Mercurial > repos > iuc > trinity

annotate trinity.xml @ 23:940901f74064 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 3b8670ad0ce9dd90d6a24429bca131362e56d17d"
author iuc
date Fri, 01 Nov 2019 08:11:57 -0400
parents c9cfec002f71
children 26d5493b20b6
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1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@">
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>
15
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6 <expand macro="requirements" />
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7 <command detect_errors="aggressive"><![CDATA[
19
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8 if [ -z "\$GALAXY_MEMORY_MB" ] ; then
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9 GALAXY_MEMORY_GB=1 ;
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10 else
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11 GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ;
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12 fi ;
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13
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14 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
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15 workdir=`pwd` ;
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16 cd "\$TRINITY_SCRATCH_DIR" ;
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17 fi ;
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18
18
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19 #if $additional_params.guided.is_guided == "yes":
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20 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' &&
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21 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' &&
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22 #end if
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23 Trinity --no_version_check
0
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24
20
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25 ## Inputs
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26 #if $pool.pool_mode == "Yes":
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27 #if str($pool.inputs.paired_or_single) == "single":
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28 --single ${ ','.join(['"%s"' % x for x in $pool.inputs.input]) }
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29 #if $pool.inputs.input[0].is_of_type('fasta'):
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30 --seqType fa
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31 #else:
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32 --seqType fq
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33 #end if
3
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34
20
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35 #if $pool.inputs.strand.is_strand_specific:
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36 --SS_lib_type $pool.inputs.strand.library_type
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37 #end if
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38 #elif str($pool.inputs.paired_or_single) == "paired":
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39 --left ${ ','.join(['"%s"' % x for x in $pool.inputs.left_input]) }
3
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40
20
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41 --right ${ ','.join(['"%s"' % x for x in $pool.inputs.right_input]) }
17
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42
20
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43 #if $pool.inputs.left_input[0].is_of_type('fasta'):
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44 --seqType fa
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45 #else:
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46 --seqType fq
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47 #end if
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48 @COMMAND_PAIRED_STRAND_JACCARD@
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49 #elif str($pool.inputs.paired_or_single) == "paired_collection":
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50 --left ${ ','.join(['"%s"' % x.forward for x in $pool.inputs.pair_input]) }
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51 --right ${ ','.join(['"%s"' % x.reverse for x in $pool.inputs.pair_input]) }
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52 #if $pool.inputs.pair_input[0].forward.is_of_type('fasta'):
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53 --seqType fa
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54 #else:
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55 --seqType fq
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56 #end if
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57 @COMMAND_PAIRED_STRAND_JACCARD@
0
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58 #end if
20
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59 #elif $pool.pool_mode == "No":
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60 #if $pool.inputs.paired_or_single == "unmerged_paired_collection":
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61 --left $pool.inputs.pair_input.forward
0
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62
20
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63 --right $pool.inputs.pair_input.reverse
3
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64
20
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65 #if $pool.inputs.pair_input.forward.is_of_type('fasta'):
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66 --seqType fa
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67 #else:
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68 --seqType fq
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69 #end if
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70 @COMMAND_PAIRED_STRAND_JACCARD@
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71 #elif $pool.inputs.paired_or_single == "unmerged_single_collection":
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72 --single $pool.inputs.input
3
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73
20
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74 #if $pool.inputs.input.is_of_type('fasta'):
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75 --seqType fa
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76 #else:
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77 --seqType fq
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78 #end if
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79
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80 #if $pool.inputs.strand.is_strand_specific:
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81 --SS_lib_type $pool.inputs.strand.library_type
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82 #end if
0
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83 #end if
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84 #end if
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85 $norm
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86
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87 ## Additional parameters.
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88 #if $additional_params.min_contig_length:
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89 --min_contig_length $additional_params.min_contig_length
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90 #end if
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91 #if $additional_params.long_reads:
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92 --long_reads $additional_params.long_reads
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93 #end if
1
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94 #if $additional_params.guided.is_guided == "yes":
18
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95 --genome_guided_bam 'localbam.bam'
0
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96
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97 #if $additional_params.guided.genome_guided_min_coverage:
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98 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage
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99 #end if
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100
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101 #if $additional_params.guided.genome_guided_min_reads_per_partition:
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102 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
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103 #end if
3
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104
18
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105 #if $additional_params.guided.genome_guided_max_intron:
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106 --genome_guided_max_intron $additional_params.guided.genome_guided_max_intron
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107 #end if
0
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108 #end if
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109
10
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110 #if $additional_params.min_kmer_cov:
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111 --min_kmer_cov $additional_params.min_kmer_cov
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112 #end if
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113
0
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114 ## CPU and butterfly options.
