Mercurial > repos > iuc > data_manager_salmon_index_builder

annotate data_manager/salmon_index_builder.xml @ 9:ad0ad1f6623e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit 940b8237169a0a16541bd3bc340b085c95fb5bd7
author iuc
date Fri, 07 Nov 2025 07:58:18 +0000
parents e1bbef81b470
children
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befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
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1 <tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.0">
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2 <description>index builder</description>
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iuc
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.10.1</token>
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5 <token name="@VERSION_SUFFIX@">1</token>
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6 <token name="@PROFILE@">24.0</token>
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iuc
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7 <token name="@IDX_VERSION@">q7</token>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
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8 </macros>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
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11 </requirements>
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12 <version_command><![CDATA[salmon --no-version-check --version | cut -d" " -f2]]></version_command>
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13 <command detect_errors="exit_code"><![CDATA[
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14 ## salmon uses one thread to much
ad0ad1f6623e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit 940b8237169a0a16541bd3bc340b085c95fb5bd7
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15 ## https://github.com/COMBINE-lab/salmon/issues/993
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16 SLOTS=\$(( \${GALAXY_SLOTS:-12} > 1 ? \${GALAXY_SLOTS:-12} - 1 : 1 ));
e1bbef81b470 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit 1ea9e99e1c7a7cd0f012467466e0740b6bdeb90e
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17
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18 ## https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
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19 ## https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
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20 #for $transcripts in $transcriptome.fields.path.split(",")
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
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21 (zcat '$transcripts' 2>/dev/null || cat '$transcripts') >> gentrome.fa &&
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
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22 #end for
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23 (zcat '$all_fasta_source.fields.path' 2>/dev/null || cat '$all_fasta_source.fields.path') >> gentrome.fa &&
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
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befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
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25 (zcat '$all_fasta_source.fields.path' 2>/dev/null || cat '$all_fasta_source.fields.path') | awk '{if($1 ~ /^>/) print $1}' | cut -c2- | tr -d " " > decoys.txt &&
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
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27 mkdir '$out_file.extra_files_path' &&
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
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28
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29 salmon --no-version-check index
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30 -k $kmer_size
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31 -t gentrome.fa
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32 -d decoys.txt
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33 -i '$out_file.extra_files_path'
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34 -p "\$SLOTS"
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35 $gencode
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36 &&
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38 cp '$dmjson' '$out_file'
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39 ]]></command>
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40 <configfiles>
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41 <configfile name="dmjson"><![CDATA[#slurp
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42 #import os
ad0ad1f6623e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit 940b8237169a0a16541bd3bc340b085c95fb5bd7
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43 #def combine(strings, sep):
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44 #set lcp = os.path.commonprefix(strings)
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45 #set value = lcp + sep.join([s[len(lcp):] for s in strings])
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46 #return $value
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47 #end def
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48 #if str($sequence_id).strip() == ""
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49 #set sequence_id = $combine($transcriptome.fields.value.split(","), "_")
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50 #end if
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51 #if str($sequence_name).strip() == ""
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52 #set sequence_name = $combine($transcriptome.fields.name.split(","), " + ")
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53 #end if
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54 {
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55 "data_tables":{
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56 "salmon_indexes_versioned":[
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57 {
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58 "value": "$sequence_id",
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59 "dbkey": "$all_fasta_source.fields.dbkey",
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60 "name": "$sequence_name",
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61 "path": "$out_file.extra_files_path",
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62 "version": "@IDX_VERSION@"
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63 }
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64 ]
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65 }
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66 }]]></configfile>
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67 </configfiles>
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68 <inputs>
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69 <param label="Transcriptome sequences" name="transcriptome" optional="false" multiple="true" type="select">
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70 <options from_data_table="transcriptomes" />
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71 </param>
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72 <param label="Genome" name="all_fasta_source" optional="false" type="select">
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73 <options from_data_table="all_fasta"/>
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74 </param>
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75 <param name="sequence_name" type="text" value="" label="Name of sequence" help="default: common prefix of the transcriptome names plus the non-common parts joined by ' + '" />
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76 <param name="sequence_id" type="text" value="" label="ID for sequence" help="default: common prefix of the transcriptome IDs plus the non-common parts joined by '_'"/>
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77 <param name="kmer_size" type="integer" optional='true' value="31" max="32" label="The size of the k-mer on which the index is built"
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78 help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, the more distinct they will be. We generally recommend using a k-mer size of at least 20. MUST BE AN ODD VALUE ">
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79 <validator type="expression" message="Only odd values">value % 2 == 1</validator>
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80 </param>
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81 <param name="gencode" type="boolean" label="Transcript sequences are in gencode format" truevalue="--gencode" falsevalue="" checked="false" help="Will split the transcript name at the first '|' character. These reduced names will be used in the output and when looking for these transcripts in a gene to transcript GTF."/>
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82 </inputs>
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83 <outputs>
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84 <data name="out_file" format="data_manager_json" />
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85 </outputs>
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86 <tests>
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87 <test>
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88 <param name="transcriptome" value="phiX1741,phiX1742"/>
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89 <param name="all_fasta_source" value="phiX174"/>
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90 <output name="out_file">
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91 <assert_contents>
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92 <has_text text='"salmon_indexes_versioned"' />
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93 <has_text text='"dbkey": "phiX174"' />
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94 <has_text text='"name": "phiX174: 1 + 2"' />
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95 <has_text text='"value": "phiX1741_2"' />
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96 <has_text text='"version": "q7"' />
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97 <has_text text='"path":' />
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98 </assert_contents>
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99 </output>
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100 </test>
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101 <test>
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102 <param name="transcriptome" value="phiX1741"/>
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103 <param name="all_fasta_source" value="phiX174"/>
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104 <output name="out_file">
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105 <assert_contents>
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106 <has_text text='"salmon_indexes_versioned"' />
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107 <has_text text='"dbkey": "phiX174"' />
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108 <has_text text='"name": "phiX174: 1"' />
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109 <has_text text='"value": "phiX1741"' />
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110 <has_text text='"version": "q7"' />
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111 <has_text text='"path":' />
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112 </assert_contents>
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113 </output>
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114 </test>
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115 <test>
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116 <param name="transcriptome" value="phiX1741"/>
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117 <param name="all_fasta_source" value="phiX174"/>
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118 <param name="sequence_name" value="name_override"/>
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119 <param name="sequence_id" value="value_override"/>
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120 <output name="out_file">
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121 <assert_contents>
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122 <has_text text='"salmon_indexes_versioned"' />
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123 <has_text text='"dbkey": "phiX174"' />
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124 <has_text text='"name": "name_override"' />
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125 <has_text text='"value": "value_override"' />
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126 <has_text text='"version": "q7"' />
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127 <has_text text='"path":' />
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128 </assert_contents>
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129 </output>
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130 </test>
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131 </tests>
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132 <help>
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133 <![CDATA[
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134 .. class:: infomark
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135
5
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136 Indices are constructed as described here: https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/
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137
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138 See also https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode
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139
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140 **Notice:** If you leave name, description, or id blank, it the dbkey of the genome will be used.
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141 ]]>
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142 </help>
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143 <citations>
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144 <citation type="doi">https://doi.org/10.1038/nmeth.4197</citation>
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145 </citations>
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146 </tool>