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comparison stringtie.xml @ 11:6e45b443ef1f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf
author iuc
date Thu, 01 Jun 2017 12:16:04 -0400
parents c84d44519b2e
children 76d290331481
comparison
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10:c84d44519b2e 11:6e45b443ef1f
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command> 9 <command><![CDATA[
10 <![CDATA[
11 mkdir -p ./special_de_output/sample1/ && 10 mkdir -p ./special_de_output/sample1/ &&
12 #if str($guide.use_guide) == 'yes': 11 #if str($guide.use_guide) == 'yes':
13 ln -s '$guide.guide_gff' ./special_de_output/sample1/guide.gtf && 12 ln -s '$guide.guide_gff' ./special_de_output/sample1/guide.gtf &&
14 #end if 13 #end if
15 14
40 -M '$option_set.bundle_fraction' $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping 39 -M '$option_set.bundle_fraction' $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping
41 #if $option_set.abundance_estimation: 40 #if $option_set.abundance_estimation:
42 -A "$gene_abundance_estimation" 41 -A "$gene_abundance_estimation"
43 #end if 42 #end if
44 #if str($option_set.omit_sequences).strip() != "": 43 #if str($option_set.omit_sequences).strip() != "":
45 -x "$option_set.omit_sequences" 44 -x '$option_set.omit_sequences'
46 #end if 45 #end if
47 #end if 46 #end if
48 47
49 #if str($guide.use_guide) == 'yes': 48 #if str($guide.use_guide) == 'yes':
50 #if $guide.special_outputs.special_outputs_select == 'deseq2': 49 #if $guide.special_outputs.special_outputs_select == 'deseq2':
69 sed -i.bak 's/,/\t/g' transcripts_count_matrix.tsv 68 sed -i.bak 's/,/\t/g' transcripts_count_matrix.tsv
70 && 69 &&
71 sed -i.bak 's/,/\t/g' gene_cout_matrix.tsv 70 sed -i.bak 's/,/\t/g' gene_cout_matrix.tsv
72 #end if 71 #end if
73 #end if 72 #end if
74 73 ]]></command>
75 ]]>
76 </command>
77 <inputs> 74 <inputs>
78 <param format="sam,bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" /> 75 <param name="input_bam" type="data" format="sam,bam" label="Mapped reads to assemble transcripts from" />
79 <conditional name="guide"> 76 <conditional name="guide">
80 <param label="Use GFF file to guide assembly" name="use_guide" type="select"> 77 <param name="use_guide" type="select" label="Use GFF file to guide assembly">
81 <option value="yes">Use GFF/GTF</option> 78 <option value="yes">Use GFF/GTF</option>
82 <option selected="True" value="no">Do not use GFF/GTF</option> 79 <option selected="True" value="no">Do not use GFF/GTF</option>
83 </param> 80 </param>
84 <when value="no" /> 81 <when value="no" />
85 <when value="yes"> 82 <when value="yes">
86 <param argument="-G" format="gtf,gff3" name="guide_gff" type="data" 83 <param name="guide_gff" argument="-G" type="data" format="gtf,gff3"
87 help="" label="Reference annotation to use for guiding the assembly process" /> 84 label="Reference annotation to use for guiding the assembly process" />
88 <param argument="-e" name="input_estimation" truevalue="-e" type="boolean" falsevalue="" 85 <param name="input_estimation" argument="-e" type="boolean" truevalue="-e" falsevalue=""
89 help="" label="Perform abundance estimation only of input transcripts" /> 86 label="Perform abundance estimation only of input transcripts" />
90 <conditional name="special_outputs"> 87 <conditional name="special_outputs">
91 <param label="Output additional files for use in..." name="special_outputs_select" type="select"> 88 <param name="special_outputs_select" type="select" label="Output additional files for use in...">
92 <option value="ballgown">Ballgown</option> 89 <option value="ballgown">Ballgown</option>
93 <option selected="True" value="deseq2">DESeq2/EdgeR</option> 90 <option selected="True" value="deseq2">DESeq2/EdgeR</option>
94 <option value="no">No addional output</option> 91 <option value="no">No addional output</option>
95 </param> 92 </param>
96 <when value="ballgown" /> 93 <when value="ballgown" />
97 <when value="deseq2"> 94 <when value="deseq2">
98 <param label="Average read length" name="read_length" type="integer" value="75" help="" /> 95 <param name="read_length" type="integer" value="75" label="Average read length" />
99 <param label="Whether to cluster genes that overlap with different gene IDs" 96 <param name="clustering" type="boolean" truevalue="--cluster" falsevalue="" label="Whether to cluster genes that overlap with different gene IDs" help="ignoring ones with geneID pattern" />
100 name="clustering"
101 truevalue="--cluster"
102 type="boolean" help="ignoring ones with geneID pattern" falsevalue="" />
103 </when> 97 </when>
98 <when value="no" />
