Mercurial > repos > iuc > kallisto_pseudo
comparison kallisto_pseudo.xml @ 2:1c75aa5de15e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
author | iuc |
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date | Sat, 09 Dec 2017 05:34:01 -0500 |
parents | 2953303df011 |
children | 5ae5c312d718 |
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1:63f76b9f4ba7 | 2:1c75aa5de15e |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.0"> | 2 <tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.1"> |
3 <description>- run pseudoalignment on RNA-Seq transcripts</description> | 3 <description>- run pseudoalignment on 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 = $reference_transcriptome.index.fields.path |
16 #end if | 16 #end if |
17 kallisto pseudo -i '$index_path' | 17 kallisto pseudo -i '$index_path' |
18 #if $pseudobam: | 18 #if $pseudobam: |
19 $pseudobam -o . | 19 $pseudobam -o . |
20 #else: | 20 #else: |
65 #end if | 65 #end if |
66 ]]> | 66 ]]> |
67 </configfile> | 67 </configfile> |
68 </configfiles> | 68 </configfiles> |
69 <inputs> | 69 <inputs> |
70 <conditional name="reference_genome"> | 70 <expand macro="reference_input" /> |
71 <param name="reference_genome_source" type="select" label="Reference genome for pseudoalignment"> | |
72 <option value="indexed" selected="true">Use a built-in genome</option> | |
73 <option value="history">Use a genome from history</option> | |
74 </param> | |
75 <when value="indexed"> | |
76 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy administrator"> | |
77 <options from_data_table="kallisto_indexes"> | |
78 <filter type="sort_by" column="2" /> | |
79 <validator type="no_options" message="No genomes are available for the selected input dataset" /> | |
80 </options> | |
81 </param> | |
82 </when> | |
83 <when value="history"> | |
84 <param name="reference" type="data" format="fasta" label="FASTA reference genome" /> | |
85 </when> | |
86 </conditional> | |
87 <conditional name="single_paired"> | 71 <conditional name="single_paired"> |
88 <param name="single_paired_selector" type="select" label="Single-end or paired reads"> | 72 <param name="single_paired_selector" type="select" label="Single-end or paired reads"> |
89 <option value="single" selected="true">Single-end</option> | 73 <option value="single" selected="true">Single-end</option> |
90 <option value="paired">Paired</option> | 74 <option value="paired">Paired</option> |
91 </param> | 75 </param> |
132 <filter>pseudobam</filter> | 116 <filter>pseudobam</filter> |
133 </data> | 117 </data> |
134 </outputs> | 118 </outputs> |
135 <tests> | 119 <tests> |
136 <test> | 120 <test> |
137 <param name="reference_genome_source" value="history" /> | 121 <param name="reference_transcriptome_source" value="history" /> |
138 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> | 122 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> |
139 <param name="single_paired_selector" value="paired" /> | 123 <param name="single_paired_selector" value="paired" /> |
140 <param name="collection_selector" value="datasets" /> | 124 <param name="collection_selector" value="datasets" /> |
141 <param name="umi" value="yes" /> | 125 <param name="umi" value="yes" /> |
142 <param name="forward" ftype="tabular" value="mm10_chrM.umi" /> | 126 <param name="forward" ftype="tabular" value="mm10_chrM.umi" /> |
146 <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out1.ec" ftype="tabular" /> | 130 <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out1.ec" ftype="tabular" /> |
147 <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out1.cells" ftype="tabular" /> | 131 <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out1.cells" ftype="tabular" /> |
148 </output> | 132 </output> |
149 </test> | 133 </test> |
150 <test> | 134 <test> |
151 <param name="reference_genome_source" value="history" /> | 135 <param name="reference_transcriptome_source" value="history" /> |
152 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> | 136 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> |
153 <param name="single_paired_selector" value="paired" /> | 137 <param name="single_paired_selector" value="paired" /> |
154 <param name="collection_selector" value="collection" /> | 138 <param name="collection_selector" value="collection" /> |
155 <param name="umi" value="no" /> | 139 <param name="umi" value="no" /> |
156 <param name="reads"> | 140 <param name="reads"> |
163 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out2.tab" ftype="tabular" /> | 147 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out2.tab" ftype="tabular" /> |
164 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out2.ec" ftype="tabular" /> | 148 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out2.ec" ftype="tabular" /> |
165 </output> | 149 </output> |
166 </test> | 150 </test> |
167 <test> | 151 <test> |
168 <param name="reference_genome_source" value="history" /> | 152 <param name="reference_transcriptome_source" value="history" /> |
169 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> | 153 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> |
170 <param name="single_paired_selector" value="single" /> | 154 <param name="single_paired_selector" value="single" /> |
171 <param name="collection_selector" value="collection" /> | 155 <param name="collection_selector" value="collection" /> |
172 <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" /> | 156 <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" /> |
173 <output name="sample"> | 157 <output name="sample"> |
174 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out3.tab" ftype="tabular" /> | 158 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out3.tab" ftype="tabular" /> |
175 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out3.ec" ftype="tabular" /> | 159 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out3.ec" ftype="tabular" /> |
176 </output> | 160 </output> |
177 </test> | 161 </test> |
178 <test> | 162 <test> |
179 <param name="reference_genome_source" value="history" /> | 163 <param name="reference_transcriptome_source" value="history" /> |
180 <param name="reference" ftype="fasta" value="felCat8_chrM.fa" /> | 164 <param name="reference" ftype="fasta" value="felCat8_chrM.fa" /> |
181 <param name="single_paired_selector" value="paired" /> | 165 <param name="single_paired_selector" value="paired" /> |
182 <param name="collection_selector" value="datasets" /> | 166 <param name="collection_selector" value="datasets" /> |
183 <param name="umi" value="no" /> | 167 <param name="umi" value="no" /> |
184 <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" /> | 168 <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" /> |
187 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out4.tab" ftype="tabular" /> | 171 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out4.tab" ftype="tabular" /> |
188 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out4.ec" ftype="tabular" /> | 172 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out4.ec" ftype="tabular" /> |
189 </output> | 173 </output> |
190 </test> | 174 </test> |
191 <test> | 175 <test> |
192 <param name="reference_genome_source" value="cached" /> | 176 <param name="reference_transcriptome_source" value="cached" /> |
193 <param name="single_paired_selector" value="paired" /> | 177 <param name="single_paired_selector" value="paired" /> |
194 <param name="collection_selector" value="datasets" /> | 178 <param name="collection_selector" value="datasets" /> |
195 <param name="pseudobam" value="true" /> | 179 <param name="pseudobam" value="true" /> |
196 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" /> | 180 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" /> |
197 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" /> | 181 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" /> |
200 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out5.ec" ftype="tabular" /> | 184 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out5.ec" ftype="tabular" /> |
201 </output> | 185 </output> |
202 <output name="pseudobam_output" file="kallisto_pseudo_out5.bam" ftype="bam" /> | 186 <output name="pseudobam_output" file="kallisto_pseudo_out5.bam" ftype="bam" /> |
203 </test> | 187 </test> |
204 <test> | 188 <test> |
205 <param name="reference_genome_source" value="cached" /> | 189 <param name="reference_transcriptome_source" value="cached" /> |
206 <param name="single_paired_selector" value="paired" /> | 190 <param name="single_paired_selector" value="paired" /> |
207 <param name="collection_selector" value="datasets" /> | 191 <param name="collection_selector" value="datasets" /> |
208 <param name="umi" value="yes" /> | 192 <param name="umi" value="yes" /> |
209 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" /> | 193 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" /> |
210 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" /> | 194 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" /> |