Mercurial > repos > iuc > nanocompore_sampcomp

annotate sampcomp.xml @ 4:c0fb573c1e8d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 51078f4c0eab9cc41a0cb2190000e428322631a4
author iuc
date Thu, 23 Jun 2022 17:29:34 +0000
parents 25abc2c72ff9
children
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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"?>
4
c0fb573c1e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 51078f4c0eab9cc41a0cb2190000e428322631a4
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2 <tool id="nanocompore_sampcomp" name="SampComp" version="@TOOL_VERSION@+galaxy1">
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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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3 <description>to compare Nanopolished datasets</description>
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c0fb573c1e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 51078f4c0eab9cc41a0cb2190000e428322631a4
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4 <expand macro="bio_tools"/>
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5 <macros>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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6 <import>macros.xml</import>
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7 </macros>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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8 <expand macro="requirements"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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9 <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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10 <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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11 ## initialize
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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12 ## 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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13 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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14 ## 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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15 #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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16 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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17 ln -s '$current.index' 'sample_1_${i}.tsv.idx' &&
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18 #end for
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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19 #for $i, $current in enumerate($file2_rep)
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20 ln -s '$current.file' 'sample_2_${i}.tsv' &&
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21 ln -s '$current.index' 'sample_2_${i}.tsv.idx' &&
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22 #end for
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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23
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c0fb573c1e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 51078f4c0eab9cc41a0cb2190000e428322631a4
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24 ## symlink fasta file because a .fai file is created
c0fb573c1e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 51078f4c0eab9cc41a0cb2190000e428322631a4
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25 ln -s '$fasta' reference.fa &&
c0fb573c1e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 51078f4c0eab9cc41a0cb2190000e428322631a4
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26
0
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27 ## run
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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28 nanocompore sampcomp
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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29 ## required
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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30 --label1 '$label1'
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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31 #set files1 = ','.join(['sample_1_' + str(item) + '.tsv' for item in range(len($file1_rep))])
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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32 --file_list1 '$files1'
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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33 --label2 '$label2'
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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34 #set files2 = ','.join(['sample_2_' + str(item) + '.tsv' for item in range(len($file2_rep))])
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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35 --file_list2 '$files2'
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c0fb573c1e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 51078f4c0eab9cc41a0cb2190000e428322631a4
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36 --fasta reference.fa
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37 ## optional
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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38 #if $ap.bed
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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39 --bed '$ap.bed'
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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40 #end if
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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41 --max_invalid_kmers_freq $ap.max_invalid_kmers_freq
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42 --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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43 --min_ref_length $ap.min_ref_length
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44 --comparison_methods '$ap.comparison_methods'
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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45 --sequence_context $ap.sequence_context
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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46 --sequence_context_weights '$ap.sequence_context_weights'
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47 --pvalue_thr $ap.pvalue_thr
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48 $ap.logit
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49 $ap.allow_warnings
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50 --outpath 'results'
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51 --nthreads \$threads
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52 --log_level debug
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53
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54 && 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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55 ]]></command>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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56 <inputs>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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57 <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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58 <repeat name="file1_rep" min="1" title="First condition files">
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59 <param name="file" type="data" format="tabular" label="Select NanopolishComp file" help="(--file_list1)"/>
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60 <param name="index" type="data" format="tabular" label="Select index file"/>
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61 </repeat>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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62 <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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63 <repeat name="file2_rep" min="1" title="Second condition files">
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64 <param name="file" type="data" format="tabular" label="Select NanopolishComp file" help="(--file_list2)"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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65 <param name="index" type="data" format="tabular" label="Select index file"/>
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66 </repeat>
1
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67 <param argument="--fasta" type="data" format="fasta" label="Select reference mapping fasta"/>
0
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68
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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69 <section name="ap" title="Advanced parameters">
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70 <param argument="--bed" type="data" format="bed" optional="true" label="Select mapping file with annotation of transcriptome"/>
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71 <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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72 <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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73 <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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74 <param argument="--comparison_methods" type="select" multiple="true" label="Select comparison methods">
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75 <option value="GMM" selected="true">GMM</option>
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76 <option value="KS" selected="true">KS</option>
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77 <option value="TT">TT</option>
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78 <option value="MW">MW</option>
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79 </param>
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80 <param argument="--sequence_context" type="integer" value="0" min="0" max="4" label="Set sequence context for combining p-values"/>
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81 <param argument="--sequence_context_weights" type="select" label="Select type of weights to use for combining p-values">
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diff changeset
82 <option value="uniform" selected="true">Uniform</option>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
83 <option value="harmonic">Harmonic</option>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
84 </param>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
85 <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"/>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
86 <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
87 <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
88 <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
89 <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
90 <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
91 <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
92 <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
93 </param>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
94 </section>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
95 </inputs>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
96 <outputs>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
97 <data name="out_results" format="tabular" from_work_dir="results/out_nanocompore_results.tsv" label="${tool.name} on ${on_string}: Results">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
98 <filter>'results' in ap['out']</filter>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
99 </data>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
100 <data name="out_shift" format="tabular" from_work_dir="results/out_nanocompore_shift_stats.tsv" label="${tool.name} on ${on_string}: Shift stats">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
101 <filter>'shift' in ap['out']</filter>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
102 </data>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
103 <data name="out_db" format="tar" from_work_dir="results/db.tar" label="${tool.name} on ${on_string}: Database">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
104 <filter>'db' in ap['out']</filter>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
105 </data>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
106 <data name="out_log" format="txt" from_work_dir="results/out_SampComp.log" label="${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
107 <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
108 </data>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
109 </outputs>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
110 <tests>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
111 <!-- #1 -->
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
112 <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
113 <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
114 <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
115 <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
116 </repeat>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
117 <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
118 <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
119 <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
120 </repeat>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
121 <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
122 <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
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 <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
125 <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
126 <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
127 </assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
128 </output>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
129 <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
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 <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
132 <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
133 <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
134 </assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
135 </output>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
136 <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
137 <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
138 <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
139 </assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
140 </output>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
141 </test>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
142 <!-- #2 -->
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
143 <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
144 <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
145 <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
146 <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
147 <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
148 </repeat>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
149 <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
150 <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
151 <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
152 <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
153 </repeat>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
154 <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
155 <section name="ap">
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
156 <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
157 <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
158 <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
159 <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
160 <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
161 <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
162 <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
163 <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
164 <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
165 <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
166 </section>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
167 <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
168 <assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
169 <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
170 <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
171 <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
172 </assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
173 </output>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
174 <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
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 <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
177 <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
178 <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
179 </assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
180 </output>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
181 <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
182 <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
183 <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
184 </assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
185 </output>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
186 <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
187 <assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
188 <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
189 <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
190 </assert_contents>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
191 </output>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
192 </test>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
193 </tests>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
194 <help><![CDATA[
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
195 .. class:: infomark
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
196
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
197 **What it does**
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
198
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
199 @WID@
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
200
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
201 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
parents:
diff changeset
202
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
203 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
parents:
diff changeset
204
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
205 **Input**
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
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 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
parents:
diff changeset
208
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
209 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
parents:
diff changeset
210
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
211 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"
iuc
parents:
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 **Output**
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
214
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
215 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
parents:
diff changeset
216
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
217 .. class:: infomark
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
218
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
219 **References**
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
220
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
221 @REFERENCES@
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
222 ]]></help>
557cf45ff2c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
223 <expand macro="citations"/>
2
25abc2c72ff9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit a57b5b935a80db12a0ed867b4219453a2854dd32"
iuc
parents: 1
diff changeset
224 </tool>