Mercurial > repos > bgruening > nanopolish_eventalign
annotate nanopolish_eventalign.xml @ 8:3b6f94fc7e1d draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
author | bgruening |
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date | Thu, 30 Nov 2023 17:58:54 +0000 |
parents | 855b7ba0ce9c |
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rev | line source |
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8
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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1 <tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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2 <description>- Align nanopore events to reference k-mers</description> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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3 <macros> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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4 <import>macros.xml</import> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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5 </macros> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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6 <expand macro="requirements" /> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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7 <command detect_errors="exit_code"><![CDATA[ |
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3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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8 @PREPROCESS_INPUTS@ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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9 |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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10 nanopolish eventalign |
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3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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11 -r reads.fasta |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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12 -b reads.bam |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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13 -g genome.fa |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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14 #if str($min_mapping_quality): |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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15 -q $min_mapping_quality |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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16 #end if |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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17 --threads "\${GALAXY_SLOTS:-4}" |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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18 $samples |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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19 $scale_events |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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20 $signal_index |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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21 $sam |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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22 $print_read_names |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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23 #if $w and str($w).strip(): |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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24 -w "${w}" |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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25 #end if |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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26 #if $input_models_fofn: |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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27 --models-fofn '$input_models_fofn' |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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28 #end if |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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29 #if $summary: |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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30 --summary eventalign-summary.txt |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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31 #end if |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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32 > eventalign.out |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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33 |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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34 |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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35 ]]></command> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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36 <inputs> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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37 <!-- index inputs --> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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38 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> |
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3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
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39 <param type="data" name="input_reads_raw" format="fast5.tar.xz,fast5.tar.gz,fast5.tar.bz2,fast5.tar,fast5" label="Flat archive file of raw fast5 files"/> |
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bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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40 |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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41 <!-- variants consensus inputs --> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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42 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> |
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c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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43 <conditional name="reference_source"> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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44 <param name="reference_source_selector" type="select" label="Load reference genome from"> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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45 <option value="cached">Local cache</option> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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46 <option value="history">History</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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47 </param> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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48 <when value="cached"> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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49 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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50 <options from_data_table="all_fasta"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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51 </options> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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52 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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53 </param> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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54 </when> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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55 <when value="history"> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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56 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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57 </when> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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58 </conditional> |
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59 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
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60 <section name="adv" title="Optional data inputs"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
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61 <!-- optional inputs --> |
0938217b3221
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
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62 <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/> |
0938217b3221
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
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63 </section> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 89078a214cefd31d28da75ddebb21f546fba79df-dirty
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64 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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65 <!-- optional inputs --> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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66 <param type="data" name="input_models_fofn" argument="--models-fofn" format="txt" optional="true" |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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67 label="Read alternative k-mer models (optional)" /> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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68 |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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69 <!-- optional params --> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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70 <param argument="-w" type="text" optional="true" |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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71 label="find variants in window of region chromsome:start-end" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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72 <param name="min_mapping_quality" type="integer" optional="true" value="" |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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73 label="Only use reads with mapping quality of at least this value" help="(-q)"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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74 |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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75 <!-- optional flags --> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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76 <param argument="--summary" type="boolean" truevalue="--summary" falsevalue="" checked="true" |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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77 label="Summarize the alignment of each read/strand" /> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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78 <param argument="--samples" type="boolean" truevalue="--samples" falsevalue="" checked="false" |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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79 label="Write the raw samples for the event to the tsv output" /> |
8
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
parents:
6
diff
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|
80 <param argument="--scale-events" type="boolean" truevalue="--scale-events" falsevalue="" checked="false" |
0
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
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diff
changeset
|
81 label="Scale events to the model, rather than vice-versa" /> |
8
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
parents:
6
diff
changeset
|
82 <param argument="--signal-index" type="boolean" truevalue="--signal-index" falsevalue="" checked="false" |
6
855b7ba0ce9c
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4883f9a9a2779e2b4792314bd6128c7c109c00e1"
bgruening
parents:
5
diff
changeset
|
83 label="write the raw signal start and end index values for the event to the tsv output" /> |
855b7ba0ce9c
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4883f9a9a2779e2b4792314bd6128c7c109c00e1"
bgruening
parents:
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diff
changeset
|
84 |
855b7ba0ce9c
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4883f9a9a2779e2b4792314bd6128c7c109c00e1"
bgruening
parents:
5
diff
changeset
|
85 |
0
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff
changeset
|
86 <param argument="--sam" type="boolean" truevalue="--sam" falsevalue="" checked="false" |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff
