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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
author iuc
date Wed, 11 Nov 2020 21:54:51 +0000
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60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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1 <?xml version="1.0"?>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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2 <macros>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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3 <token name="@TOOL_VERSION@">0.6.0</token>
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4 <token name="@PROFILE@">18.01</token>
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5 <xml name="requirements">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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6 <requirements>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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7 <requirement type="package" version="@TOOL_VERSION@">shasta</requirement>
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8 </requirements>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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9 </xml>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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10 <xml name="version_command">
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11 <version_command>shasta --version</version_command>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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12 </xml>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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13 <xml name="citations">
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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14 <citations>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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15 <citation type="doi">10.1038/s41587-020-0503-6</citation>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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16 <citation type="bibtex">@online{shasta,
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17 author = {TODOLastName,TODOFirstName},
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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18 title = {shasta},
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19 year = 2020,
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20 url = {https://github.com/chanzuckerberg/shasta},
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21 urldate = {2020-11-05}
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22 }</citation>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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23 </citations>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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24 </xml>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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25 <!--
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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26 input
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27 -->
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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28 <token name="@INIT_INPUT_READS@"><![CDATA[
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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29 #for $counter, $input in enumerate($in_data)
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30 #if $input.is_of_type("fasta.gz")
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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31 #set $ext = "fasta"
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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32 gzip -dcf '$input' > ./input_${counter}.${ext} &&
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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33 #elif $input.is_of_type("fastq.gz","fastqsanger.gz")
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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34 #set $ext = "fastq"
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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35 gzip -dcf '$input' > ./input_${counter}.${ext} &&
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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36 #elif $input.is_of_type("fastqsanger", "fastq"):
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37 #set $ext = "fastq"
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38 ### I tried symlinking but shasta still complained about file extensions
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39 cp '$input' ./input_${counter}.${ext} &&
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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40 #elif $input.is_of_type("fasta"):
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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41 #set $ext = "fasta"
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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42 ### I tried symlinking but shasta still complained about file extensions
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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43 cp '$input' ./input_${counter}.${ext} &&
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44 #end if
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45 #end for
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46 ]]></token>
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47
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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48 <xml name="input_reads">
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49 <param name="in_data" type="data" format="fasta,fastq,fastqsanger,fasta.gz,fastq.gz,fastqsanger.gz" multiple="true" label="Input read file(s)"/>
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50 </xml>
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51
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52 <xml name="config_selection">
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53 <param name="config_select" type="select" label="Initial config file to build off of." help="Link to the directory where these config files are stored can be found in the tool help below.">
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54 <option value="Nanopore-Dec2019.conf"></option>
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55 <option value="Nanopore-Jun2020.conf"></option>
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56 <option value="Nanopore-OldGuppy-Sep2020.conf"></option>
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57 <option value="Nanopore-Sep2020.conf"></option>
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58 <option value="Nanopore-UL-Dec2019.conf"></option>
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59 <option value="Nanopore-UL-Jun2020.conf"></option>
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60 <option value="Nanopore-UL-Sep2020.conf"></option>
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61 <option value="Nanopore-UL-iterative-Sep2020.conf"></option>
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62 <option value="PacBio-CCS-Dec2019.conf"></option>
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63 <option value="PacBio-CLR-Dec2019.conf"></option>
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64 </param>
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65 </xml>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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66 <!--
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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67 Help
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68 -->
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69
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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70 <token name="@WID@"><![CDATA[
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71 The goal of the *Shasta* long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.
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72
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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73 Computational methods used by the Shasta assembler include:
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74
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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75 Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads.
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76
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77 Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10).
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78 ]]></token>
60573349e9ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta commit 6d14992ea4fb1af09373d51b3a48166afcbd3a74"
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79 <token name="@REFERENCES@"><![CDATA[
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80 More information are available on the `documentation <https://chanzuckerberg.github.io/shasta/>`_ or the `github <https://github.com/chanzuckerberg/shasta>`_ .
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81 ]]></token>
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82 </macros>