annotate hapog.xml @ 2:ee0d6e789958 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit 0da1ca313d02ca780a671247e434a424fa67887b
author iuc
date Sun, 28 Jan 2024 23:46:07 +0000
parents 7d56a813fd24
children 5287036a797a
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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@">
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2 <description>genome polishing</description>
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3 <macros>
2
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4 <token name="@TOOL_VERSION@">1.3.7</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
2
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7 <xrefs>
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8 <xref type="bio.tools">hapog</xref>
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9 </xrefs>
0
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">hapog</requirement>
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12 </requirements>
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13 <command detect_errors="exit_code"><![CDATA[
2
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14 ##Compute samtools memory settings like in samtools_sort
ee0d6e789958 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit 0da1ca313d02ca780a671247e434a424fa67887b
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15 ##use only 75% of available: https://github.com/samtools/samtools/issues/831
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16 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
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17 ((addmemory=addmemory*75/100)) &&
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18 hapog
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19 --genome '${genome}'
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20 --output output/
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21
2
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22 --threads \${GALAXY_SLOTS:-1}
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23 --samtools-mem \$addmemory"M"
0
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24
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25 #if str( $reads.type ) == "short":
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26 #for $i in $reads.pe1
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27 --pe1 '${i}'
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28 #end for
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29 #for $i in $reads.pe2
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30 --pe2 '${i}'
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31 #end for
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32 #elif str( $reads.type ) == "short_collection":
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33 #for $i in $reads.pecol
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34 --pe1 '${i.forward}'
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35 --pe2 '${i.reverse}'
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36 #end for
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37 #elif str( $reads.type ) == "long":
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38 --single '${single}'
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39 #elif str( $reads.type ) == "bam":
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40 -b '${bam}'
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41 #end if
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42
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43 $u
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44 ]]></command>
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45 <inputs>
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46 <param argument="--genome" type="data" format="fasta" label="Genome assembly to polish"/>
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47 <conditional name="reads">
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48 <param name="type" type="select" label="Type of data used for polishing">
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49 <option value="short">Short (paired) reads</option>
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50 <option value="short_collection">Short (paired) reads collection</option>
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51 <option value="long">Long reads</option>
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52 <option value="bam">Pre-aligned reads (BAM)</option>
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53 </param>
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54 <when value="short">
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55 <param argument="--pe1" type="data" format="fastq,fastq.gz" multiple="true" label="First set of short reads"/>
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56 <param argument="--pe2" type="data" format="fastq,fastq.gz" multiple="true" label="Second set of short reads"/>
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57 </when>
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58 <when value="short_collection">
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59 <param name="pecol" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Paired collection of short reads"/>
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60 </when>
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61 <when value="long">
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62 <param argument="--single" type="data" format="fastq,fastq.gz" label="Long reads"/>
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63 </when>
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64 <when value="bam">
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65 <param name="bam" type="data" format="bam" label="Pre-aligned reads"/>
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66 </when>
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67 </conditional>
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68 <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Include unpolished sequences in final output" />
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69 </inputs>
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70 <outputs>
1
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71 <data format="fasta" name="output" label="${tool.name}: polished assembly from ${on_string}" from_work_dir="output/hapog_results/hapog.fasta"/>
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72 <data format="tsv" name="changes" label="${tool.name}: report of changes" from_work_dir="output/hapog_results/hapog.changes"/>
0
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="genome" value="genome.fa" />
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77 <conditional name="reads">
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78 <param name="type" value="short" />
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79 <param name="pe1" value="fastq1.fq" />
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80 <param name="pe2" value="fastq2.fq" />
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81 </conditional>
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82 <output name="output" file="hapog_short.fasta" />
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83 <output name="changes" file="hapog_short.changes" />
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84 </test>
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85 <test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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86 <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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87 <conditional name="reads">
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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88 <param name="type" value="short" />
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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89 <param name="pe1" 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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90 <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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91 </conditional>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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92 <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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93 <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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94 </test>
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 <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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97 <conditional name="reads">
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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98 <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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99 <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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100 </conditional>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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101 <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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102 <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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103 </test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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104 <test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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105 <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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106 <conditional name="reads">
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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107 <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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108 <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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109 </conditional>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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110 <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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111 <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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112 </test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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113 <test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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114 <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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115 <conditional name="reads">
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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116 <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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117 <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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118 </conditional>
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119 <output name="output" file="hapog_bam.fasta"/>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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120 <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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121 </test>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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122 </tests>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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123 <help><![CDATA[
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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124 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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125 ]]></help>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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126 <citations>
c61bc8bb5f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit e0b3195d9d7ae754bcc61c50bf127e13c9b1e9dc
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127 <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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128 </citations>
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129 </tool>