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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ec26c475a013d89b0f973f29250d660e79d4751f
author iuc
date Wed, 20 Sep 2023 14:54:54 +0000
parents 9fa24d5aac68
children
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8f1c3df4dd49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ec26c475a013d89b0f973f29250d660e79d4751f
iuc
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1 <tool id="trinity" name="Trinity" version="@TOOL_VERSION@+galaxy1" profile="21.05">
0
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2 <description>de novo assembly of RNA-Seq data</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 <expand macro="bio_tools"/>
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7 <expand macro="requirements">
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8 <requirement type="package" version="3.2.7">rsync</requirement>
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9 </expand>
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10 <command detect_errors="aggressive"><![CDATA[
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11 if [ -z "\$GALAXY_MEMORY_MB" ] ; then
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12 GALAXY_MEMORY_GB=1 ;
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13 else
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14 GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ;
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15 fi ;
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16
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17 TRINITY_SCRATCH_DIR=\${TRINITY_SCRATCH_DIR:-\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR}}
8f1c3df4dd49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ec26c475a013d89b0f973f29250d660e79d4751f
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18 workdir=\$(pwd)
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19 scratchfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR");
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20 emptyfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR");
8f1c3df4dd49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ec26c475a013d89b0f973f29250d660e79d4751f
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21 cd "\$scratchfolder" ;
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22
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23 #if $additional_params.guided.is_guided == "yes":
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24 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' &&
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25 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' &&
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26 #end if
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27 #if $pool.pool_mode == "Yes":
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28 #if str($pool.inputs.paired_or_single) == "single":
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29 #for i, f in enumerate($pool.inputs.input):
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30 ln -s '$f' input${i}.${f.ext} &&
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31 #end for
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32 #elif str($pool.inputs.paired_or_single) == "paired":
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33 #for i, f in enumerate($pool.inputs.left_input):
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34 ln -s '$f' left_input${i}.${f.ext} &&
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35 #end for
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36 #for i, f in enumerate($pool.inputs.right_input):
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37 ln -s '$f' right_input${i}.${f.ext} &&
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38 #end for
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39 #elif str($pool.inputs.paired_or_single) == "paired_collection":
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40 #for i, f in enumerate($pool.inputs.pair_input):
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41 ln -s '$f.forward' 'left_input${i}.${f.forward.ext}' &&
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42 ln -s '$f.reverse' 'right_input${i}.${f.reverse.ext}' &&
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43 #end for
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44 #end if
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45 #elif $pool.pool_mode == "No":
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46 #if $pool.inputs.paired_or_single == "unmerged_paired_collection":
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47 ln -s '$pool.inputs.pair_input.forward' 'left_input.${$pool.inputs.pair_input.forward.ext}' &&
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48 ln -s '$pool.inputs.pair_input.reverse' 'right_input.${pool.inputs.pair_input.reverse.ext}' &&
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49 #elif $pool.inputs.paired_or_single == "unmerged_single_collection":
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50 ln -s '$pool.inputs.input' 'input.${pool.inputs.input.ext}' &&
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51 #end if
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52 #end if
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53
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54 Trinity --no_version_check
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55 --output ./trinity_out_dir
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56 ## do not try to run the high-mem normalization stats generator in parallel for paired-end fastqs
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57 --no_parallel_norm_stats
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58 ## Inputs
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59 #if $pool.pool_mode == "Yes":
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60 #if str($pool.inputs.paired_or_single) == "single":
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61 --single ${ ','.join(["'input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.input)]) }
20
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62 #if $pool.inputs.input[0].is_of_type('fasta'):
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63 --seqType fa
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64 #else:
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65 --seqType fq
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66 #end if
3
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67
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68 #if $pool.inputs.strand.is_strand_specific == 'true':
20
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69 --SS_lib_type $pool.inputs.strand.library_type
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70 #end if
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71 #elif str($pool.inputs.paired_or_single) == "paired":
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72 --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.left_input)]) }
3
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73
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74 --right ${ ','.join(["'right_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.right_input)]) }
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75
20
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76 #if $pool.inputs.left_input[0].is_of_type('fasta'):
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77 --seqType fa
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78 #else:
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79 --seqType fq
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80 #end if
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81 @COMMAND_PAIRED_STRAND_JACCARD@
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82 #elif str($pool.inputs.paired_or_single) == "paired_collection":
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83 --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.forward.ext) for i, f in enumerate($pool.inputs.pair_input)]) }
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84 --right ${ ','.join(["'right_input%s.%s'" % ($i, $f.reverse.ext) for i, f in enumerate($pool.inputs.pair_input)]) }
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85 #if $pool.inputs.pair_input[0].forward.is_of_type('fasta'):
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86 --seqType fa
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87 #else:
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88 --seqType fq
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89 #end if
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90 @COMMAND_PAIRED_STRAND_JACCARD@
0
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91 #end if
20
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92 #elif $pool.pool_mode == "No":
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93 #if $pool.inputs.paired_or_single == "unmerged_paired_collection":
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94 --left 'left_input.${$pool.inputs.pair_input.forward.ext}'
0
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95
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96 --right 'right_input.${pool.inputs.pair_input.reverse.ext}'
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97
20
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98 #if $pool.inputs.pair_input.forward.is_of_type('fasta'):
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99 --seqType fa
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100 #else:
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101 --seqType fq
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102 #end if
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103 @COMMAND_PAIRED_STRAND_JACCARD@
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104 #elif $pool.inputs.paired_or_single == "unmerged_single_collection":
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105 --single 'input.${pool.inputs.input.ext}'
3
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106
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107 #if $pool.inputs.input.is_of_type('fasta'):
20
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108 --seqType fa
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109 #else:
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110 --seqType fq
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111 #end if
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112
32
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113 #if $pool.inputs.strand.is_strand_specific == 'true':
20
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114 --SS_lib_type $pool.inputs.strand.library_type
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115 #end if
0
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116 #end if
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117 #end if
32
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118 $no_normalize_reads
0
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119
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120 ## Additional parameters.
