Mercurial > repos > bgruening > nanopolish_variants
annotate nanopolish_variants.xml @ 0:639b3a5bb415 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
author | bgruening |
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date | Wed, 30 May 2018 11:56:35 -0400 |
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children | 1ebed8b65752 |
rev | line source |
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0
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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1 <tool id="nanopolish_variants" name="Nanopolish variants" version="0.1.0"> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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2 <description>- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences</description> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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3 <macros> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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4 <import>macros.xml</import> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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5 </macros> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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6 <expand macro="requirements" /> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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7 <command detect_errors="exit_code"><![CDATA[ |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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8 ln -s '$input_merged' reads.fasta && |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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9 |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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10 #if $input_reads_raw.extension == 'fast5': |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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11 mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 && |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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12 #else |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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13 ln -s '$input_reads_raw' fast5_files.tar.gz && |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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14 mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files && |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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15 #end if |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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16 |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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17 nanopolish index -d fast5_files/ reads.fasta && |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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18 ln -s '$b' reads.bam && |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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19 ln -s '${b.metadata.bam_index}' reads.bam.bai && |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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20 ln -s '$g' genome.fa && |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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21 |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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22 nanopolish variants |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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23 -r reads.fasta |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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24 -b reads.bam |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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25 -g genome.fa |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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26 -o variants.vcf |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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27 #if $consensus: |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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28 --consensus polished.fa |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
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29 #end if |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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30 |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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31 $snps |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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32 $verbose |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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33 $homopolymer |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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34 $faster |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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35 $all_bases |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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36 |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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37 -m $min_candidate_frequency |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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38 -d $min_candidate_depth |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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39 -x $max_haplotypes |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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40 --max-rounds $max_rounds |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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41 #if $ploidy != -1: |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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42 --ploidy $ploidy |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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43 #end if |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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44 |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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45 #if $w and str($w).strip(): |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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46 -w "${w}" |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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47 #end if |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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48 #if $methylation_aware and str($methylation_aware).strip(): |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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49 -q "${methylation_aware}" |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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50 #end if |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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51 |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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52 #if $adv.input_events_bam: |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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53 -e '$adv.input_events_bam' |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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54 #end if |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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55 #if $adv.input_genotype: |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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56 --genotype '$adv.input_genotype' |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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57 #end if |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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58 #if $adv.input_candidates: |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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59 -c '$adv.input_candidates' |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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60 #end if |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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61 #if $adv.input_alt_bc_bam: |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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62 -a '$adv.input_alt_bc_bam' |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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63 #end if |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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64 #if $adv.input_models_fofn: |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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65 --models-fofn '$input_models_fofn' |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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66 #end if |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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67 |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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68 |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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69 |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
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70 ]]></command> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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71 <inputs> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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72 <!-- index inputs --> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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73 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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74 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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75 |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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76 <!-- variants consensus inputs --> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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77 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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78 <param type="data" argument="-g" format="fasta" label="The reference genome"/> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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79 |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