104 </conditional> 99 </conditional>
105 </when> 100 </when>
106 </conditional> 101 </conditional>
107 <conditional name="option_set"> 102 <conditional name="option_set">
108 <param help="" label="Options" name="options" type="select"> 103 <param name="options" type="select" label="Options">
109 <option selected="True" value="default">Use defaults</option> 104 <option selected="True" value="default">Use defaults</option>
110 <option value="advanced">Specify advanced options</option> 105 <option value="advanced">Specify advanced options</option>
111 </param> 106 </param>
112 <when value="default" /> 107 <when value="default" />
113 <when value="advanced"> 108 <when value="advanced">
114 <param argument="-t" falsevalue="" name="disable_trimming" truevalue="-t" type="boolean" 109 <param name="disable_trimming" argument="-t" type="boolean" truevalue="-t" falsevalue=""
115 label="Disable trimming of predicted transcripts based on coverage" /> 110 label="Disable trimming of predicted transcripts based on coverage" />
116 <param argument="-S" falsevalue="" 111 <param name="sensitive" argument="-S" type="boolean" truevalue="-S" falsevalue=""
117 label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" /> 112 label="Increase sensitivity" />
118 <param argument="-l" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" /> 113 <param name="name_prefix" argument="-l" type="text" value="STRG" label="Name prefix for output transcripts" />
119 <param argument="-f" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" /> 114 <param name="fraction" argument="-f" type="float" value="0.15" min="0.0" max="1.0" label="Minimum isoform fraction" />
120 <param argument="-m" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" /> 115 <param name="min_tlen" argument="-m" type="integer" value="200" label="Minimum assembled transcript length" />
121 <param argument="-a" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" /> 116 <param name="min_anchor_len" argument="-a" type="integer" value="10" label="Minimum anchor length for junctions" />
122 <param argument="-j" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" /> 117 <param name="min_anchor_cov" argument="-j" type="integer" value="1" label="Minimum junction coverage" />
123 <param argument="-c" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" /> 118 <param name="min_bundle_cov" argument="-c" type="integer" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" />
124 <param argument="-g" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" /> 119 <param name="bdist" argument="-g" type="integer" value="50" label="Gap between read mappings triggering a new bundle" />
125 <param argument="-M" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" /> 120 <param name="bundle_fraction" argument="-M" type="float" value="0.95" label="Fraction of bundle allowed to be covered by multi-hit reads" />
126 <param argument="-x" name="omit_sequences" type="text" value="" 121 <param name="omit_sequences" argument="-x" type="text" value=""
127 help="e.g. chrM,chrX" label="Do not assemble any transcripts on these reference sequence(s)" /> 122 label="Do not assemble any transcripts on these reference sequence(s)" help="e.g. chrM,chrX" />
128 <param argument="-A" falsevalue="" name="abundance_estimation" truevalue="-A" type="boolean" 123 <param name="abundance_estimation" argument="-A" type="boolean" truevalue="-A" falsevalue=""
129 label="Additional gene abundance estimation output file" /> 124 label="Additional gene abundance estimation output file" />
130 <param argument="-u" falsevalue="" truevalue="-u" type="boolean" 125 <param name="multi_mapping" argument="-u" type="boolean" truevalue="-u" falsevalue=""
131 label="Disable multi-mapping correction" name="multi_mapping" /> 126 label="Disable multi-mapping correction" />
132 </when> 127 </when>
133 </conditional> 128 </conditional>
134 </inputs> 129 </inputs>
135 <outputs> 130 <outputs>
136 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" /> 131 <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" />
137 <data format="gtf" label="${tool.name} on ${on_string}: Gene abundance estimates" name="gene_abundance_estimation"> 132 <data name="gene_abundance_estimation" format="gtf" label="${tool.name} on ${on_string}: Gene abundance estimates">
138 <filter>option_set['options'] == 'advanced' and option_set['abundance_estimation']</filter> 133 <filter>option_set['options'] == 'advanced' and option_set['abundance_estimation']</filter>
139 </data> 134 </data>
140 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage"> 135 <data name="coverage" format="gff3" label="${tool.name} on ${on_string}: Coverage">