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121 #if $additional_params.min_contig_length:
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122 --min_contig_length $additional_params.min_contig_length
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123 #end if
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124 #if $additional_params.long_reads:
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125 --long_reads $additional_params.long_reads
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126 #end if
1
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127 #if $additional_params.guided.is_guided == "yes":
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128 --genome_guided_bam 'localbam.bam'
0
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129
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130 #if $additional_params.guided.genome_guided_min_coverage:
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131 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage
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132 #end if
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133
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134 #if $additional_params.guided.genome_guided_min_reads_per_partition:
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135 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
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136 #end if
3
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137
18
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138 #if $additional_params.guided.genome_guided_max_intron:
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139 --genome_guided_max_intron $additional_params.guided.genome_guided_max_intron
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140 #end if
0
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141 #end if
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142
10
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143 #if $additional_params.min_kmer_cov:
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144 --min_kmer_cov $additional_params.min_kmer_cov
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145 #end if
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146
0
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147 ## CPU and butterfly options.
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148 --CPU \${GALAXY_SLOTS:-4} --max_memory \${GALAXY_MEMORY_GB:-1}G --bflyHeapSpaceMax \${GALAXY_MEMORY_GB:-1}G --bfly_opts '-V 10 --stderr'
3
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149
19
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150 &&
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151
29
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152 ## Trinity can create millions of files in the same directory, so the cleaning task makes use of rsync
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153 ## for ensuring better performances.
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154 ## see: https://web.archive.org/web/20130929001850/http://linuxnote.net/jianingy/en/linux/a-fast-way-to-remove-huge-number-of-files.html
34
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155 rsync -a --delete "\$emptyfolder/" "\$scratchfolder/" --exclude=trinity_out_dir.Trinity.fasta --exclude=trinity_out_dir.Trinity.fasta.gene_trans_map;
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156 mv "\$scratchfolder/trinity_out_dir.Trinity.fasta" '$assembled_transcripts';
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157 mv "\$scratchfolder/trinity_out_dir.Trinity.fasta.gene_trans_map" '$gene_to_trans';
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158 cd "\$workdir";
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159 rmdir "\$emptyfolder" "\$scratchfolder"
0
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160 ]]></command>
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161 <inputs>
20
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162 <conditional name="pool">
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163 <param name="pool_mode" type="select" label="Are you pooling sequence datasets?" help="" >
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164 <option value="No">No</option>
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165 <option value="Yes" selected="True">Yes</option>
0
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166 </param>
20
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167 <when value="Yes" >
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168 <conditional name="inputs">
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169 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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170 <option value="single" selected="true">Single-end</option>
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171 <option value="paired">Paired-end</option>
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172 <option value="paired_collection">Paired-end collection</option>
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173 </param>
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174 <when value="single">
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175 <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Single-end reads" help=""/>
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176 <expand macro="is_strand_specific_f_r"/>
0
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177 </when>
20
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178 <when value="paired">
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179 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Left/Forward strand reads" />
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180 <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Right/Reverse strand reads" />
20
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181 <expand macro="input_paired_strand_jaccard" />
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182 </when>
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183 <when value="paired_collection">
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184 <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger,fastqsanger.gz" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/>
20
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185 <expand macro="input_paired_strand_jaccard" />
0
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186 </when>
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187 </conditional>
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188 </when>
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189 <when value="No">
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190 <conditional name="inputs">
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191 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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192 <option value="unmerged_single_collection">Single-end</option>
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193 <option value="unmerged_paired_collection">Paired-end</option>
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194 </param>
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195 <when value="unmerged_single_collection">
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196 <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Single-end reads" help="Elements of collection will NOT be merged"/>
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197 <expand macro="is_strand_specific_f_r"/>
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198 </when>
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199 <when value="unmerged_paired_collection">
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200 <param name="pair_input" type="data_collection" collection_type="paired" format="fasta,fastqsanger,fastqsanger.gz" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Pair dataset collection. The paired datasets will NOT be merged"/>
20
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201 <expand macro="input_paired_strand_jaccard" />
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202 </when>
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203 </conditional>
17
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204 </when>
0
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205 </conditional>
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206 <param argument="--no_normalize_reads" type="boolean" truevalue="" falsevalue="--no_normalize_reads" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
0
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207 <section name="additional_params" title="Additional Options" expanded="False">
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208 <param argument="--min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
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209
0
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210 <conditional name="guided">
1
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211 <param name="is_guided" type="select" label="Use the genome guided mode?" help="If you already mapped the reads to the genome, Trinity can use this information">
0
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212 <option value="no">No</option>
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213 <option value="yes">Yes</option>
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214 </param>
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215 <when value="no">
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216 </when>
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217 <when value="yes">
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218 <param argument="--genome_guided_bam" type="data" format="bam" label="Coordinate-sorted BAM file" />
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219 <param argument="--genome_guided_max_intron" type="integer" value="" min="1" label="Maximum allowed intron length (also maximum fragment span on genome)"/>
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220 <param argument="--genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
