Mercurial > repos > iuc > nanocompore_sampcomp

annotate sampcomp.xml @ 2:25abc2c72ff9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit a57b5b935a80db12a0ed867b4219453a2854dd32"
author iuc
date Wed, 17 Jun 2020 13:28:27 -0400
parents c43f4b80f5a9
children c0fb573c1e8d
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557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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1 <?xml version="1.0"?>
2
25abc2c72ff9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit a57b5b935a80db12a0ed867b4219453a2854dd32"
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2 <tool id="nanocompore_sampcomp" name="SampComp" version="@TOOL_VERSION@+galaxy0">
0
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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3 <description>to compare Nanopolished datasets</description>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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4 <macros>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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5 <import>macros.xml</import>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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6 </macros>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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7 <expand macro="requirements"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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8 <version_command><![CDATA[nanocompore --version]]></version_command>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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9 <command detect_errors="exit_code"><![CDATA[
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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10 ## initialize
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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11 ## requires a minimum of 3 threads
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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12 threads=\$((3 > \${GALAXY_SLOTS:-3} ? 3 : \${GALAXY_SLOTS:-3})) &&
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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13 ## same name pattern required
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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14 #for $i, $current in enumerate($file1_rep)
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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15 ln -s '$current.file' 'sample_1_${i}.tsv' &&
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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16 ln -s '$current.index' 'sample_1_${i}.tsv.idx' &&
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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17 #end for
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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18 #for $i, $current in enumerate($file2_rep)
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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19 ln -s '$current.file' 'sample_2_${i}.tsv' &&
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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20 ln -s '$current.index' 'sample_2_${i}.tsv.idx' &&
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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21 #end for
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22
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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23 ## run
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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24 nanocompore sampcomp
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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25 ## required
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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26 --label1 '$label1'
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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27 #set files1 = ','.join(['sample_1_' + str(item) + '.tsv' for item in range(len($file1_rep))])
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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28 --file_list1 '$files1'
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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29 --label2 '$label2'
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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30 #set files2 = ','.join(['sample_2_' + str(item) + '.tsv' for item in range(len($file2_rep))])
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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31 --file_list2 '$files2'
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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32 --fasta '$fasta'
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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33 ## optional
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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34 #if $ap.bed
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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35 --bed '$ap.bed'
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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36 #end if
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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37 --max_invalid_kmers_freq $ap.max_invalid_kmers_freq
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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38 --min_coverage $ap.min_coverage
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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39 --min_ref_length $ap.min_ref_length
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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40 --comparison_methods '$ap.comparison_methods'
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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41 --sequence_context $ap.sequence_context
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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42 --sequence_context_weights '$ap.sequence_context_weights'
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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43 --pvalue_thr $ap.pvalue_thr
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44 $ap.logit
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45 $ap.allow_warnings
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46 --outpath 'results'
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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47 --nthreads \$threads
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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48 --log_level debug
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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49
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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50 && tar -cf 'results/db.tar' 'results/out_SampComp.db.bak' 'results/out_SampComp.db.dir' 'results/out_SampComp.db.dat'
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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51 ]]></command>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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52 <inputs>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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53 <param argument="--label1" type="text" value="Condition 1" label="Set label of first condition"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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54 <repeat name="file1_rep" min="1" title="First condition files">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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55 <param name="file" type="data" format="tabular" label="Select NanopolishComp file" help="(--file_list1)"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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56 <param name="index" type="data" format="tabular" label="Select index file"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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57 </repeat>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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58 <param argument="--label2" type="text" value="Condition 2" label="Set label of second condition"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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59 <repeat name="file2_rep" min="1" title="Second condition files">
