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comparison microrunqc.xml @ 16:b07d5fec5942 draft

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author estrain
date Thu, 18 Jan 2024 20:14:55 +0000
parents c3eb197a283b
children 5083f8406e34
comparison
equal deleted inserted replaced
15:c3eb197a283b 16:b07d5fec5942
1 <tool id="microrunqc" name="microrunqc" version="1.0.1"> 1 <tool id="microrunqc" name="microrunqc" version="1.0.2">
2 2
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.4.0">skesa</requirement> 4 <requirement type="package" version="2.4.0">skesa</requirement>
5 <requirement type="package" version="2.23.0">mlst</requirement> 5 <requirement type="package" version="2.23.0">mlst</requirement>
6 <requirement type="package" version="0.7.17">bwa</requirement> 6 <requirement type="package" version="0.7.17">bwa</requirement>
89 > ${outname}.fasta; 89 > ${outname}.fasta;
90 90
91 bwa index ${outname}.fasta; 91 bwa index ${outname}.fasta;
92 bwa mem -t $num_cores ${outname}.fasta ${bwalist} | python $__tool_directory__/median_size.py > insert.median; 92 bwa mem -t $num_cores ${outname}.fasta ${bwalist} | python $__tool_directory__/median_size.py > insert.median;
93 93
94 mlst --nopath --threads $num_cores 94 mlst --nopath --threads $num_cores --datadir $mlst_databases.fields.path/pubmlst --blastdb $mlst_databases.fields.path/blast/mlst.fa
95 #if $options.select=="advanced" 95 #if $options.select=="advanced"
96 #if $options.minid 96 #if $options.minid
97 --minid $options.minid 97 --minid $options.minid
98 #end if 98 #end if
99 #if $options.mincov 99 #if $options.mincov
156 <param name="minid" type="integer" label="Minimum DNA %identity" value="95" min="0" max="100" help="Minimum DNA %identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" /> 156 <param name="minid" type="integer" label="Minimum DNA %identity" value="95" min="0" max="100" help="Minimum DNA %identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" />
157 <param name="minscore" type="integer" label="Minimum score to match scheme" value="50" min="0" max="100" help="Minumum score out of 100 to match a scheme" optional="true" /> 157 <param name="minscore" type="integer" label="Minimum score to match scheme" value="50" min="0" max="100" help="Minumum score out of 100 to match a scheme" optional="true" />
158 </when> 158 </when>
159 <when value="basic"/> 159 <when value="basic"/>
160 </conditional> 160 </conditional>
161
162 <param name="mlst_databases" label="Select a mlst database" type="select">
163 <options from_data_table="mlst">
164 <validator message="No database is available" type="no_options" />
165 </options>
166 </param>
167
161 </inputs> 168 </inputs>
162 <outputs> 169 <outputs>
163 <data format="fasta" name="results.skesa.fasta" label="${tool.name} on ${on_string}: Contigs" from_work_dir="*.fasta"/> 170 <data format="fasta" name="results.skesa.fasta" label="${tool.name} on ${on_string}: Contigs" from_work_dir="*.fasta"/>
164 <data format="tabular" name="results.mlst.tsv" label="${tool.name} on ${on_string}: MLST" from_work_dir="*.mlst.tsv"/> 171 <data format="tabular" name="results.mlst.tsv" label="${tool.name} on ${on_string}: MLST" from_work_dir="*.mlst.tsv"/>
165 <data format="tabular" name="qc_results.tsv" label="${tool.name} on ${on_string}: MLST" from_work_dir="*.txt"/> 172 <data format="tabular" name="qc_results.tsv" label="${tool.name} on ${on_string}: MLST" from_work_dir="*.txt"/>