19
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115 --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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116
2
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117 ## > $trinity_log 2>&1
19
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118
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119 &&
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120
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121 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
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122 mkdir -p "\$workdir/trinity_out_dir";
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123 cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir";
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124 cd "\$workdir";
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125 fi ;
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126
0
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127 ]]></command>
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128 <inputs>
20
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129 <conditional name="pool">
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130 <param name="pool_mode" type="select" label="Are you pooling sequence datasets?" help="" >
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131 <option value="No">No</option>
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132 <option value="Yes" selected="True">Yes</option>
0
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133 </param>
20
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134 <when value="Yes" >
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135 <conditional name="inputs">
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136 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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137 <option value="single" selected="true">Single-end</option>
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138 <option value="paired">Paired-end</option>
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139 <option value="paired_collection">Paired-end collection</option>
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140 </param>
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141 <when value="single">
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142 <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/>
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143 <conditional name="strand">
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144 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
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145 <when value="false">
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146 </when>
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147 <when value="true">
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148 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
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149 <option value="F">F</option>
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150 <option value="R">R</option>
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151 </param>
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152 </when>
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153 </conditional>
0
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154 </when>
20
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155 <when value="paired">
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156 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger" multiple="true" label="Left/Forward strand reads" />
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157 <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger" multiple="true" label="Right/Reverse strand reads" />
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158 <expand macro="input_paired_strand_jaccard" />
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159 </when>
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160 <when value="paired_collection">
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161 <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/>
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162 <expand macro="input_paired_strand_jaccard" />
0
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163 </when>
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164 </conditional>
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165 </when>
20
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166 <when value="No">
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167 <conditional name="inputs">
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168 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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169 <option value="unmerged_single_collection">Single-end</option>
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170 <option value="unmerged_paired_collection">Paired-end</option>
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171 </param>
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172 <when value="unmerged_single_collection">
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173 <param name="input" argument="--single" type="data" format="fasta,fastqsanger" label="Single-end reads" help="Elements of collection will NOT be merged"/>
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174 <conditional name="strand">
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175 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
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176 <when value="false">
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177 </when>
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178 <when value="true">
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179 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
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180 <option value="F">F</option>
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181 <option value="R">R</option>
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182 </param>
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183 </when>
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184 </conditional>
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185 </when>
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186 <when value="unmerged_paired_collection">
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187 <param name="pair_input" type="data_collection" collection_type="paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Pair dataset collection. The paired datasets will NOT be merged"/>
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188 <expand macro="input_paired_strand_jaccard" />
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189 </when>
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190 </conditional>
17
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191 </when>
0
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192 </conditional>
22
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193 <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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194 <section name="additional_params" title="Additional Options" expanded="False">
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195 <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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196
0
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197 <conditional name="guided">
1
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198 <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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199 <option value="no">No</option>
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200 <option value="yes">Yes</option>
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201 </param>
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202 <when value="no">
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203 </when>
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204 <when value="yes">
18
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205 <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
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206 <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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207 <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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208 <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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209 </when>
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210 </conditional>
3
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211
17
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212 <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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213
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214 <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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215 </section>
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216 </inputs>
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217 <outputs>
17
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218 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
20
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219 <data name="gene_to_trans" format="tabular" label="${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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220 </outputs>
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221 <tests>
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222 <test>
20
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223 <param name="pool_mode" value="No" />
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224 <param name="paired_or_single" value="unmerged_paired_collection"/>
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225 <param name="pair_input">
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226 <collection type="paired">
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227 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
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228 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
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229 </collection>
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230 </param>
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231 <param name="is_strand_specific" value="true"/>
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232 <param name="norm" value="true"/>
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233 <param name="library_type" value="RF"/>
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234 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" />
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235 <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" />
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236 </test>
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237 <test>
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238 <param name="pool_mode" value="No" />
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239 <param name="paired_or_single" value="unmerged_single_collection"/>
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240 <param name="input" value="reads.left.fq" ftype="fastqsanger"/>
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241 <param name="is_strand_specific" value="true"/>
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242 <param name="norm" value="false"/>
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243 <param name="library_type" value="F"/>
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244 <output name="assembled_transcripts" file="raw/Trinity_single_unmerged_1.fasta" compare="sim_size" delta="500" />
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245 <output name="gene_to_trans" file="raw/Trinity_single_unmerged_1.map" compare="sim_size" />
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246 </test>
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247 <test>
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248 <param name="pool_mode" value="Yes" />
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249 <param name="paired_or_single" value="paired"/>
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250 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
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251 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
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252 <param name="is_strand_specific" value="true"/>
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253 <param name="norm" value="false"/>
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254 <param name="library_type" value="RF"/>
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255 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
20
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256 <output name="gene_to_trans" file="raw/Trinity.map" compare="sim_size" />
0
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257 </test>
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258 <test>
20
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259 <param name="pool_mode" value="Yes" />
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260 <param name="paired_or_single" value="paired"/>
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261 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
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262 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
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263 <param name="is_strand_specific" value="true"/>
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264 <param name="norm" value="true"/>
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265 <param name="library_type" value="RF"/>
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266 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
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267 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" />
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268 </test>
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269 <test>
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270 <param name="pool_mode" value="Yes" />
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271 <param name="paired_or_single" value="paired_collection"/>
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272 <param name="pair_input">
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273 <collection type="list:paired">
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274 <element name="pair1">
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275 <collection type="paired">
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276 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
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277 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
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278 </collection>
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279 </element>
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280 <element name="pair2">
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281 <collection type="paired">
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282 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
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283 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
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284 </collection>
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285 </element>
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286 </collection>
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287 </param>
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288 <param name="is_strand_specific" value="true"/>
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289 <param name="norm" value="true"/>
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290 <param name="library_type" value="RF"/>
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291 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
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292 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" />
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293 </test>
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294 </tests>
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295 <help>
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296 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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297
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298 .. _Trinity: http://trinityrnaseq.github.io
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299 </help>
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300 <expand macro="citation" />
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301 </tool>