Mercurial > repos > iuc > slamdunk

comparison slamdunk.xml @ 5:8b62f89924a7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 64bbe6ec9a3f3cd6241fa4cf0e0548e0e67629a0"
author iuc
date Sat, 18 Jan 2020 12:59:37 -0500
parents 24657d5edede
children 141f65f7c7c8
comparison
equal deleted inserted replaced
4:fe3fe68b09a7 5:8b62f89924a7
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>