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comparison kallisto_quant.xml @ 4:b818b23df1e0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
author iuc
date Sat, 09 Dec 2017 05:33:38 -0500
parents 2754990eb583
children 10c98fab6c5a
comparison
equal deleted inserted replaced
3:2754990eb583 4:b818b23df1e0
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.2"> 2 <tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.3">
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" />
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
9 <![CDATA[ 9 <![CDATA[
10 #if $reference_genome.reference_genome_source == "history": 10 #if $reference_transcriptome.reference_transcriptome_source == "history":
11 ln -s '$reference_genome.reference' reference.fa && 11 ln -s '$reference_transcriptome.reference' reference.fa &&
12 kallisto index reference.fa -i reference.kallisto && 12 kallisto index reference.fa -i reference.kallisto &&
13 #set index_path = 'reference.kallisto' 13 #set index_path = 'reference.kallisto'
14 #else: 14 #else:
15 #set index_path = $reference_genome.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 $pseudobam
19 #if $pseudobam: 19 #if $pseudobam:
20 -o . 20 -o .
44 #end if 44 #end if
45 && cat run_info.json 45 && cat run_info.json
46 ]]> 46 ]]>
47 </command> 47 </command>
48 <inputs> 48 <inputs>
49 <conditional name="reference_genome"> 49 <expand macro="reference_input" />
50 <param name="reference_genome_source" type="select" label="Reference genome for quantification">
51 <option value="indexed" selected="true">Use a built-in genome</option>
52 <option value="history">Use a genome from history</option>
53 </param>
54 <when value="indexed">
55 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy administrator">
56 <options from_data_table="kallisto_indexes">
57 <filter type="sort_by" column="2" />
58 <validator type="no_options" message="No genomes are available for the selected input dataset" />
59 </options>
60 </param>
61 </when>
62 <when value="history">
63 <param name="reference" type="data" format="fasta" label="FASTA reference genome" />
64 </when>
65 </conditional>
66 <conditional name="single_paired"> 50 <conditional name="single_paired">
67 <param name="single_paired_selector" type="select" label="Single-end or paired reads"> 51 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
68 <option value="single" selected="true">Single-end</option> 52 <option value="single" selected="true">Single-end</option>
69 <option value="paired">Paired</option> 53 <option value="paired">Paired</option>
70 </param> 54 </param>
105 <filter>fusion</filter> 89 <filter>fusion</filter>
106 </data> 90 </data>
107 </outputs> 91 </outputs>
108 <tests> 92 <tests>
109 <test> 93 <test>
110 <param name="reference_genome_source" value="history" /> 94 <param name="reference_transcriptome_source" value="history" />
111 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> 95 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
112 <param name="single_paired_selector" value="paired" /> 96 <param name="single_paired_selector" value="paired" />
113 <param name="collection_selector" value="datasets" /> 97 <param name="collection_selector" value="datasets" />
114 <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" /> 98 <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />
115 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" /> 99 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
116 <output name="abundance_tab" file="kallisto_quant_out1.tab" ftype="tabular" /> 100 <output name="abundance_tab" file="kallisto_quant_out1.tab" ftype="tabular" />
117 </test> 101 </test>
118 <test> 102 <test>
119 <param name="reference_genome_source" value="history" /> 103 <param name="reference_transcriptome_source" value="history" />
120 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> 104 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
121 <param name="single_paired_selector" value="paired" /> 105 <param name="single_paired_selector" value="paired" />
122 <param name="collection_selector" value="collection" /> 106 <param name="collection_selector" value="collection" />
123 <param name="reads"> 107 <param name="reads">
124 <collection type="paired"> 108 <collection type="paired">
127 </collection> 111 </collection>
128 </param> 112 </param>
129 <output name="abundance_tab" file="kallisto_quant_out2.tab" ftype="tabular" /> 113 <output name="abundance_tab" file="kallisto_quant_out2.tab" ftype="tabular" />
130 </test> 114 </test>
131 <test> 115 <test>
132 <param name="reference_genome_source" value="history" /> 116 <param name="reference_transcriptome_source" value="history" />
133 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> 117 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
134 <param name="single_paired_selector" value="single" /> 118 <param name="single_paired_selector" value="single" />
135 <param name="collection_selector" value="collection" /> 119 <param name="collection_selector" value="collection" />
136 <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" /> 120 <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />
137 <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" /> 121 <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" />
138 </test> 122 </test>
139 <test> 123 <test>
140 <param name="reference_genome_source" value="history" /> 124 <param name="reference_transcriptome_source" value="history" />
141 <param name="reference" ftype="fasta" value="felCat8_chrM.fa" /> 125 <param name="reference" ftype="fasta" value="felCat8_chrM.fa" />
142 <param name="single_paired_selector" value="paired" /> 126 <param name="single_paired_selector" value="paired" />
143 <param name="collection_selector" value="datasets" /> 127 <param name="collection_selector" value="datasets" />
144 <param name="pseudobam" value="true" /> 128 <param name="pseudobam" value="true" />
145 <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" /> 129 <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />
146 <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" /> 130 <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" />
147 <output name="abundance_tab" file="kallisto_quant_out4.tab" ftype="tabular" /> 131 <output name="abundance_tab" file="kallisto_quant_out4.tab" ftype="tabular" />
148 <output name="pseudobam_output" file="kallisto_quant_out4.bam" ftype="bam" /> 132 <output name="pseudobam_output" file="kallisto_quant_out4.bam" ftype="bam" />
149 </test> 133 </test>
150 <test> 134 <test>
151 <param name="reference_genome_source" value="cached" /> 135 <param name="reference_transcriptome_source" value="cached" />
152 <param name="single_paired_selector" value="paired" /> 136 <param name="single_paired_selector" value="paired" />
153 <param name="collection_selector" value="datasets" /> 137 <param name="collection_selector" value="datasets" />
154 <param name="pseudobam" value="true" /> 138 <param name="pseudobam" value="true" />
155 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" /> 139 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />
156 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" /> 140 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" />
157 <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" /> 141 <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" />
158 <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" /> 142 <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" />
159 </test> 143 </test>
160 <test> 144 <test>
161 <param name="reference_genome_source" value="history" /> 145 <param name="reference_transcriptome_source" value="history" />
162 <param name="reference" ftype="fasta" value="hg38_transcripts.fa" /> 146 <param name="reference" ftype="fasta" value="hg38_transcripts.fa" />
163 <param name="single_paired_selector" value="paired" /> 147 <param name="single_paired_selector" value="paired" />
164 <param name="collection_selector" value="datasets" /> 148 <param name="collection_selector" value="datasets" />
165 <param name="fusion" value="true" /> 149 <param name="fusion" value="true" />
166 <param name="forward" ftype="fastq" dbkey="hg38" value="hg38_F.fq.gz" /> 150 <param name="forward" ftype="fastq" dbkey="hg38" value="hg38_F.fq.gz" />