changeset
|
87 label="write output in SAM format" /> |
8
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
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diff
changeset
|
88 <param argument="--print-read-names" type="boolean" truevalue="--print-read-names" falsevalue="" checked="false" |
0
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff
changeset
|
89 label="Print read names instead of indexes" /> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff
changeset
|
90 </inputs> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff
changeset
|
91 |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff
changeset
|
92 <outputs> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
|
93 <!-- variants consensus outputs --> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
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diff
changeset
|
94 <data name="output_summary" format="txt" from_work_dir="eventalign-summary.txt" label="eventalign summary of reads/strands" /> |
1
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents:
0
diff
changeset
|
95 <data name="output_eventalign" format="txt" from_work_dir="eventalign.out" label="Aligned squiggles"/> |
0
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff
changeset
|
96 </outputs> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
|
97 <tests> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff
changeset
|
98 <test> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff
changeset
|
99 <param name="input_merged" ftype="fasta" value="reads.fasta" /> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
diff
changeset
|
100 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
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diff
changeset
|
101 <param name="b" value="reads.sorted.bam" /> |
1
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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|
102 <param name="reference_source_selector" value="history" /> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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|
103 <param name="ref_file" value="draft.fa" /> |
0
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
parents:
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changeset
|
104 <param name="w" value="tig00000001:200000-200010" /> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
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changeset
|
105 <param name="sam" value="true" /> |
8
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
parents:
6
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|
106 <output name="output_summary" file="eventalign-summary.txt" compare="sim_size"> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
parents:
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|
107 <assert_contents> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
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changeset
|
108 <has_n_lines n="144"/> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
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|
109 <has_n_columns n="14"/> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
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110 <has_line_matching expression="read_index\sread_name\sfast5_path\smodel_name\sstrand\snum_events\snum_steps\snum_skips\snum_stays\stotal_duration\sshift\sscale\sdrift\svar"/> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
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6
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changeset
|
111 <has_text text="d57afb7d-903e-46cf-a43d-0e17fb0949d8"/> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
parents:
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changeset
|
112 <has_text text="15727"/> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
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113 <has_text text="fast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch378_read5665_strand.fast5"/> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
parents:
6
diff
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|
114 </assert_contents> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
parents:
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|
115 </output> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
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6
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|
116 <output name="output_eventalign" file="reads-draft.eventalign.sam" compare="sim_size"> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
parents:
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|
117 <assert_contents> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
parents:
6
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|
118 <has_n_lines n="148"/> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
parents:
6
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|
119 <has_line_matching expression="@SQ\sSN:tig00000001\sLN:4376233"/> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
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|
120 <has_text text="d57afb7d-903e-46cf-a43d-0e17fb0949d8"/> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
parents:
6
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|
121 <has_text text="191118"/> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
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122 <has_text text="274S1M2I3M1I2M2I9M1I1M1I1M1I9M6I3M1I1M2I2M2I2M1"/> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
parents:
6
diff
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|
123 </assert_contents> |
3b6f94fc7e1d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
bgruening
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6
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|
124 </output> |
0
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
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changeset
|
125 </test> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
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|
126 <test> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
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127 <param name="input_merged" ftype="fasta" value="reads.fasta" /> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
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|
128 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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129 <param name="b" value="reads.sorted.bam" /> |
1
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
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130 <param name="reference_source_selector" value="history" /> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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131 <param name="ref_file" value="draft.fa" /> |
0
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
bgruening
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132 <param name="w" value="tig00000001:200000-200010" /> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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133 <param name="sam" value="false" /> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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134 <param name="summary" value="false" /> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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|
135 <param name="scale_events" value="true" /> |
bee42f615f28
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
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|
136 <param name="print_read_names" value="true" /> |
1
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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137 <param name="min_mapping_quality" value="0" /> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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138 <output name="output_summary" file="t2-eventalign-summary.txt" /> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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139 <output name="output_eventalign"> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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140 <assert_contents> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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141 <has_text text="contig" /> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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142 <has_text text="position" /> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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143 <has_text text="event_index" /> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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|
144 <has_text text="tig00000001" /> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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|
145 </assert_contents> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
parents:
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|
146 </output> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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147 </test> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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148 <test> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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|
149 <!-- test data table reference --> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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150 <param name="input_merged" ftype="fasta" value="reads.fasta" /> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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|
151 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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|
152 <param name="b" value="reads.sorted.bam" /> |
4
d219b6d8158a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 25c22b467760e4784e199125292927bd2274a189-dirty
bgruening
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153 <param name="reference_source_selector" value="history" /> |
d219b6d8158a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 25c22b467760e4784e199125292927bd2274a189-dirty
bgruening
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154 <param name="ref_file" value="draft.fa"/> |
1
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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|
155 <param name="w" value="tig00000001:200000-200010" /> |
c8c5caecfacc
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
bgruening
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|
156 <param name="sam" value="false" /> |
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157 <param name="summary" value="false" /> |
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158 <param name="scale_events" value="true" /> |
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159 <param name="print_read_names" value="true" /> |
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160 <param name="min_mapping_quality" value="0" /> |
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161 <output name="output_summary" file="t2-eventalign-summary.txt" /> |
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162 <output name="output_eventalign"> |
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163 <assert_contents> |
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164 <has_text text="contig" /> |
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165 <has_text text="position" /> |
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166 <has_text text="event_index" /> |
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167 <has_text text="tig00000001" /> |
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168 </assert_contents> |
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169 </output> |
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170 </test> |
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171 </tests> |
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172 <help><![CDATA[ |
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173 Usage: nanopolish eventalign [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa |
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174 Align nanopore events to reference k-mers |
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175 |
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176 Tutorial and manual available at: |
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177 http://nanopolish.readthedocs.io/en/latest/quickstart_eventalign.html |
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178 |
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179 ]]></help> |
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180 <expand macro="citations" /> |
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181 </tool> |