141 <filter>guide['use_guide'] == 'yes'</filter> 136 <filter>guide['use_guide'] == 'yes'</filter>
142 </data> 137 </data>
143 <data format="tabular" from_work_dir="special_de_output/sample1/e_data.ctab" 138 <data name="exon_expression" format="tabular" from_work_dir="special_de_output/sample1/e_data.ctab"
144 label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression"> 139 label="${tool.name} on ${on_string}: exon-level expression measurements">
145 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter> 140 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
146 </data> 141 </data>
147 <data format="tabular" from_work_dir="special_de_output/sample1/i_data.ctab" 142 <data name="intron_expression" format="tabular" from_work_dir="special_de_output/sample1/i_data.ctab"
148 label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression"> 143 label="${tool.name} on ${on_string}: intron-level expression measurements">
149 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter> 144 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
150 </data> 145 </data>
151 <data format="tabular" from_work_dir="special_de_output/sample1/t_data.ctab" 146 <data name="transcript_expression" format="tabular" from_work_dir="special_de_output/sample1/t_data.ctab"
152 label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression"> 147 label="${tool.name} on ${on_string}: transcript-level expression measurements">
153 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter> 148 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
154 </data> 149 </data>
155 <data format="tabular" from_work_dir="special_de_output/sample1/e2t.ctab" 150 <data name="exon_transcript_mapping" format="tabular" from_work_dir="special_de_output/sample1/e2t.ctab"
156 label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping"> 151 label="${tool.name} on ${on_string}: exon to transcript mapping">
157 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter> 152 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
158 </data> 153 </data>
159 <data format="tabular" from_work_dir="special_de_output/sample1/i2t.ctab" 154 <data name="intron_transcript_mapping" format="tabular" from_work_dir="special_de_output/sample1/i2t.ctab"
160 label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping"> 155 label="${tool.name} on ${on_string}: intron to transcript mapping">
161 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter> 156 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
162 </data> 157 </data>
163 158 <data name="gene_counts" format="tabular" from_work_dir="gene_cout_matrix.tsv"
164 <data format="tabular" from_work_dir="gene_cout_matrix.tsv" 159 label="${tool.name} on ${on_string}: Gene counts">
165 label="${tool.name} on ${on_string}: Gene counts" name="gene_counts">
166 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter> 160 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
167 </data> 161 </data>
168 <data format="tabular" from_work_dir="transcripts_count_matrix.tsv" 162 <data name="transcript_counts" format="tabular" from_work_dir="transcripts_count_matrix.tsv"
169 label="${tool.name} on ${on_string}: Transcript counts" name="transcript_counts"> 163 label="${tool.name} on ${on_string}: Transcript counts">
170 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter> 164 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
171 </data> 165 </data>
172 <data format="tabular" from_work_dir="legend.tsv" 166 <data name="legend" format="tabular" from_work_dir="legend.tsv"
173 label="${tool.name} on ${on_string}: legend" name="legend"> 167 label="${tool.name} on ${on_string}: legend">
174 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2' and guide['special_outputs']['clustering'] is True</filter> 168 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2' and guide['special_outputs']['clustering'] is True</filter>
175 </data> 169 </data>
176 </outputs> 170 </outputs>
177 <tests> 171 <tests>
178 <test> 172 <test>
173 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
174 <param name="use_guide" value="no" />
175 <param name="options" value="default" />
176 <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" lines_diff="2" />
177 </test>
178 <test>
179 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
180 <param name="use_guide" value="no" />
181 <param name="options" value="advanced" />
182 <param name="fraction" value="0.17" />
183 <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" lines_diff="2" />
184 </test>
185 <test>
179 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 186 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
