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annotate trinity.xml @ 19:cee61b3fcf78 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
author iuc
date Mon, 22 Jan 2018 11:26:29 -0500
parents d3b1249af60c
children 171b827eadf2
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1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.2">
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="requirements" />
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7 <command detect_errors="aggressive"><![CDATA[
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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 ;
cee61b3fcf78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
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13
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14 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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15 workdir=`pwd` ;
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16 cd "\$TRINITY_SCRATCH_DIR" ;
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17 fi ;
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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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25 ## Inputs.
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26 #if $inputs.paired_or_single == "paired":
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28 --left ${ ','.join(['"%s"' % x for x in $inputs.left_input]) }
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30 --right ${ ','.join(['"%s"' % x for x in $inputs.right_input]) }
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32 #if $inputs.left_input[0].is_of_type('fasta'):
0
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33 --seqType fa
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34 #else:
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35 --seqType fq
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36 #end if
3
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37
17
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38 @COMMAND_PAIRED_STRAND_JACCARD@
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39
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40 #elif $inputs.paired_or_single == "paired_collection"
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41 --left ${ ','.join(['"%s"' % x.forward for x in $inputs.pair_input]) }
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43 --right ${ ','.join(['"%s"' % x.reverse for x in $inputs.pair_input]) }
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45 #if $inputs.pair_input[0].forward.is_of_type('fasta'):
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46 --seqType fa
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47 #else:
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48 --seqType fq
0
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49 #end if
3
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50
17
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51 @COMMAND_PAIRED_STRAND_JACCARD@
0
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53 #else:
3
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54 --single ${ ','.join(['"%s"' % x for x in $inputs.input]) }
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56 #if $inputs.input[0].is_of_type('fasta'):
0
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57 --seqType fa
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58 #else:
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59 --seqType fq
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60 #end if
3
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61
0
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62 #if $inputs.strand.is_strand_specific:
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63 --SS_lib_type $inputs.strand.library_type
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64 #end if
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65 #end if
3
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66
0
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67 $norm
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68
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69 ## Additional parameters.
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70 #if $additional_params.min_contig_length:
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71 --min_contig_length $additional_params.min_contig_length
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72 #end if
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73 #if $additional_params.long_reads:
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74 --long_reads $additional_params.long_reads
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75 #end if
1
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76 #if $additional_params.guided.is_guided == "yes":
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77 --genome_guided_bam 'localbam.bam'
0
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78
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79 #if $additional_params.guided.genome_guided_min_coverage:
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80 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage
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81 #end if
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82
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83 #if $additional_params.guided.genome_guided_min_reads_per_partition:
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84 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
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85 #end if
3
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86
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87 #if $additional_params.guided.genome_guided_max_intron:
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88 --genome_guided_max_intron $additional_params.guided.genome_guided_max_intron
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89 #end if
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90
0
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91 #end if
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92
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93 #if $additional_params.min_kmer_cov:
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94 --min_kmer_cov $additional_params.min_kmer_cov
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95 #end if
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96
0
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97 ## CPU and butterfly options.
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98 --CPU \${GALAXY_SLOTS:-4} --max_memory \${GALAXY_MEMORY_GB:-1}G --bflyHeapSpaceMax \${GALAXY_MEMORY_GB:-1}G --bfly_opts '-V 10 --stderr'
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99
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100 ## > $trinity_log 2>&1
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101
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102 &&
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103
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104 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
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105 mkdir -p "\$workdir/trinity_out_dir";
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106 cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir";
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107 cd "\$workdir";
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108 fi ;
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109
0
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110 ]]></command>
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111 <inputs>
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112 <conditional name="inputs">
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113 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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114 <option value="single">Single-end</option>
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115 <option value="paired" selected="true">Paired-end</option>
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116 <option value="paired_collection">Paired-end collection</option>
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117 </param>
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118 <when value="single">
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119 <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/>
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120 <conditional name="strand">
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121 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
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122 <when value="false">
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123 </when>
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124 <when value="true">
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125 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
0
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126 <option value="F">F</option>
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127 <option value="R">R</option>
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128 </param>
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129 </when>
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130 </conditional>
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131 </when>
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132 <when value="paired">
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133 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger" multiple="true" label="Left/Forward strand reads" />
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134 <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger" multiple="true" label="Right/Reverse strand reads" />
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135 <expand macro="input_paired_strand_jaccard" />
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136 </when>
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137 <when value="paired_collection">
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138 <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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139 <expand macro="input_paired_strand_jaccard" />
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140 </when>
0
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141 </conditional>
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142
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143 <param name="norm" type="boolean" argument="--normalize_reads" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
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144
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145 <section name="additional_params" title="Additional Options" expanded="False">
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146 <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"/>
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147
0
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148 <conditional name="guided">
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149 <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">
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150 <option value="no">No</option>
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151 <option value="yes">Yes</option>
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152 </param>
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153 <when value="no">
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154 </when>
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155 <when value="yes">
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156 <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
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157 <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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158 <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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159 <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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160 </when>
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161 </conditional>
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162
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163 <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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164
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165 <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"/>
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166 </section>
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167 </inputs>
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168 <outputs>
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169 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
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170 </outputs>
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171 <tests>
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172 <test>
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173 <param name="paired_or_single" value="paired"/>
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174 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
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175 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
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176 <param name="is_strand_specific" value="true"/>
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177 <param name="norm" value="false"/>
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178 <param name="library_type" value="RF"/>
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179 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
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180 </test>
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181 <test>
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182 <param name="paired_or_single" value="paired"/>
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183 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
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184 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
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185 <param name="is_strand_specific" value="true"/>
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186 <param name="norm" value="true"/>
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187 <param name="library_type" value="RF"/>
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188 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
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189 </test>
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190 <test>
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191 <param name="paired_or_single" value="paired_collection"/>
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192 <param name="pair_input">
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193 <collection type="list:paired">
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194 <element name="pair1">
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195 <collection type="paired">
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196 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
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197 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
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198 </collection>
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199 </element>
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200 <element name="pair2">
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201 <collection type="paired">
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202 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
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203 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
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204 </collection>
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205 </element>
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206 </collection>
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207 </param>
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208 <param name="is_strand_specific" value="true"/>
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209 <param name="norm" value="true"/>
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210 <param name="library_type" value="RF"/>
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211 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
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212 </test>
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213 </tests>
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214 <help>
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215 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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216
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217 .. _Trinity: http://trinityrnaseq.github.io
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218 </help>
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219
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220 <expand macro="citation" />
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221 </tool>