Mercurial > repos > iuc > data_manager_salmon_index_builder

annotate data_manager/salmon_index_builder.xml @ 8:ec2a1f280d67 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit 1ea9e99e1c7a7cd0f012467466e0740b6bdeb90e
author iuc
date Thu, 23 Oct 2025 17:05:46 +0000
parents 9fc154508622
children d31d59516633
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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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3 <macros>
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4 <token name="@TOOL_VERSION@">1.10.1</token>
ec2a1f280d67 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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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <token name="@PROFILE@">24.0</token>
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7 <token name="@IDX_VERSION@">q7</token>
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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 <command detect_errors="exit_code"><![CDATA[
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13 ## salmon uses one thread to much
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14 SLOTS=\$(( \${GALAXY_SLOTS:-12} > 1 ? \${GALAXY_SLOTS:-12} - 1 : 1 ));
ec2a1f280d67 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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15
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16 ## https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/
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17 ## https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode
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19 #for $transcripts in $transcriptome.fields.path.split(",")
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20 (zcat '$transcripts' 2>/dev/null || cat '$transcripts') >> gentrome.fa &&
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21 #end for
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22 (zcat '$all_fasta_source.fields.path' 2>/dev/null || cat '$all_fasta_source.fields.path') >> gentrome.fa &&
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24 (zcat '$all_fasta_source.fields.path' 2>/dev/null || cat '$all_fasta_source.fields.path') | awk '{if($1 ~ /^>/) print $1}' | cut -c2- | tr -d " " > decoys.txt &&
4d92281e3b30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
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26 mkdir '$out_file.extra_files_path' &&
4d92281e3b30 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 salmon index
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29 -k $kmer_size
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30 -t gentrome.fa
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31 -d decoys.txt
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32 -i '$out_file.extra_files_path'
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33 -p "\$SLOTS"
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34 $gencode
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35 &&
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37 cp '$dmjson' '$out_file'
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38 ]]></command>
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39 <configfiles>
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40 <configfile name="dmjson"><![CDATA[{
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41 #if str($sequence_id).strip() == ""
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42 #set sequence_id = $transcriptome.fields.value
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43 #end if
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44 #if str($sequence_name).strip() == ""
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45 #set sequence_name = $transcriptome.fields.name
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46 #end if
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47
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48 "data_tables":{
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49 "salmon_indexes_versioned":[
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50 {
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51 "value": "$sequence_id",
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52 "dbkey": "$all_fasta_source.fields.dbkey",
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53 "name": "$sequence_name",
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54 "path": "$out_file.extra_files_path",
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55 "version": "@IDX_VERSION@"
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56 }
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57 ]
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58 }
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59 }]]></configfile>
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60 </configfiles>
0
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61 <inputs>
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62 <param label="Transcriptome sequences" name="transcriptome" optional="false" type="select">
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63 <options from_data_table="transcriptomes" />
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64 </param>
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65 <param label="Genome" name="all_fasta_source" optional="false" type="select">
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66 <options from_data_table="all_fasta" />
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67 </param>
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68 <param name="sequence_name" type="text" value="" label="Name of sequence" />
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69 <param name="sequence_id" type="text" value="" label="ID for sequence" />
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70 <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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71 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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72 <validator type="expression" message="Only odd values">value % 2 == 1</validator>
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73 </param>
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74 <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."/>
0
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75 </inputs>
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76 <outputs>
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77 <data name="out_file" format="data_manager_json" />
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78 </outputs>
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79 <tests>
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80 <test>
5
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81 <param name="transcriptome" value="phiX174"/>
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82 <param name="all_fasta_source" value="phiX174"/>
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83 <param name="sequence_name" value="sequence_name"/>
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84 <param name="sequence_id" value="sequence_id"/>
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85 <output name="out_file">
6b0f2bdcc1b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit dcd9b028532258b62cfe15b60d5bef05cac9ed69"
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86 <assert_contents>
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87 <has_text text='"salmon_indexes_versioned"' />
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88 <has_text text='"dbkey": "phiX174"' />
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89 <has_text text='"name": "sequence_name"' />
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90 <has_text text='"value": "sequence_id"' />
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91 <has_text text='"version": "q7"' />
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92 <has_text text='"path":' />
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93 </assert_contents>
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94 </output>
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95 </test>
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96 <test>
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97 <param name="transcriptome" value="phiX174"/>
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98 <param name="all_fasta_source" value="phiX174"/>
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99 <param name="sequence_name" value=""/>
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100 <param name="sequence_id" value=""/>
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101 <output name="out_file">
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102 <assert_contents>
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103 <has_text text='"salmon_indexes_versioned"' />
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104 <has_text text='"dbkey": "phiX174"' />
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105 <has_text text='"name": "phiX174"' />
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106 <has_text text='"value": "phiX174"' />
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107 <has_text text='"version": "q7"' />
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108 <has_text text='"path":' />
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109 </assert_contents>
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110 </output>
0
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111 </test>
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112 </tests>
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113 <help>
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114 <![CDATA[
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115 .. class:: infomark
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116
5
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117 Indices are constructed as described here: https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/
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118
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119 See also https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode
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120
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121 **Notice:** If you leave name, description, or id blank, it the dbkey of the genome will be used.
0
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122 ]]>
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123 </help>
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124 <citations>
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125 <citation type="doi">https://doi.org/10.1038/nmeth.4197</citation>
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126 </citations>
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127 </tool>