.collection.collection_selector) == 'collection': +cell1 $single_paired.collection.reads.forward $single_paired.collection.reads.reverse +#else: +cell1 $single_paired.collection.fastq_umi.forward $single_paired.collection.fastq_umi.reverse +#end if +#end if +]]> + </configfile> + </configfiles> + <inputs> + <conditional name="reference_genome"> + <param name="reference_genome_source" type="select" label="Reference genome for pseudoalignment"> + <option value="indexed" selected="true">Use a built-in genome</option> + <option value="history">Use a genome from history</option> + </param> + <when value="indexed"> + <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy administrator"> + <options from_data_table="kallisto_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No genomes are available for the selected input dataset" /> + </options> + </param> + </when> + <when value="history"> + <param name="reference" type="data" format="fasta" label="FASTA reference genome" /> + </when> + </conditional> + <conditional name="single_paired"> + <param name="single_paired_selector" type="select" label="Single-end or paired reads"> + <option value="single" selected="true">Single-end</option> + <option value="paired">Paired</option> + </param> + <when value="single"> + <param name="reads" type="data" format="fastq" multiple="True" label="Reads in FASTQ format" /> + <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" /> + <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" /> + </when> + <when value="paired"> + <conditional name="collection"> + <param name="collection_selector" type="select" label="Collection or individual datasets"> + <option value="datasets" selected="true">Individual files</option> + <option value="collection">Pair or list of pairs</option> + </param> + <when value="datasets"> + <conditional name="fastq_umi"> + <param name="umi" type="select" label="Pseudoalignment uses UMIs"> + <option value="no" selected="true">Paired FASTQ</option> + <option value="yes">UMI</option> + </param> + <when value="yes"> + <param name="forward" type="data" format="tabular" multiple="True" label="UMI file" /> + <param name="reverse" type="data" format="fastq" multiple="True" label="FASTQ reads" /> + </when> + <when value="no"> + <param name="forward" type="data" format="fastq" multiple="True" label="Forward reads" /> + <param name="reverse" type="data" format="fastq" multiple="True" label="Reverse reads" /> + </when> + </conditional> + </when> + <when value="collection"> + <param name="reads" type="data_collection" format="fastq" collection_type="paired" label="Collection of reads" /> + </when> + </conditional> + </when> + </conditional> + <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" /> + </inputs> + <outputs> + <data format="tabular" name="sample"> + <discover_datasets pattern="(?P<designation>.+)" directory="outputs" ext="tabular" visible="true" /> + </data> + <data format="bam" name="pseudobam_output" label="${tool.name} on ${on_string}: Pseudoalignments (BAM)"> + <filter>pseudobam</filter> + </data> + </outputs> + <tests> + <test> + <param name="reference_genome_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="umi" value="yes" /> + <param name="forward" ftype="tabular" value="mm10_chrM.umi" /> + <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" /> + <output name="sample"> + <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out1.tab" ftype="tabular" /> + <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out1.ec" ftype="tabular" /> + <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out1.cells" ftype="tabular" /> + </output> + </test> + <test> + <param name="reference_genome_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="umi" value="no" /> + <param name="reads"> + <collection type="paired"> + <element name="forward" value="mm10_chrM-1.f.fq" /> + <element name="reverse" value="mm10_chrM-1.r.fq" /> + </collection> + </param> + <output name="sample"> + <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out2.tab" ftype="tabular" /> + <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out2.ec" ftype="tabular" /> + </output> + </test> + <test> + <param name="reference_genome_source" value="history" /> + <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> + <param name="single_paired_selector" value="single" /> + <param name="collection_selector" value="collection" /> + <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" /> + <output name="sample"> + <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out3.tab" ftype="tabular" /> + <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out3.ec" ftype="tabular" /> + </output> + </test> + <test> + <param name="reference_genome_source" value="history" /> + <param name="reference" ftype="fasta" value="felCat8_chrM.fa" /> + <param name="single_paired_selector" value="paired" /> + <param name="collection_selector" value="datasets" /> + <param name="umi" value="no" /> + <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" /> + <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" /> + <output name="sample"> + <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out4.tab" ftype="tabular" /> + <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out4.ec" ftype="tabular" /> + </output> + </test> + <test> + <param name="reference_genome_source" value="cached" /> + <param name="single_paired_selector" value="paired" /> + <param name="collection_selector" value="datasets" /> + <param name="pseudobam" value="true" /> + <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" /> + <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" /> + <output name="sample"> + <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out5.tab" ftype="tabular" /> + <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out5.ec" ftype="tabular" /> + </output> + <output name="pseudobam_output" file="kallisto_pseudo_out5.bam" ftype="bam" /> + </test> + <test> + <param name="reference_genome_source" value="cached" /> + <param name="single_paired_selector" value="paired" /> + <param name="collection_selector" value="datasets" /> + <param name="umi" value="yes" /> + <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" /> + <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" /> + <output name="sample"> + <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out6.tab" ftype="tabular" /> + <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out6.ec" ftype="tabular" /> + <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out6.cells" ftype="tabular" /> + </output> + </test> + </tests> + <help> + <![CDATA[ + `kallisto <https://pachterlab.github.io/kallisto/manual>`__ 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. + ]]> + </help> + <expand macro="citations" /> +</tool>