180 <param name="use_guide" value="no" /> 187 <param name="use_guide" value="yes" />
181 <param name="options" value="default" /> 188 <param name="special_outputs_select" value="no" />
182 <output file="stringtie_out1.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> 189 <param name="guide_gff" value="stringtie_in.gtf" />
183 </test> 190 <param name="options" value="default" />
184 <test> 191 <output file="stringtie_out3.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
185 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 192 </test>
186 <param name="use_guide" value="no" /> 193 <test>
194 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
195 <param name="use_guide" value="yes" />
196 <param name="special_outputs_select" value="no" />
197 <param name="guide_gff" value="stringtie_in.gtf" />
187 <param name="options" value="advanced" /> 198 <param name="options" value="advanced" />
188 <param name="fraction" value="0.17" /> 199 <param name="fraction" value="0.17" />
189 <output file="stringtie_out2.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> 200 <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" />
190 </test> 201 </test>
191 <test> 202 <test>
192 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 203 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
193 <param name="use_guide" value="yes" />
194 <param name="special_outputs_select" value="no" />
195 <param name="guide_gff" value="stringtie_in.gtf" />
196 <param name="options" value="default" />
197 <output file="stringtie_out3.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
198 </test>
199 <test>
200 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
201 <param name="use_guide" value="yes" />
202 <param name="special_outputs_select" value="no" />
203 <param name="guide_gff" value="stringtie_in.gtf" />
204 <param name="options" value="advanced" />
205 <param name="fraction" value="0.17" />
206 <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
207 </test>
208 <test>
209 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
210 <param name="use_guide" value="yes" /> 204 <param name="use_guide" value="yes" />
211 <param name="special_outputs_select" value="ballgown" /> 205 <param name="special_outputs_select" value="ballgown" />
212 <param name="guide_gff" value="stringtie_in.gtf" /> 206 <param name="guide_gff" value="stringtie_in.gtf" />
213 <param name="options" value="default" /> 207 <param name="options" value="default" />
214 <output file="./ballgown/e_data.ctab" ftype="tabular" name="exon_expression" /> 208 <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular" />
215 <output file="./ballgown/i_data.ctab" ftype="tabular" name="intron_expression" /> 209 <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular" />
216 <output file="./ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" /> 210 <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular" />
217 <output file="./ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" /> 211 <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular" />
218 <output file="./ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" /> 212 <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular" />
219 <output file="stringtie_out5.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> 213 <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" lines_diff="2" />
220 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" /> 214 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gff3" />
221 </test> 215 </test>
222 <test> 216 <test>
223 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 217 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
224 <param name="use_guide" value="yes" /> 218 <param name="use_guide" value="yes" />
225 <param name="special_outputs_select" value="deseq2" /> 219 <param name="special_outputs_select" value="deseq2" />
226 <param name="input_estimation" value="True" /> 220 <param name="input_estimation" value="True" />
227 <param name="guide_gff" value="stringtie_in.gtf" /> 221 <param name="guide_gff" value="stringtie_in.gtf" />
228 <param name="options" value="default" /> 222 <param name="options" value="default" />
229 <param name="clustering" value="True" /> 223 <param name="clustering" value="True" />
230 <output file="./deseq2/gene_counts.tsv" ftype="tabular" lines_diff="2" name="gene_counts" /> 224 <output name="gene_counts" file="./deseq2/gene_counts.tsv" ftype="tabular" lines_diff="2" />
231 <output file="./deseq2/transcript_counts.tsv" ftype="tabular" name="transcript_counts" /> 225 <output name="transcript_counts" file="./deseq2/transcript_counts.tsv" ftype="tabular" />
