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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit cb48fa8b0d1a3e4e2483b4b0ecea6011d4f71200
author iuc
date Mon, 28 Apr 2025 07:17:49 +0000
parents 27a56ecc88ee
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27a56ecc88ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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1 <tool id="syri" name="SyRI" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
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2 <description>Synteny and Rearrangement Identifier</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <xrefs>
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7 <xref type="bio.tools">SyRI</xref>
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8 </xrefs>
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9 <expand macro="requirements"/>
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10 <stdio>
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11 <exit_code range="1:" level="fatal" description="Error"/>
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12 <regex match="- ERROR -" source="both" level="fatal" description="Error"/>
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13 </stdio>
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14 <version_command>syri --version</version_command>
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15 <command>
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16 <![CDATA[
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17 syri
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18 ## Input files
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19 #if $alnfile.is_of_type("bam")
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20 -F B
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21 #elif $alnfile.is_of_type("sam")
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22 -F S
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23 #elif $alnfile.is_of_type("paf")
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24 -F P
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25 #end if
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26 ## Additional arguments
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27 #if $additional_options.aln_filter
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28 '${additional_options.aln_filter}'
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29 #end if
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30 #if $additional_options.seed
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31 --seed '${additional_options.seed}'
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32 #end if
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33 #if $additional_options.sample_name
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34 --samplename '${additional_options.sample_name}'
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35 #end if
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36 ## SR identification
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37 #if $sr_options.nosr
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38 '${sr_options.nosr}'
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39 #end if
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40 #if $sr_options.invgaplen
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41 --invgaplen '${sr_options.invgaplen}'
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42 #end if
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43 #if $sr_options.tdgaplen
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44 --tdgaplen '${sr_options.tdgaplen}'
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45 #end if
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46 #if $sr_options.tdmaxolp
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47 --tdmaxolp '${sr_options.tdmaxolp}'
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48 #end if
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49 #if $sr_options.bruteruntime
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50 -b '${sr_options.bruteruntime}'
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51 #end if
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52 #if $sr_options.unic
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53 --unic '${sr_options.unic}'
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54 #end if
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55 #if $sr_options.unip
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56 --unip '${sr_options.unip}'
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57 #end if
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58 #if $sr_options.inc
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59 --inc '${sr_options.inc}'
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60 #end if
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61 #if $sr_options.no_chrmatch
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62 '${sr_options.no_chrmatch}'
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63 #end if
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64 ## ShV identification
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65 #if $shv_options.nosv
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66 '${shv_options.nosv}'
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67 #end if
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68 #if $shv_options.nosnp
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69 '${shv_options.nosnp}'
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70 #end if
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71 #if $shv_options.all
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72 '${shv_options.all}'
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73 #end if
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74 #if $shv_options.offset
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75 --allow-offset '${shv_options.offset}'
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76 #end if
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77 #if $shv_options.hdrseq
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78 '${shv_options.hdrseq}'
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79 #end if
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80 #if $shv_options.maxsize
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81 --maxsize '${shv_options.maxsize}'
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82 #end if
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83 -c '${alnfile}' -r '${refgenome}' -q '${qrygenome}' -k --prefix galaxy_ --nc \${GALAXY_SLOTS:-2}
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84 ]]> </command>
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85 <inputs>
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86 <param type="data" label="Alignment file" name="alnfile" optional="false" format="sam,paf,bam"/>
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87 <param type="data" label="Reference genome" name="refgenome" optional="false" format="fasta"/>
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88 <param type="data" label="Query genome" name="qrygenome" optional="false" format="fasta"/>
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89 <section name="additional_options" title="Additional options">
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90 <param argument="--seed" type="integer" label="Seed for generating random numbers (default: 1)" min="1" max="10000" optional="true"/>