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60 <param name="file" type="data" format="tabular" label="Select NanopolishComp file" help="(--file_list2)"/>
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61 <param name="index" type="data" format="tabular" label="Select index file"/>
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62 </repeat>
1
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
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63 <param argument="--fasta" type="data" format="fasta" label="Select reference mapping fasta"/>
0
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64
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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65 <section name="ap" title="Advanced parameters">
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66 <param argument="--bed" type="data" format="bed" optional="true" label="Select mapping file with annotation of transcriptome"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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67 <param argument="--max_invalid_kmers_freq" type="float" value="0.1" min="0.0" max="1.0" label="Set max fequency of invalid kmers"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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68 <param argument="--min_coverage" type="integer" value="30" min="0" label="Set minimum coverage required in each condition to do the comparison"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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69 <param argument="--min_ref_length" type="integer" value="100" min="0" label="Set minimum length of a reference transcript to include it in the analysis"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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70 <param argument="--comparison_methods" type="select" multiple="true" label="Select comparison methods">
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71 <option value="GMM" selected="true">GMM</option>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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72 <option value="KS" selected="true">KS</option>
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73 <option value="TT">TT</option>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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74 <option value="MW">MW</option>
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75 </param>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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76 <param argument="--sequence_context" type="integer" value="0" min="0" max="4" label="Set sequence context for combining p-values"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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77 <param argument="--sequence_context_weights" type="select" label="Select type of weights to use for combining p-values">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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78 <option value="uniform" selected="true">Uniform</option>
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79 <option value="harmonic">Harmonic</option>
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80 </param>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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81 <param argument="--pvalue_thr" type="float" value="0.05" min="0.0" max="1.0" label="Set adjusted p-value threshold for reporting significant sites"/>
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diff changeset
82 <param argument="--logit" type="boolean" truevalue="--logit" falsevalue="" label="Use logistic regression testing also when all conditions have replicates?"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
83 <param argument="--allow_warnings" type="boolean" truevalue="--allow_warnings" falsevalue="" label="Should runtime warnings during the ANOVA tests raise an error?"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
84 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
85 <option value="results" selected="true">Results</option>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
86 <option value="shift" selected="true">Shift stats</option>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
87 <option value="db" selected="true">Database (*.db.dir, *.db.bak, *.db.dat)</option>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
88 <option value="log">Log</option>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
89 </param>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
90 </section>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
91 </inputs>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
92 <outputs>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
93 <data name="out_results" format="tabular" from_work_dir="results/out_nanocompore_results.tsv" label="${tool.name} on ${on_string}: Results">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
94 <filter>'results' in ap['out']</filter>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
95 </data>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
96 <data name="out_shift" format="tabular" from_work_dir="results/out_nanocompore_shift_stats.tsv" label="${tool.name} on ${on_string}: Shift stats">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
97 <filter>'shift' in ap['out']</filter>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
98 </data>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
99 <data name="out_db" format="tar" from_work_dir="results/db.tar" label="${tool.name} on ${on_string}: Database">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
100 <filter>'db' in ap['out']</filter>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
101 </data>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
102 <data name="out_log" format="txt" from_work_dir="results/out_SampComp.log" label="${tool.name} on ${on_string}: log">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
103 <filter>'log' in ap['out']</filter>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
104 </data>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
105 </outputs>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
106 <tests>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
107 <!-- #1 -->
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
108 <test expect_num_outputs="3">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
109 <repeat name="file1_rep">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
110 <param name="file" value="sample1.tsv"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
111 <param name="index" value="sample1.tsv.idx"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
112 </repeat>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
113 <repeat name="file2_rep">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
114 <param name="file" value="sample2.tsv"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
115 <param name="index" value="sample2.tsv.idx"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
116 </repeat>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
117 <param name="fasta" value="reference.fa"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
118 <output name="out_results">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
119 <assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
120 <has_n_lines n="3"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
121 <has_text_matching expression="pos&#09;chr.+"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
122 <has_text_matching expression="22102&#09;NA.+"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
123 </assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
124 </output>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
125 <output name="out_shift">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
126 <assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
127 <has_n_lines n="3"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
128 <has_text_matching expression="ref\_id&#09;pos.+"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
129 <has_text_matching expression="chr&#09;22102.+"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
130 </assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
131 </output>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
132 <output name="out_db">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
133 <assert_contents>
1
