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1 <tool id="stringtie" name="StringTie" version="1.0.1">
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2 <description>RNA-Seq assembler</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.1">stringtie</requirement>
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5 </requirements>
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6 <command><![CDATA[
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7 stringtie "$input_bam"
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8 -o "$output_gtf"
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9 -p "\${GALAXY_SLOTS:-1}"
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10 #if str($guide.use_guide) == 'yes':
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11 -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation
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12 #if str($guide.output_ballgown) == '-b':
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13 $guide.output_ballgown `pwd`
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14 #end if
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15 #end if
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16 #if str($option_set.options) == 'advanced':
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17 -l "$option_set.name_prefix"
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18 -f "$option_set.fraction"
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19 -m "$option_set.min_tlen"
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20 -a "$option_set.min_anchor_len"
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21 -j "$option_set.min_anchor_cov"
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22 -c "$option_set.min_bundle_cov"
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23 -s "$option_set.maxcov"
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24 -g "$option_set.bdist"
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25 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming
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26 #end if
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27 ]]>
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28 </command>
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29 <inputs>
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30 <param format="bam" label="BAM file to assemble" name="input_bam" type="data" />
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31 <conditional name="guide">
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32 <param label="Use GFF file to guide assembly" name="use_guide" type="select">
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33 <option value="yes">Use GFF</option>
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34 <option selected="True" value="no">Do not use GFF</option>
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35 </param>
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36 <when value="no" />
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37 <when value="yes">
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38 <param format="gtf,gff3" help="(-G)" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" />
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39 <param falsevalue="" help="(-e)" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" />
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40 <param falsevalue="" help="(-b)" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" />
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41 </when>
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42 </conditional>
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43 <conditional name="option_set">
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44 <param label="Options" name="options" type="select">
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45 <option selected="True" value="default">Use defaults</option>
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46 <option value="advanced">Specify advanced options</option>
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47 </param>
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48 <when value="default" />
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49 <when value="advanced">
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50 <param falsevalue="" help="(-t)" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" />
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51 <param falsevalue="" help="(-S)" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" />
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52 <param help="(-l)" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" />
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53 <param help="(-f)" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" />
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54 <param help="(-m)" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" />
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55 <param help="(-a)" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" />
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56 <param help="(-j)" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" />
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57 <param help="(-c)" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" />
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58 <param help="(-s)" label="Coverage saturation threshold" name="maxcov" type="integer" value="1000000" />
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59 <param help="(-g)" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" />
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60 <param help="(-M)" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" />
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61 </when>
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62 </conditional>
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63 </inputs>
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64 <outputs>
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65 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
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66 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
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67 <filter>guide['use_guide'] == "yes"</filter>
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68 </data>
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69 <data format="tabular" from_work_dir="e_data.ctab" label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression">
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70 <filter>guide['output_ballgown']</filter>
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71 </data>
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72 <data format="tabular" from_work_dir="i_data.ctab" label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression">
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73 <filter>guide['output_ballgown']</filter>
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74 </data>
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75 <data format="tabular" from_work_dir="t_data.ctab" label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression">
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76 <filter>guide['output_ballgown']</filter>
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77 </data>
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78 <data format="tabular" from_work_dir="e2t.ctab" label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping">
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79 <filter>guide['output_ballgown']</filter>
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80 </data>
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81 <data format="tabular" from_work_dir="i2t.ctab" label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping">
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82 <filter>guide['output_ballgown']</filter>
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83 </data>
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84 </outputs>
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85 <tests>
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86 <test>
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87 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
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88 <param name="use_guide" value="no" />
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89 <param name="options" value="default" />
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90 <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" />
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91 </test>
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92 <test>
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93 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
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94 <param name="use_guide" value="no" />
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95 <param name="options" value="advanced" />
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96 <param name="fraction" value="0.17" />
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97 <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" />
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98 </test>
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99 <test>
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100 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
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101 <param name="use_guide" value="yes" />
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102 <param name="guide_gff" value="stringtie_in.gtf" />
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103 <param name="options" value="default" />
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104 <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" />
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105 </test>
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106 <test>
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107 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
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108 <param name="use_guide" value="yes" />
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109 <param name="guide_gff" value="stringtie_in.gtf" />
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110 <param name="options" value="advanced" />
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111 <param name="fraction" value="0.17" />
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112 <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" />
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113 </test>
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114 <test>
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115 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
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116 <param name="use_guide" value="yes" />
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117 <param name="output_ballgown" value="yes" />
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118 <param name="guide_gff" value="stringtie_in.gtf" />
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119 <param name="options" value="default" />
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120 <output file="ballgown/e_data.ctab" ftype="tabular" name="exon_expression" />
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121 <output file="ballgown/i_data.ctab" ftype="tabular" name="intron_expression" />
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122 <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />
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123 <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />
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124 <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />
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125 <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" />
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126 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
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127 </test>
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128 </tests>
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129 <help>
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130 <![CDATA[
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131 StringTie v1.0.1 usage:
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132 stringtie <input.bam> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]
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133 [-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-n sens]
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134 [-C <coverage_file_name>] [-s <maxcov>] [-c <min_bundle_cov>] [-g <bdist>]
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135 {-B | -b <dir_path>} [-e]
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136
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137 Assemble RNA-Seq alignments into potential transcripts.
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138
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139 Options:
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140 -G reference annotation to use for guiding the assembly process (GTF/GFF3)
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141 -l name prefix for output transcripts (default: STRG)
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142 -f minimum isoform fraction (default: 0.1)
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143 -m minimum assembled transcript length to report (default 200bp)
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144 -o output path/file name for the assembled transcripts GTF (default: stdout)
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145 -a minimum anchor length for junctions (default: 10)
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146 -j minimum junction coverage (default: 1)
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147 -t disable trimming of predicted transcripts based on coverage
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148 (default: coverage trimming is enabled)
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149 -c minimum reads per bp coverage to consider for transcript assembly (default: 2.5)
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150 -s coverage saturation threshold; further read alignments will be
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151 ignored in a region where a local coverage depth of <maxcov>
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152 is reached (default: 1,000,000);
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153 -v verbose (log bundle processing details)
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154 -g gap between read mappings triggering a new bundle (default: 50)
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155 -C output file with reference transcripts that are covered by reads
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156 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
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157 -p number of threads (CPUs) to use (default: 1)
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158 -B enable output of Ballgown table files which will be created in the
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159 same directory as the output GTF (requires -G, -o recommended)
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160 -b enable output of Ballgown table files but these files will be
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161 created under the directory path given as <dir_path>
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162 -e only estimates the abundance of given reference transcripts (requires -G)
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163 ]]>
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164 </help>
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165 <citations>
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166 <citation type="doi">doi:10.1038/nbt.3122</citation>
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167 </citations>
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168 </tool>
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