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annotate hapog.xml @ 1:7d56a813fd24 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit 34255461a89adf6cdd9e781ac1fe47e8c41227ba
author iuc
date Tue, 10 Oct 2023 17:29:42 +0000
parents c61bc8bb5f1e
children ee0d6e789958
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c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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1 <tool id="hapog" name="Hapo-G" profile="21.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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2 <description>genome polishing</description>
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3 <macros>
1
7d56a813fd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit 34255461a89adf6cdd9e781ac1fe47e8c41227ba
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4 <token name="@TOOL_VERSION@">1.3.6</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">hapog</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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11 hapog
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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12 --genome '${genome}'
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13 --output output/
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14
1
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15 ## setting default threads to 2 until
7d56a813fd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit 34255461a89adf6cdd9e781ac1fe47e8c41227ba
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16 ## https://github.com/institut-de-genomique/HAPO-G/issues/34
7d56a813fd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit 34255461a89adf6cdd9e781ac1fe47e8c41227ba
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17 ## gets addressed, at least
7d56a813fd24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit 34255461a89adf6cdd9e781ac1fe47e8c41227ba
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18 --threads \${GALAXY_SLOTS:-2}
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19
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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20 #if str( $reads.type ) == "short":
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21 #for $i in $reads.pe1
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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22 --pe1 '${i}'
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23 #end for
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24 #for $i in $reads.pe2
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25 --pe2 '${i}'
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26 #end for
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27 #elif str( $reads.type ) == "short_collection":
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28 #for $i in $reads.pecol
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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29 --pe1 '${i.forward}'
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30 --pe2 '${i.reverse}'
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31 #end for
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32 #elif str( $reads.type ) == "long":
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33 --single '${single}'
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34 #elif str( $reads.type ) == "bam":
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35 -b '${bam}'
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36 #end if
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37
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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38 $u
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39 ]]></command>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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40 <inputs>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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41 <param argument="--genome" type="data" format="fasta" label="Genome assembly to polish"/>
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42 <conditional name="reads">
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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43 <param name="type" type="select" label="Type of data used for polishing">
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44 <option value="short">Short (paired) reads</option>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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45 <option value="short_collection">Short (paired) reads collection</option>
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46 <option value="long">Long reads</option>
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47 <option value="bam">Pre-aligned reads (BAM)</option>
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48 </param>
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49 <when value="short">
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50 <param argument="--pe1" type="data" format="fastq,fastq.gz" multiple="true" label="First set of short reads"/>
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51 <param argument="--pe2" type="data" format="fastq,fastq.gz" multiple="true" label="Second set of short reads"/>
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52 </when>
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53 <when value="short_collection">
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54 <param name="pecol" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Paired collection of short reads"/>
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55 </when>
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56 <when value="long">
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57 <param argument="--single" type="data" format="fastq,fastq.gz" label="Long reads"/>
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58 </when>
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59 <when value="bam">
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60 <param name="bam" type="data" format="bam" label="Pre-aligned reads"/>
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61 </when>
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62 </conditional>
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63 <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Include unpolished sequences in final output" />
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64 </inputs>
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65 <outputs>
1
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66 <data format="fasta" name="output" label="${tool.name}: polished assembly from ${on_string}" from_work_dir="output/hapog_results/hapog.fasta"/>
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67 <data format="tsv" name="changes" label="${tool.name}: report of changes" from_work_dir="output/hapog_results/hapog.changes"/>
0
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param name="genome" value="genome.fa" />
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72 <conditional name="reads">
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73 <param name="type" value="short" />
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74 <param name="pe1" value="fastq1.fq" />
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75 <param name="pe2" value="fastq2.fq" />
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76 </conditional>
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77 <output name="output" file="hapog_short.fasta" />
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78 <output name="changes" file="hapog_short.changes" />
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79 </test>
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80 <test>
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81 <param name="genome" value="genome.fa" />
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82 <conditional name="reads">
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83 <param name="type" value="short" />
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84 <param name="pe1" value="fastq1.fq.gz" />
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85 <param name="pe2" value="fastq2.fq.gz" />
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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86 </conditional>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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87 <output name="output" file="hapog_short.fasta"/>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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88 <output name="changes" file="hapog_short.changes" />
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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89 </test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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90 <test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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91 <param name="genome" value="genome.fa" />
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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92 <conditional name="reads">
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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93 <param name="type" value="long" />
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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94 <param name="single" value="fastq1.fq" />
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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95 </conditional>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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96 <output name="output" file="hapog_long.fasta" />
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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97 <output name="changes" file="hapog_long.changes" />
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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98 </test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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99 <test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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100 <param name="genome" value="genome.fa" />
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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101 <conditional name="reads">
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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102 <param name="type" value="long" />
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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103 <param name="single" value="fastq1.fq.gz" />
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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104 </conditional>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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105 <output name="output" file="hapog_long.fasta"/>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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106 <output name="changes" file="hapog_long.changes" />
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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107 </test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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108 <test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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109 <param name="genome" value="genome.fa" />
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110 <conditional name="reads">
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111 <param name="type" value="bam" />
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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112 <param name="bam" value="input.bam" />
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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113 </conditional>
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114 <output name="output" file="hapog_bam.fasta"/>
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115 <output name="changes" file="hapog_bam.changes" />
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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116 </test>
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117 </tests>
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118 <help><![CDATA[
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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119 Hapo-G uses alignments produced by BWA (or any other aligner that produces SAM files) to polish the consensus of a genome assembly.
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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120 ]]></help>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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121 <citations>
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122 <citation type="doi">10.1093/nargab/lqab034</citation>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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123 </citations>
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124 </tool>