232 <output file="./deseq2/legend.tsv" ftype="tabular" name="legend" /> 226 <output name="legend" file="./deseq2/legend.tsv" ftype="tabular" />
233 <output file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> 227 <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" />
234 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" /> 228 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gff3" />
235 </test> 229 </test>
236 <test> 230 <test>
237 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 231 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
238 <param name="use_guide" value="yes" /> 232 <param name="use_guide" value="yes" />
239 <param name="guide_gff" value="stringtie_in.gtf" /> 233 <param name="guide_gff" value="stringtie_in.gtf" />
240 <param name="options" value="advanced" /> 234 <param name="options" value="advanced" />
241 <param name="fraction" value="0.17" /> 235 <param name="fraction" value="0.17" />
242 <param name="abundance_estimation" value="True" /> 236 <param name="abundance_estimation" value="True" />
243 <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> 237 <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" />
244 <output file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" name="gene_abundance_estimation" /> 238 <output name="gene_abundance_estimation" file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" />
245 </test> 239 </test>
246 <test> 240 <test>
247 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 241 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
248 <param name="use_guide" value="yes" /> 242 <param name="use_guide" value="yes" />
249 <param name="special_outputs_select" value="no" /> 243 <param name="special_outputs_select" value="no" />
250 <param name="guide_gff" value="stringtie_in.gtf" /> 244 <param name="guide_gff" value="stringtie_in.gtf" />
251 <param name="options" value="advanced" /> 245 <param name="options" value="advanced" />
252 <param name="fraction" value="0.15" /> 246 <param name="fraction" value="0.15" />
253 <param name="c" value="test_chromosome" /> 247 <param name="c" value="test_chromosome" />
254 <output file="stringtie_out8.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> 248 <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="2" />
255 </test> 249 </test>
256 </tests> 250 </tests>
257 <help> 251 <help><![CDATA[
258 <![CDATA[
259
260 **What it does?** 252 **What it does?**
261 253
262 StringTie_ is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional *de novo* assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads.To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs. 254 StringTie_ is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional *de novo* assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads.To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs.
263 255
264 .. _StringTie: http://ccb.jhu.edu/software/stringtie/ 256 .. _StringTie: http://ccb.jhu.edu/software/stringtie/
265 257 ]]></help>
266 ------
267
268 StringTie has the following options::
269
270 -G reference annotation to use for guiding the assembly process (GTF/GFF3)
271 -l name prefix for output transcripts (default: STRG)
272 -f minimum isoform fraction (default: 0.1)
273 -m minimum assembled transcript length (default: 200)
274 -o output path/file name for the assembled transcripts GTF (default: stdout)
275 -a minimum anchor length for junctions (default: 10)
276 -j minimum junction coverage (default: 1)
277 -t disable trimming of predicted transcripts based on coverage
278 (default: coverage trimming is enabled)
279 -c minimum reads per bp coverage to consider for transcript assembly (default: 2.5)
280 -v verbose (log bundle processing details)
281 -g gap between read mappings triggering a new bundle (default: 50)
282 -C output file with reference transcripts that are covered by reads
283 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
284 -p number of threads (CPUs) to use (default: 1)
285 -A gene abundance estimation output file
286 -B enable output of Ballgown table files which will be created in the
287 same directory as the output GTF (requires -G, -o recommended)
288 -b enable output of Ballgown table files but these files will be
289 created under the directory path given as <dir_path>
290 -e only estimates the abundance of given reference transcripts (requires -G)
291 -x do not assemble any transcripts on these reference sequence(s)
292 -u no multi-mapping correction default: false)
293
294 ]]>
295 </help>
296 <expand macro="citations" /> 258 <expand macro="citations" />
297 </tool> 259 </tool>