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comparison kallisto_quant.xml @ 5:10c98fab6c5a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 4364e7d61b72e12afb7ef294955b1c1e57f757b0
author iuc
date Fri, 30 Nov 2018 06:26:27 -0500
parents b818b23df1e0
children 60f888039fb2
comparison
equal deleted inserted replaced
4:b818b23df1e0 5:10c98fab6c5a
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.3"> 2 <tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.4">
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" />
13 #set index_path = 'reference.kallisto' 13 #set index_path = 'reference.kallisto'
14 #else: 14 #else:
15 #set index_path = $reference_transcriptome.index.fields.path 15 #set index_path = $reference_transcriptome.index.fields.path
16 #end if 16 #end if
17 kallisto quant -i '$index_path' 17 kallisto quant -i '$index_path'
18 $bias --bootstrap-samples $bootstrap_samples --seed $seed $fusion $pseudobam 18 $bias --bootstrap-samples $bootstrap_samples --seed $seed $fusion $lib_type $pseudobam
19 #if $pseudobam: 19 #if $pseudobam:
20 -o . 20 -o .
21 #else: 21 #else:
22 --threads \${GALAXY_SLOTS:-1} 22 --threads \${GALAXY_SLOTS:-1}
23 -o . 23 -o .
75 </conditional> 75 </conditional>
76 <param argument="--bias" type="boolean" truevalue="--bias" falsevalue="" label="Perform sequence based bias correction" /> 76 <param argument="--bias" type="boolean" truevalue="--bias" falsevalue="" label="Perform sequence based bias correction" />
77 <param name="bootstrap_samples" argument="--bootstrap-samples" type="integer" value="0" label="Number of bootstrap samples" help="default: 0" /> 77 <param name="bootstrap_samples" argument="--bootstrap-samples" type="integer" value="0" label="Number of bootstrap samples" help="default: 0" />
78 <param argument="--seed" type="integer" value="42" label="Seed for the bootstrap sampling" help="default: 42" /> 78 <param argument="--seed" type="integer" value="42" label="Seed for the bootstrap sampling" help="default: 42" />
79 <param argument="--fusion" type="boolean" truevalue="--fusion" falsevalue="" label="Search for fusions" help="for Pizzly" /> 79 <param argument="--fusion" type="boolean" truevalue="--fusion" falsevalue="" label="Search for fusions" help="for Pizzly" />
80 <param name="lib_type" type="select" label="Library strandness information">
81 <option value="">Unstranded</option>
82 <option value="--fr-stranded">Strand specific reads, first read forward</option>
83 <option value="--rf-stranded">Strand specific reads, first read reverse</option>
84 </param>
80 <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" /> 85 <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" />
81 </inputs> 86 </inputs>
82 <outputs> 87 <outputs>
83 <data format="h5" name="abundance_h5" from_work_dir="abundance.h5" label="${tool.name} on ${on_string}: Abundances (HDF5)" /> 88 <data format="h5" name="abundance_h5" from_work_dir="abundance.h5" label="${tool.name} on ${on_string}: Abundances (HDF5)" />
84 <data format="tabular" name="abundance_tab" from_work_dir="abundance.tsv" label="${tool.name} on ${on_string}: Abundances (tabular)" /> 89 <data format="tabular" name="abundance_tab" from_work_dir="abundance.tsv" label="${tool.name} on ${on_string}: Abundances (tabular)" />
96 <param name="single_paired_selector" value="paired" /> 101 <param name="single_paired_selector" value="paired" />
97 <param name="collection_selector" value="datasets" /> 102 <param name="collection_selector" value="datasets" />
98 <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" /> 103 <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />
99 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" /> 104 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
100 <output name="abundance_tab" file="kallisto_quant_out1.tab" ftype="tabular" /> 105 <output name="abundance_tab" file="kallisto_quant_out1.tab" ftype="tabular" />
106 </test>
107 <test>
108 <param name="reference_transcriptome_source" value="history" />
109 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
110 <param name="single_paired_selector" value="paired" />
111 <param name="collection_selector" value="datasets" />
112 <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />
113 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
114 <param name="lib_type" value="--fr-stranded"/>
115 <output name="abundance_tab" >
116 <assert_contents>
117 <has_text_matching expression="chrM\t16299\t15804.2\t37\t1e\+06" />
118 </assert_contents>
119 </output>
101 </test> 120 </test>
102 <test> 121 <test>
103 <param name="reference_transcriptome_source" value="history" /> 122 <param name="reference_transcriptome_source" value="history" />
104 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> 123 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
105 <param name="single_paired_selector" value="paired" /> 124 <param name="single_paired_selector" value="paired" />