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents: 0
diff changeset
134 <has_size value="5416960" delta="10000"/>
0
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
135 </assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
136 </output>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
137 </test>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
138 <!-- #2 -->
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
139 <test expect_num_outputs="4">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
140 <param name="label1" value="C1"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
141 <repeat name="file1_rep">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
142 <param name="file" value="sample1.tsv"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
143 <param name="index" value="sample1.tsv.idx"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
144 </repeat>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
145 <param name="label2" value="C2"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
146 <repeat name="file2_rep">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
147 <param name="file" value="sample2.tsv"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
148 <param name="index" value="sample2.tsv.idx"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
149 </repeat>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
150 <param name="fasta" value="reference.fa"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
151 <section name="ap">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
152 <param name="max_invalid_kmers_freq" value="0.2"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
153 <param name="min_coverage" value="31"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
154 <param name="min_ref_length" value="101"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
155 <param name="comparison_methods" value="GMM,KS,TT,MW"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
156 <param name="sequence_context" value="1"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
157 <param name="sequence_context_weights" value="harmonic"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
158 <param name="pvalue_thr" value="0.06"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
159 <param name="logit" value="true"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
160 <param name="allow_warnings" value="true"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
161 <param name="out" value="results,shift,db,log"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
162 </section>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
163 <output name="out_results">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
164 <assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
165 <has_n_lines n="3"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
166 <has_text_matching expression="pos&#09;chr.+"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
167 <has_text_matching expression="22102&#09;NA.+"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
168 </assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
169 </output>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
170 <output name="out_shift">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
171 <assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
172 <has_n_lines n="3"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
173 <has_text_matching expression="ref\_id&#09;pos.+"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
174 <has_text_matching expression="chr&#09;22102.+"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
175 </assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
176 </output>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
177 <output name="out_db">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
178 <assert_contents>
1
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents: 0
diff changeset
179 <has_size value="5416960" delta="10000"/>
0
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
180 </assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
181 </output>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
182 <output name="out_log">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
183 <assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
184 <has_n_lines n="31"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
185 <has_text_matching expression=".+package\_name.+"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
186 </assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
187 </output>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
188 </test>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
189 </tests>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
190 <help><![CDATA[
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
191 .. class:: infomark
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
192
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
193 **What it does**
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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194
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
195 @WID@
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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196
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
197 SampComp provides a very flexible analysis framework with a few mandatory options and many optional parameters.
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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198
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
199 First, SampComp parses the sample eventalign collapse files and then the observed results are piled-up per reference at position level. In a second time, positions are compared using various statistical methods and the statistics are stored in a shelve DBM database containing the results for all positions with sufficient coverage.
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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200
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
201 **Input**
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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202
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
203 SampComp requires sample files obtained with NanopolishComp EventalignCollapse as explained before (see data preparation) for both the control and the experimental conditions. 2 conditions are expected and at least 2 replicates per conditions are highly recommended.
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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204
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
205 A transcriptome FASTA reference file is required to extract kmer sequences during the analyses. The reference has to be the same as the one used at the mapping step.
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
206
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
207 Optionally, a BED file containing the genome annotations corresponding to the transcriptome fasta file can be provided. In that case Nanocompore will also convert the transcript coordinates into the genome space.
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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208
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
209 **Output**
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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210
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
211 The database object returned by Sampcomp is a Python GDBM object database indexed by reference id and can be be used with SampCompDB.
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
212
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
213 .. class:: infomark
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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214
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
215 **References**
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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216
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
217 @REFERENCES@
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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218 ]]></help>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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219 <expand macro="citations"/>
2
25abc2c72ff9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit a57b5b935a80db12a0ed867b4219453a2854dd32"
iuc
parents: 1
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220 </tool>