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91 <param argument="-f" name="aln_filter" type="boolean" label="Disable filtering of low-quality and small alignments" checked="false" truevalue="-f" falsevalue=""/>
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92 <param argument="--samplename" name="sample_name" type="text" label="Sample name for the output VCF file. (default: sample)">
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93 <validator type="regex" message="Invalid characters in sample name">^[a-zA-Z0-9\-_]*$</validator>
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94 </param>
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95 </section>
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96 <section name="sr_options" title="SR identification">
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97 <param argument="--nosr" type="boolean" label="Set to skip structural rearrangement identification (default: False)" checked="false" truevalue="--nosr" falsevalue=""/>
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98 <param argument="--invgaplen" type="integer" label="Maximum allowed gap-length between two alignments of a multi-alignment inversion. (default: 1,000,000,000)" optional="true"/>
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99 <param argument="--tdgaplen" type="integer" label="Maximum allowed gap-length between two alignments of a multi-alignment translocation or duplication. (default: 500,000)" optional="true"/>
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100 <param argument="--tdmaxolp" type="float" min="0" max="1" label="Maximum allowed overlap between two translocations. Value should be in range (0,1]. (default: 0.8)" optional="true"/>
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101 <param argument="-b" name="bruteruntime" type="integer" min="1" label="Cutoff to restrict brute force methods from running too long (in seconds). (default: 60)" optional="true"/>
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102 <param argument="--unic" type="integer" min="1" label="Number of unique base pairs for selecting translocations. (default: 1,000)" optional="true"/>
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103 <param argument="--unip" type="float" min="0" max="100" label="Percent of unique region required to select translocation. (default: 0.5)" optional="true"/>
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104 <param argument="--inc" type="integer" min="0" label="Minimum score increase required to add another alignment to a translocation cluster solution. (default: 1,000)" optional="true"/>
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105 <param argument="--no-chrmatch" type="boolean" label="Prevent automatic matching of chromosome IDs between genomes. (default: False)" checked="false" truevalue="--no-chrmatch" falsevalue=""/>
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106 </section>
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107 <section name="shv_options" title="ShV identification">
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108 <param argument="--nosv" type="boolean" label="Set to skip structural variation identification (default: False)" checked="false" truevalue="--nosv" falsevalue=""/>
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109 <param argument="--nosnp" type="boolean" label="Set to skip SNP/Indel (within alignment) identification (default: False)" checked="false" truevalue="--nosnp" falsevalue=""/>
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110 <param argument="--all" type="boolean" label="Use duplications too for variant identification (default: False)" checked="false" truevalue="--all" falsevalue=""/>
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111 <param argument="--allow-offset" name="offset" type="integer" label="Number of base pairs allowed to overlap. (default: 5)" optional="true"/>
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112 <param argument="--hdrseq" type="boolean" label="Output highly-diverged regions (HDRs) sequences. (default: False)" checked="false" truevalue="--hdrseq" falsevalue="" optional="true"/>
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113 <param argument="--maxsize" type="integer" label="Maximum size for printing sequences of large structural variants. Larger variants will be printed as symbolic SVs. (default: -1)" optional="true"/>
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114 </section>
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115 </inputs>
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116 <outputs>
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117 <data name="syri_out" from_work_dir="galaxy_syri.out" format="tabular" label="${tool.name} on ${on_string} : OUT"/>
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118 <data name="syri_summary" from_work_dir="galaxy_syri.summary" format="tabular" label="${tool.name} on ${on_string} : Summary"> </data>
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119 <data name="syri_vcf" from_work_dir="galaxy_syri.vcf" format="vcf" label="${tool.name} on ${on_string} : VCF"/>
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120 <data name="mapids" from_work_dir="galaxy_mapids.txt" format="tabular" label="${tool.name} on ${on_string} : Map IDs"/>
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121 </outputs>
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122 <tests>
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123 <test expect_num_outputs="4">
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124 <param name="alnfile" value="aln.bam"/>
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125 <param name="refgenome" value="ref.fa.gz"/>
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126 <param name="qrygenome" value="qry.fa.gz"/>
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127 <section name="additional_options">
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128 <param name="sample_name" value="syri_user_1"/>
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129 </section>
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130 <output name="syri_vcf">
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131 <assert_contents>
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132 <has_text text="syri_user_1"/>
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133 </assert_contents>
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134 </output>
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135 </test>
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136 <test expect_num_outputs="4">
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137 <param name="alnfile" value="aln.paf"/>
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138 <param name="refgenome" value="ref.fa.gz"/>
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139 <param name="qrygenome" value="qry.fa.gz"/>
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140 <output name="mapids">
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141 <assert_contents>
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142 <has_text_matching expression="NC_001133.9\tNC_047487.1"/>
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143 </assert_contents>
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144 </output>
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145 </test>
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146 </tests>
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147 <expand macro="help"/>
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148 <expand macro="citations"/>
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149 </tool>