Mercurial > repos > iuc > slamdunk
comparison slamdunk.xml @ 5:8b62f89924a7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 64bbe6ec9a3f3cd6241fa4cf0e0548e0e67629a0"
author | iuc |
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date | Sat, 18 Jan 2020 12:59:37 -0500 |
parents | 24657d5edede |
children | 141f65f7c7c8 |
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4:fe3fe68b09a7 | 5:8b62f89924a7 |
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123 <output_collection name="outputBam"> | 123 <output_collection name="outputBam"> |
124 <element name="reads_slamdunk_mapped_filtered" ftype="bam" file="reads1.bam" compare="sim_size" /> | 124 <element name="reads_slamdunk_mapped_filtered" ftype="bam" file="reads1.bam" compare="sim_size" /> |
125 </output_collection> | 125 </output_collection> |
126 <output_collection name="outputTsv"> | 126 <output_collection name="outputTsv"> |
127 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" | 127 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" |
128 lines_diff="2" /> | 128 compare="re_match" /> |
129 </output_collection> | 129 </output_collection> |
130 <output_collection name="outputVcf"> | 130 <output_collection name="outputVcf"> |
131 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" /> | 131 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" /> |
132 </output_collection> | 132 </output_collection> |
133 </test> | 133 </test> |
134 <test> | 134 <test> |
135 <!--Ensure built-in fasta works --> | 135 <!--Ensure built-in fasta works --> |
136 <param name="reference_source_selector" value="cached" /> | 136 <param name="reference_source_selector" value="cached" /> |
137 <param name="ref_file" value="hg38full" /> | |
137 <param name="Reference" value="actb.bed" /> | 138 <param name="Reference" value="actb.bed" /> |
138 <param name="reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" /> | 139 <param name="reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" /> |
139 <param name="readLength" value="100" /> | 140 <param name="readLength" value="100" /> |
140 <section name="quantseq"> | 141 <section name="quantseq"> |
141 <param name="trim5" value="0" /> | 142 <param name="trim5" value="0" /> |
146 <output_collection name="outputBam"> | 147 <output_collection name="outputBam"> |
147 <element name="reads_slamdunk_mapped_filtered" ftype="bam" file="reads1.bam" compare="sim_size" /> | 148 <element name="reads_slamdunk_mapped_filtered" ftype="bam" file="reads1.bam" compare="sim_size" /> |
148 </output_collection> | 149 </output_collection> |
149 <output_collection name="outputTsv"> | 150 <output_collection name="outputTsv"> |
150 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" | 151 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" |
151 lines_diff="2" /> | 152 compare="re_match" /> |
152 </output_collection> | 153 </output_collection> |
153 <output_collection name="outputVcf"> | 154 <output_collection name="outputVcf"> |
154 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" /> | 155 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" /> |
155 </output_collection> | 156 </output_collection> |
156 </test> | 157 </test> |