Mercurial > repos > iuc > trinity

annotate trinity.xml @ 28:48636f857c4b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
author iuc
date Fri, 10 Sep 2021 22:46:16 +0000
parents 5b60313a6ce7
children d5e8807a407d
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iuc
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1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@+galaxy1">
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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2 <description>de novo assembly of RNA-Seq data</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>macros.xml</import>
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="aggressive"><![CDATA[
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9 if [ -z "\$GALAXY_MEMORY_MB" ] ; then
cee61b3fcf78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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10 GALAXY_MEMORY_GB=1 ;
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11 else
cee61b3fcf78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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12 GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ;
cee61b3fcf78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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13 fi ;
cee61b3fcf78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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14
cee61b3fcf78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
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15 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
cee61b3fcf78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
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16 workdir=`pwd` ;
cee61b3fcf78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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17 cd "\$TRINITY_SCRATCH_DIR" ;
cee61b3fcf78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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18 fi ;
cee61b3fcf78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
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19
18
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20 #if $additional_params.guided.is_guided == "yes":
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21 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' &&
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22 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' &&
d3b1249af60c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
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23 #end if
27
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24 #if $pool.pool_mode == "Yes":
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25 #if str($pool.inputs.paired_or_single) == "single":
5b60313a6ce7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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26 #for i, f in enumerate($pool.inputs.input):
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27 ln -s '$f' input${i}.${f.ext} &&
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28 #end for
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iuc
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29 #elif str($pool.inputs.paired_or_single) == "paired":
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iuc
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30 #for i, f in enumerate($pool.inputs.left_input):
5b60313a6ce7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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31 ln -s '$f' left_input${i}.${f.ext} &&
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32 #end for
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33 #for i, f in enumerate($pool.inputs.right_input):
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34 ln -s '$f' right_input${i}.${f.ext} &&
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35 #end for
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iuc
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36 #elif str($pool.inputs.paired_or_single) == "paired_collection":
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iuc
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37 #for i, f in enumerate($pool.inputs.pair_input):
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38 ln -s '$f.forward' 'left_input${i}.${f.forward.ext}' &&
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iuc
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39 ln -s '$f.reverse' 'right_input${i}.${f.reverse.ext}' &&
5b60313a6ce7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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40 #end for
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41 #end if
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42 #elif $pool.pool_mode == "No":
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43 #if $pool.inputs.paired_or_single == "unmerged_paired_collection":
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44 ln -s '$pool.inputs.pair_input.forward' 'left_input.${$pool.inputs.pair_input.forward.ext}' &&
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45 ln -s '$pool.inputs.pair_input.reverse' 'right_input.${pool.inputs.pair_input.reverse.ext}' &&
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46 #elif $pool.inputs.paired_or_single == "unmerged_single_collection":
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47 ln -s '$pool.inputs.input' 'input.${pool.inputs.input.ext}' &&
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48 #end if
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49 #end if
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50
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51 Trinity --no_version_check
0
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52
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53 ## Inputs
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54 #if $pool.pool_mode == "Yes":
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55 #if str($pool.inputs.paired_or_single) == "single":
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56 --single ${ ','.join(["'input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.input)]) }
20
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57 #if $pool.inputs.input[0].is_of_type('fasta'):
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58 --seqType fa
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59 #else:
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60 --seqType fq
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61 #end if
3
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62
20
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63 #if $pool.inputs.strand.is_strand_specific:
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64 --SS_lib_type $pool.inputs.strand.library_type
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65 #end if
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66 #elif str($pool.inputs.paired_or_single) == "paired":
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67 --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.left_input)]) }
3
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68
27
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69 --right ${ ','.join(["'right_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.right_input)]) }
17
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70
20
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71 #if $pool.inputs.left_input[0].is_of_type('fasta'):
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72 --seqType fa
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73 #else:
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74 --seqType fq
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75 #end if
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76 @COMMAND_PAIRED_STRAND_JACCARD@
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77 #elif str($pool.inputs.paired_or_single) == "paired_collection":
27
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78 --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.forward.ext) for i, f in enumerate($pool.inputs.pair_input)]) }
5b60313a6ce7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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79 --right ${ ','.join(["'right_input%s.%s'" % ($i, $f.reverse.ext) for i, f in enumerate($pool.inputs.pair_input)]) }
20
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80 #if $pool.inputs.pair_input[0].forward.is_of_type('fasta'):
171b827eadf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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81 --seqType fa
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82 #else:
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83 --seqType fq
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84 #end if
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85 @COMMAND_PAIRED_STRAND_JACCARD@
0
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86 #end if
20
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87 #elif $pool.pool_mode == "No":
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88 #if $pool.inputs.paired_or_single == "unmerged_paired_collection":
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89 --left 'left_input.${$pool.inputs.pair_input.forward.ext}'
0
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90
27
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91 --right 'right_input.${pool.inputs.pair_input.reverse.ext}'
3
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92
20
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93 #if $pool.inputs.pair_input.forward.is_of_type('fasta'):
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94 --seqType fa
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95 #else:
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96 --seqType fq
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97 #end if
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98 @COMMAND_PAIRED_STRAND_JACCARD@
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99 #elif $pool.inputs.paired_or_single == "unmerged_single_collection":
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100 --single 'input.${pool.inputs.input.ext}'
3
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101
27
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102 #if $pool.inputs.input.is_of_type('fasta'):
20
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103 --seqType fa
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104 #else:
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105 --seqType fq
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106 #end if
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107
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108 #if $pool.inputs.strand.is_strand_specific:
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109 --SS_lib_type $pool.inputs.strand.library_type
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110 #end if
0
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111 #end if
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112 #end if
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113 $norm
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114
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115 ## Additional parameters.
