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annotate hapog.xml @ 0:c61bc8bb5f1e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
author iuc
date Fri, 16 Sep 2022 13:48:54 +0000
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children 7d56a813fd24
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0
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>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.3.3</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}'
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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13 --output output/
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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14
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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15 --threads \${GALAXY_SLOTS:-1}
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16
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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17 #if str( $reads.type ) == "short":
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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18 #for $i in $reads.pe1
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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19 --pe1 '${i}'
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20 #end for
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21 #for $i in $reads.pe2
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22 --pe2 '${i}'
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23 #end for
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24 #elif str( $reads.type ) == "short_collection":
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25 #for $i in $reads.pecol
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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26 --pe1 '${i.forward}'
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27 --pe2 '${i.reverse}'
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28 #end for
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29 #elif str( $reads.type ) == "long":
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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30 --single '${single}'
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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31 #elif str( $reads.type ) == "bam":
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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32 -b '${bam}'
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33 #end if
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34
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35 $u
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36 ]]></command>
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37 <inputs>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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38 <param argument="--genome" type="data" format="fasta" label="Genome assembly to polish"/>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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39 <conditional name="reads">
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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40 <param name="type" type="select" label="Type of data used for polishing">
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41 <option value="short">Short (paired) reads</option>
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42 <option value="short_collection">Short (paired) reads collection</option>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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43 <option value="long">Long reads</option>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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44 <option value="bam">Pre-aligned reads (BAM)</option>
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45 </param>
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46 <when value="short">
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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47 <param argument="--pe1" type="data" format="fastq,fastq.gz" multiple="true" label="First set of short reads"/>
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48 <param argument="--pe2" type="data" format="fastq,fastq.gz" multiple="true" label="Second set of short reads"/>
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49 </when>
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50 <when value="short_collection">
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51 <param name="pecol" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Paired collection of short reads"/>
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52 </when>
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53 <when value="long">
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54 <param argument="--single" type="data" format="fastq,fastq.gz" label="Long reads"/>
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55 </when>
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56 <when value="bam">
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57 <param name="bam" type="data" format="bam" label="Pre-aligned reads"/>
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58 </when>
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59 </conditional>
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60 <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Include unpolished sequences in final output" />
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61 </inputs>
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62 <outputs>
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63 <data format="fasta" name="output" from_work_dir="output/hapog_results/hapog.fasta"/>
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64 <data format="tsv" name="changes" from_work_dir="output/hapog_results/hapog.changes"/>
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65 </outputs>
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66 <tests>
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67 <test>
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68 <param name="genome" value="genome.fa" />
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69 <conditional name="reads">
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70 <param name="type" value="short" />
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71 <param name="pe1" value="fastq1.fq" />
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72 <param name="pe2" value="fastq2.fq" />
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73 </conditional>
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74 <output name="output" file="hapog_short.fasta" />
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75 <output name="changes" file="hapog_short.changes" />
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76 </test>
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77 <test>
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78 <param name="genome" value="genome.fa" />
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79 <conditional name="reads">
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80 <param name="type" value="short" />
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81 <param name="pe1" value="fastq1.fq.gz" />
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82 <param name="pe2" value="fastq2.fq.gz" />
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83 </conditional>
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84 <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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85 <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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86 </test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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87 <test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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88 <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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89 <conditional name="reads">
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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90 <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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91 <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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92 </conditional>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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93 <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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94 <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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95 </test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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96 <test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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97 <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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98 <conditional name="reads">
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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99 <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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100 <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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101 </conditional>
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102 <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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103 <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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104 </test>
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105 <test>
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106 <param name="genome" value="genome.fa" />
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107 <conditional name="reads">
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108 <param name="type" value="bam" />
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109 <param name="bam" value="input.bam" />
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110 </conditional>
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111 <output name="output" file="hapog_bam.fasta"/>
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112 <output name="changes" file="hapog_bam.changes" />
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113 </test>
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114 </tests>
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115 <help><![CDATA[
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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116 Hapo-G uses alignments produced by BWA (or any other aligner that produces SAM files) to polish the consensus of a genome assembly.
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117 ]]></help>
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118 <citations>
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119 <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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120 </citations>
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121 </tool>