Mercurial > repos > florianbegusch > qiime2_all
comparison qiime_quality-control_evaluate-seqs.xml @ 0:09b7bcb72fa7 draft
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| author | florianbegusch |
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| date | Thu, 24 May 2018 02:11:44 -0400 |
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| -1:000000000000 | 0:09b7bcb72fa7 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_quality-control_evaluate-seqs" name="qiime quality-control evaluate-seqs" version="2018.4"> | |
| 3 <description> - Compare query (observed) vs. reference (expected) sequences.</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2018.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command> | |
| 8 <![CDATA[ | |
| 9 qiime quality-control evaluate-seqs --i-reference-sequences=$ireferencesequences --i-query-sequences=$iquerysequences | |
| 10 | |
| 11 #if str($cmdconfig) != 'None': | |
| 12 --cmd-config=$cmdconfig | |
| 13 | |
| 14 #if $pshowalignments: | |
| 15 --p-show-alignments | |
| 16 #else | |
| 17 --p-no-show-alignments | |
| 18 #end if | |
| 19 | |
| 20 #end if | |
| 21 --o-visualization=ovisualization; | |
| 22 | |
| 23 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path' | |
| 24 && cp -r out/* '$ovisualization.files_path' | |
| 25 && mv '$ovisualization.files_path/index.html' '$ovisualization' | |
| 26 ]]> | |
| 27 </command> | |
| 28 <inputs> | |
| 29 <param format="qza,no_unzip.zip" label="--i-query-sequences: FeatureData[Sequence] Sequences to test for exclusion [required]" name="iquerysequences" optional="False" type="data"/> | |
| 30 <param format="qza,no_unzip.zip" label="--i-reference-sequences: FeatureData[Sequence] Reference sequences to align against feature sequences [required]" name="ireferencesequences" optional="False" type="data"/> | |
| 31 | |
| 32 <param label=" --p-show-alignments / --p-no-show-alignments | |
| 33 Option to plot pairwise alignments of query | |
| 34 sequences and their top hits. [default: | |
| 35 False]" name="pshowalignments" checked="False" type="boolean"/> | |
| 36 | |
| 37 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/> | |
| 38 </inputs> | |
| 39 <outputs> | |
| 40 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> | |
| 41 </outputs> | |
| 42 <help> | |
| 43 <![CDATA[ | |
| 44 Compare query (observed) vs. reference (expected) sequences. | |
| 45 ------------------------------------------------------------- | |
| 46 | |
| 47 This action aligns a set of query (e.g., observed) sequences against a set | |
| 48 of reference (e.g., expected) sequences to evaluate the quality of | |
| 49 alignment. The intended use is to align observed sequences against expected | |
| 50 sequences (e.g., from a mock community) to determine the frequency of | |
| 51 mismatches between observed sequences and the most similar expected | |
| 52 sequences, e.g., as a measure of sequencing/method error. However, any | |
| 53 sequences may be provided as input to generate a report on pairwise | |
| 54 alignment quality against a set of reference sequences. | |
| 55 | |
| 56 Parameters | |
| 57 ---------- | |
| 58 query_sequences : FeatureData[Sequence] | |
| 59 Sequences to test for exclusion | |
| 60 reference_sequences : FeatureData[Sequence] | |
| 61 Reference sequences to align against feature sequences | |
| 62 show_alignments : Bool, optional | |
| 63 Option to plot pairwise alignments of query sequences and their top | |
| 64 hits. | |
| 65 | |
| 66 Returns | |
| 67 ------- | |
| 68 visualization : Visualization | |
| 69 \ | |
| 70 ]]> | |
| 71 </help> | |
| 72 </tool> |