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116 #if $additional_params.min_contig_length:
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117 --min_contig_length $additional_params.min_contig_length
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118 #end if
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119 #if $additional_params.long_reads:
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120 --long_reads $additional_params.long_reads
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121 #end if
1
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122 #if $additional_params.guided.is_guided == "yes":
18
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123 --genome_guided_bam 'localbam.bam'
0
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124
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125 #if $additional_params.guided.genome_guided_min_coverage:
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126 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage
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127 #end if
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128
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129 #if $additional_params.guided.genome_guided_min_reads_per_partition:
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130 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
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131 #end if
3
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132
18
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133 #if $additional_params.guided.genome_guided_max_intron:
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134 --genome_guided_max_intron $additional_params.guided.genome_guided_max_intron
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135 #end if
0
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136 #end if
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137
10
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138 #if $additional_params.min_kmer_cov:
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139 --min_kmer_cov $additional_params.min_kmer_cov
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140 #end if
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141
0
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142 ## CPU and butterfly options.
19
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143 --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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144
2
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145 ## > $trinity_log 2>&1
19
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146
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147 &&
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148
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149 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
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150 mkdir -p "\$workdir/trinity_out_dir";
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151 cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir";
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152 cd "\$workdir";
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153 fi ;
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154
0
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155 ]]></command>
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156 <inputs>
20
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157 <conditional name="pool">
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158 <param name="pool_mode" type="select" label="Are you pooling sequence datasets?" help="" >
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159 <option value="No">No</option>
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160 <option value="Yes" selected="True">Yes</option>
0
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161 </param>
20
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162 <when value="Yes" >
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163 <conditional name="inputs">
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164 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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165 <option value="single" selected="true">Single-end</option>
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166 <option value="paired">Paired-end</option>
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167 <option value="paired_collection">Paired-end collection</option>
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168 </param>
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169 <when value="single">
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170 <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Single-end reads" help=""/>
20
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171 <conditional name="strand">
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172 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
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173 <when value="false">
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174 </when>
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175 <when value="true">
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176 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
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177 <option value="F">F</option>
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178 <option value="R">R</option>
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179 </param>
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180 </when>
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181 </conditional>
0
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182 </when>
20
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183 <when value="paired">
26
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184 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Left/Forward strand reads" />
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185 <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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186 <expand macro="input_paired_strand_jaccard" />
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187 </when>
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188 <when value="paired_collection">
26
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189 <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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190 <expand macro="input_paired_strand_jaccard" />
0
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191 </when>
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192 </conditional>
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193 </when>
20
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parents: 19
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194 <when value="No">
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195 <conditional name="inputs">
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196 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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197 <option value="unmerged_single_collection">Single-end</option>
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198 <option value="unmerged_paired_collection">Paired-end</option>
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199 </param>
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200 <when value="unmerged_single_collection">
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201 <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Single-end reads" help="Elements of collection will NOT be merged"/>
20
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202 <conditional name="strand">
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203 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
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204 <when value="false">
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205 </when>
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206 <when value="true">
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207 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
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208 <option value="F">F</option>
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209 <option value="R">R</option>
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210 </param>
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211 </when>
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212 </conditional>
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213 </when>
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214 <when value="unmerged_paired_collection">
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215 <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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216 <expand macro="input_paired_strand_jaccard" />
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217 </when>
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218 </conditional>
17
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219 </when>
0
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220 </conditional>
22
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221 <param name="norm" type="boolean" argument="--no_normalize_reads" 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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222 <section name="additional_params" title="Additional Options" expanded="False">
10
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223 <param name="min_contig_length" 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"/>
3
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224
0
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225 <conditional name="guided">
1
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226 <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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227 <option value="no">No</option>
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228 <option value="yes">Yes</option>
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229 </param>
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230 <when value="no">
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231 </when>
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232 <when value="yes">
18
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233 <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