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221 <param argument="--genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
0
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222 </when>
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223 </conditional>
3
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224
32
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225 <param argument="--long_reads" type="data" format="fasta" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads"
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226 help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
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227 <param argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
0
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228 </section>
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229 </inputs>
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230 <outputs>
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231 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts"/>
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232 <data name="gene_to_trans" format="tabular" label="${tool.name} on ${on_string}: Gene to transcripts map"/>
0
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233 </outputs>
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234 <tests>
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235 <test>
20
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236 <param name="pool_mode" value="No" />
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237 <param name="paired_or_single" value="unmerged_paired_collection"/>
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238 <param name="pair_input">
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239 <collection type="paired">
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240 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
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241 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
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242 </collection>
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243 </param>
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244 <param name="is_strand_specific" value="true"/>
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245 <param name="no_normalize_reads" value="true"/>
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246 <param name="library_type" value="RF"/>
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247 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" />
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248 <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" />
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249 </test>
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250 <test>
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251 <param name="pool_mode" value="No" />
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252 <param name="paired_or_single" value="unmerged_paired_collection"/>
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253 <param name="pair_input">
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254 <collection type="paired">
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255 <element name="forward" value="reads.left.fq.gz" ftype="fastqsanger.gz" />
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256 <element name="reverse" value="reads.right.fq.gz" ftype="fastqsanger.gz" />
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257 </collection>
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258 </param>
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259 <param name="is_strand_specific" value="true"/>
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260 <param name="no_normalize_reads" value="true"/>
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261 <param name="library_type" value="RF"/>
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262 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" />
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263 <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" />
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264 </test>
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265 <test>
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266 <param name="pool_mode" value="No" />
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267 <param name="paired_or_single" value="unmerged_single_collection"/>
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268 <param name="input" value="reads.left.fq" ftype="fastqsanger"/>
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269 <param name="is_strand_specific" value="true"/>
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270 <param name="no_normalize_reads" value="false"/>
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271 <param name="library_type" value="F"/>
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272 <output name="assembled_transcripts" file="raw/Trinity_single_unmerged_1.fasta" compare="sim_size" delta="500" />
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273 <output name="gene_to_trans" file="raw/Trinity_single_unmerged_1.map" compare="sim_size" />
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274 </test>
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275 <test>
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276 <param name="pool_mode" value="Yes" />
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277 <param name="paired_or_single" value="paired"/>
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278 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
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279 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
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280 <param name="is_strand_specific" value="true"/>
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281 <param name="no_normalize_reads" value="false"/>
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282 <param name="library_type" value="RF"/>
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283 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
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284 <output name="gene_to_trans" file="raw/Trinity.map" compare="sim_size" />
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285 </test>
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286 <test>
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287 <param name="pool_mode" value="Yes" />
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288 <param name="paired_or_single" value="paired"/>
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289 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
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290 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
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291 <param name="is_strand_specific" value="true"/>
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292 <param name="no_normalize_reads" value="true"/>
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293 <param name="library_type" value="RF"/>
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294 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
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295 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" />
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296 </test>
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297 <test>
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298 <param name="pool_mode" value="Yes" />
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299 <param name="paired_or_single" value="paired_collection"/>
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300 <param name="pair_input">
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301 <collection type="list:paired">
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302 <element name="pair1">
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303 <collection type="paired">
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304 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
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305 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
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306 </collection>
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307 </element>
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308 <element name="pair2">
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309 <collection type="paired">
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310 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
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311 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
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312 </collection>
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313 </element>
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314 </collection>
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315 </param>
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316 <param name="is_strand_specific" value="true"/>
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317 <param name="no_normalize_reads" value="true"/>
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318 <param name="library_type" value="RF"/>
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319 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
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320 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" />
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321 </test>
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322 </tests>
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323 <help>
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324 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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325
33
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326 .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
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327 </help>
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328 <expand macro="citation" />
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329 </tool>