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80 <section name="adv" title="Optional data inputs"> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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81 <!-- optional inputs --> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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82 <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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83 <param type="data" name="input_events_bam" format="bam" optional="true" label="Events aligned to the reference genome" help="(-e)" /> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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84 <param type="data" name="input_genotype" format="vcf" optional="true" label="Call genotypes for the variants in the vcf file" help="(--genotype)" /> |
639b3a5bb415
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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85 <param type="data" name="input_candidates" format="vcf" optional="true" |
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86 label="Use variant candidates, rather than discovering them from aligned reads" help="(-c)" /> |
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87 <param type="data" name="input_alt_bc_bam" format="bam" optional="true" label="Alternative basecaller used that does not output event annotations" help="(-a)" /> |
639b3a5bb415
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88 <param type="data" name="input_models_fofn" format="txt" optional="true" label="Read alternative k-mer models" help="(--models-fofn)" /> |
639b3a5bb415
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89 </section> |
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90 |
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91 <!-- optional params --> |
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92 <!-- optional params --> |
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93 <param argument="-w" type="text" optional="true" |
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94 label="find variants in window of region chromsome:start-end" /> |
639b3a5bb415
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95 <param name="methylation_aware" type="text" optional="true" label="methylation aware polishing and test motifs given" help="(-q)"/> |
639b3a5bb415
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96 <param name="min_candidate_frequency" type="float" optional="true" value="0.2" label="Extarct if the variant frequency is at least F" help="(-m)"/> |
639b3a5bb415
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97 <param name="min_candidate_depth" type="integer" optional="true" value="20" label="Extarct if the depth is at least D" help="(-d)"/> |
639b3a5bb415
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98 <param name="max_haplotypes" type="integer" optional="true" value="1000" label="Consider at most N haplotype combinations" help="(-x)"/> |
639b3a5bb415
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99 <param name="max_rounds" type="integer" optional="true" value="50" label="Perform N rounds of consensus sequence improvement" help="(--max_rounds)"/> |
639b3a5bb415
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100 <param name="ploidy" type="integer" optional="true" value="-1" label="The ploidy level of the sequenced genome. -1:disabled" help="(-p)"/> |
639b3a5bb415
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101 |
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102 <!-- optional flags --> |
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103 <param argument="--consensus" type="boolean" truevalue="--consensus" falsevalue="" checked="true" label="Consensus calling mode and output polished sequence" /> |
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104 <param argument="--snps" type="boolean" truevalue="--snps" falsevalue="" checked="false" label="only call SNPs"/> |
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105 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="verbose output"/> |
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106 <param name="homopolymer" type="boolean" argument="--fix-homopolymers" truevalue="--fix-homopolymers" falsevalue="" checked="false" label="homopolymer caller" /> |
639b3a5bb415
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107 <param argument="--faster" type="boolean" truevalue="--faster" falsevalue="" checked="false" |
639b3a5bb415
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108 label="speedup while slightly reducing consensus accuracy"/> |
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109 <param name="all_bases" type="boolean" argument="--calculate-all-support" truevalue="--calculate-all-support" falsevalue="" checked="false" |
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110 label="calculate the support of the 3 other possible bases" /> |
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111 </inputs> |
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112 |
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113 <outputs> |
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114 <!-- variants consensus outputs --> |
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115 <data name="output_polished" format="fasta" from_work_dir="polished.fa" label="polished sequence by consensus calling mode" /> |
639b3a5bb415
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116 <data name="output_variants" format="vcf" from_work_dir="variants.vcf" label="Computed variants"/> |
639b3a5bb415
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117 </outputs> |
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118 <tests> |
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119 <test> |
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120 <!-- index test --> |
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121 <param name="input_merged" ftype="fasta" value="reads.fasta" /> |
639b3a5bb415
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122 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> |
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123 |
639b3a5bb415
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124 <!-- variants consensus test --> |
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125 <param name="b" value="reads.sorted.bam" /> |
639b3a5bb415
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126 <param name="g" value="draft.fa" /> |
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127 <param name="w" value="tig00000001:200000-202000" /> |
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128 |
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129 <output name="output_polished" file="polished.fa" /> |
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130 <output name="output_variants" file="variants.vcf"/> |
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131 </test> |
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132 <test> |
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133 <!-- index test --> |
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134 <param name="input_merged" ftype="fasta" value="reads.fasta" /> |
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135 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> |
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136 |
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137 <!-- variants consensus test --> |
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138 <param name="b" value="reads.sorted.bam" /> |
639b3a5bb415
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139 <param name="g" value="draft.fa" /> |
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140 <param name="w" value="tig00000001:200000-202000" /> |
639b3a5bb415
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141 <param name="ploidy" value="2" /> |
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142 <param name="snps" value="true" /> |
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143 <param name="faster" value="true" /> |
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144 <param name="all_bases" value="true" /> |
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145 <param name="consensus" value="false" /> |
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146 <output name="output_polished" file="t2-polished.fa" /> |
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147 <output name="output_variants" file="t2-variants.vcf"/> |
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148 </test> |
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149 |
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150 </tests> |
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151 <help><![CDATA[ |
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152 |
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153 Build an index mapping from basecalled reads to the signals measured by the sequencer |
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154 and |
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155 Find SNPs using a signal-level HMM |
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156 |
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157 Tutorial and manual available at: |
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158 http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html |
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159 |
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160 |
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161 ]]></help> |
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162 <expand macro="citations" /> |
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163 </tool> |