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234 <param name="genome_guided_max_intron" 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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235 <param name="genome_guided_min_coverage" 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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236 <param name="genome_guided_min_reads_per_partition" 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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237 </when>
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238 </conditional>
3
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239
17
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240 <param name="long_reads" argument="--long_reads" type="data" format="fasta" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
3
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241
10
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242 <param name="min_kmer_cov" 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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243 </section>
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244 </inputs>
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245 <outputs>
17
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246 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
20
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247 <data name="gene_to_trans" format="tabular" label="${tool.name} on ${on_string}: Gene to transcripts map" from_work_dir="trinity_out_dir/Trinity.fasta.gene_trans_map"/>
0
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248 </outputs>
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249 <tests>
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250 <test>
20
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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">
26
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255 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
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256 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
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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="norm" value="true"/>
26d5493b20b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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261 <param name="library_type" value="RF"/>
26d5493b20b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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262 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" />
26d5493b20b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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263 <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" />
26d5493b20b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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264 </test>
26d5493b20b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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265 <test>
26d5493b20b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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266 <param name="pool_mode" value="No" />
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267 <param name="paired_or_single" value="unmerged_paired_collection"/>
26d5493b20b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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268 <param name="pair_input">
26d5493b20b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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269 <collection type="paired">
27
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270 <element name="forward" value="reads.left.fq.gz" ftype="fastqsanger.gz" />
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271 <element name="reverse" value="reads.right.fq.gz" ftype="fastqsanger.gz" />
20
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272 </collection>
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273 </param>
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274 <param name="is_strand_specific" value="true"/>
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275 <param name="norm" value="true"/>
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276 <param name="library_type" value="RF"/>
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277 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" />
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278 <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" />
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279 </test>
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280 <test>
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281 <param name="pool_mode" value="No" />
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282 <param name="paired_or_single" value="unmerged_single_collection"/>
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283 <param name="input" value="reads.left.fq" ftype="fastqsanger"/>
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284 <param name="is_strand_specific" value="true"/>
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285 <param name="norm" value="false"/>
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286 <param name="library_type" value="F"/>
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287 <output name="assembled_transcripts" file="raw/Trinity_single_unmerged_1.fasta" compare="sim_size" delta="500" />
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288 <output name="gene_to_trans" file="raw/Trinity_single_unmerged_1.map" compare="sim_size" />
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289 </test>
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290 <test>
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291 <param name="pool_mode" value="Yes" />
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292 <param name="paired_or_single" value="paired"/>
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293 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
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294 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
0
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295 <param name="is_strand_specific" value="true"/>
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296 <param name="norm" value="false"/>
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297 <param name="library_type" value="RF"/>
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298 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
20
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299 <output name="gene_to_trans" file="raw/Trinity.map" compare="sim_size" />
0
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300 </test>
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301 <test>
20
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302 <param name="pool_mode" value="Yes" />
0
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303 <param name="paired_or_single" value="paired"/>
3
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304 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
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305 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
0
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306 <param name="is_strand_specific" value="true"/>
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307 <param name="norm" value="true"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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308 <param name="library_type" value="RF"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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309 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
20
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310 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" />
0
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311 </test>
17
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312 <test>
20
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313 <param name="pool_mode" value="Yes" />
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314 <param name="paired_or_single" value="paired_collection"/>
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315 <param name="pair_input">
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316 <collection type="list:paired">
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317 <element name="pair1">
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318 <collection type="paired">
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319 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
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320 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
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321 </collection>
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322 </element>
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323 <element name="pair2">
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324 <collection type="paired">
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325 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
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326 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
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327 </collection>
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328 </element>
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329 </collection>
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330 </param>
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331 <param name="is_strand_specific" value="true"/>
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332 <param name="norm" value="true"/>
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333 <param name="library_type" value="RF"/>
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334 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
20
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335 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" />
17
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336 </test>
0
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337 </tests>
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338 <help>
17
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339 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
0
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340
17
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341 .. _Trinity: http://trinityrnaseq.github.io
0
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342 </help>
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343 <expand macro="citation" />
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344 </tool>