Mercurial > repos > bgruening > nanopolish_eventalign
comparison nanopolish_eventalign.xml @ 4:d219b6d8158a draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 25c22b467760e4784e199125292927bd2274a189-dirty
| author | bgruening |
|---|---|
| date | Sun, 23 Jun 2019 05:36:00 -0400 |
| parents | 0938217b3221 |
| children | 8fdb079ddaf0 |
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| 3:0938217b3221 | 4:d219b6d8158a |
|---|---|
| 1 <tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="0.1.0"> | 1 <tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="0.11.1"> |
| 2 <description>- Align nanopore events to reference k-mers</description> | 2 <description>- Align nanopore events to reference k-mers</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 65 | 65 |
| 66 ]]></command> | 66 ]]></command> |
| 67 <inputs> | 67 <inputs> |
| 68 <!-- index inputs --> | 68 <!-- index inputs --> |
| 69 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> | 69 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> |
| 70 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/> | 70 <param type="data" name="input_reads_raw" format="fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/> |
| 71 | 71 |
| 72 <!-- variants consensus inputs --> | 72 <!-- variants consensus inputs --> |
| 73 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> | 73 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> |
| 74 <conditional name="reference_source"> | 74 <conditional name="reference_source"> |
| 75 <param name="reference_source_selector" type="select" label="Load reference genome from"> | 75 <param name="reference_source_selector" type="select" label="Load reference genome from"> |
| 159 <test> | 159 <test> |
| 160 <!-- test data table reference --> | 160 <!-- test data table reference --> |
| 161 <param name="input_merged" ftype="fasta" value="reads.fasta" /> | 161 <param name="input_merged" ftype="fasta" value="reads.fasta" /> |
| 162 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> | 162 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> |
| 163 <param name="b" value="reads.sorted.bam" /> | 163 <param name="b" value="reads.sorted.bam" /> |
| 164 <param name="reference_source_selector" value="cached" /> | 164 <param name="reference_source_selector" value="history" /> |
| 165 <param name="ref_file" value="draft"/> | 165 <param name="ref_file" value="draft.fa"/> |
| 166 <param name="w" value="tig00000001:200000-200010" /> | 166 <param name="w" value="tig00000001:200000-200010" /> |
| 167 <param name="sam" value="false" /> | 167 <param name="sam" value="false" /> |
| 168 <param name="summary" value="false" /> | 168 <param name="summary" value="false" /> |
| 169 <param name="scale_events" value="true" /> | 169 <param name="scale_events" value="true" /> |
| 170 <param name="print_read_names" value="true" /> | 170 <param name="print_read_names" value="true" /> |