Mercurial > repos > estrain > microrunqc
comparison microrunqc.xml @ 16:b07d5fec5942 draft
Uploaded
author | estrain |
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date | Thu, 18 Jan 2024 20:14:55 +0000 |
parents | c3eb197a283b |
children | 5083f8406e34 |
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15:c3eb197a283b | 16:b07d5fec5942 |
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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"/> |