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comparison stringtie.xml @ 15:457d00d0005d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
author iuc
date Tue, 04 Apr 2017 12:58:13 -0400
parents f70601406e0e
children bc451c12cd18
comparison
equal deleted inserted replaced
14:0f5a352b3f04 15:457d00d0005d
1 <tool id="stringtie" name="StringTie" version="1.2.3"> 1 <tool id="stringtie" name="StringTie" version="1.3.3">
2 <description>transcript assembly and quantification</description> 2 <description>transcript assembly and quantification</description>
3 <macros> 3 <macros>
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>
10 <![CDATA[ 10 <![CDATA[
11 mkdir -p ./special_de_output/sample1/ &&
12 #if str($guide.use_guide) == 'yes':
13 ln -s '$guide.guide_gff' ./special_de_output/sample1/guide.gtf &&
14 #end if
15
11 #if $input_bam.metadata.ftype == 'sam': 16 #if $input_bam.metadata.ftype == 'sam':
12 samtools sort -@ \${GALAXY_SLOTS:-1} "$input_bam" | stringtie 17 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_bam' | stringtie
13 #else 18 #else
14 stringtie "$input_bam" 19 stringtie '$input_bam'
15 #end if 20 #end if
21
16 -o "$output_gtf" 22 -o "$output_gtf"
17 -p "\${GALAXY_SLOTS:-1}" 23 -p "\${GALAXY_SLOTS:-1}"
18 #if str($guide.use_guide) == 'yes': 24 #if str($guide.use_guide) == 'yes':
19 -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation 25 -C '$coverage'
20 #if $guide.output_ballgown: 26 -G '$guide.guide_gff'
21 -b . 27 $guide.input_estimation
28 #if $guide.special_outputs != 'no':
29 -b ./special_de_output/sample1/
22 #end if 30 #end if
23 #end if 31 #end if
24 #if str($option_set.options) == 'advanced': 32 #if str($option_set.options) == 'advanced':
25 -l "$option_set.name_prefix" 33 -l '$option_set.name_prefix'
26 -f "$option_set.fraction" 34 -f '$option_set.fraction'
27 -m "$option_set.min_tlen" 35 -m '$option_set.min_tlen'
28 -a "$option_set.min_anchor_len" 36 -a '$option_set.min_anchor_len'
29 -j "$option_set.min_anchor_cov" 37 -j '$option_set.min_anchor_cov'
30 -c "$option_set.min_bundle_cov" 38 -c '$option_set.min_bundle_cov'
31 -g "$option_set.bdist" 39 -g '$option_set.bdist'
32 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping 40 -M '$option_set.bundle_fraction' $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping
33 #if $option_set.abundance_estimation: 41 #if $option_set.abundance_estimation:
34 -A "$gene_abundance_estimation" 42 -A "$gene_abundance_estimation"
35 #end if 43 #end if
36 #if str($option_set.omit_sequences).strip() != "": 44 #if str($option_set.omit_sequences).strip() != "":
37 -x "$option_set.omit_sequences" 45 -x "$option_set.omit_sequences"
38 #end if 46 #end if
39 #end if 47 #end if
48
49 #if str($guide.use_guide) == 'yes':
50 #if $guide.special_outputs.special_outputs_select == 'deseq2':
51 &&
52 prepDE.py
53 -i ./special_de_output/
54 -g gene_cout_matrix.tsv
55 -t transcripts_count_matrix.tsv
56 -l $guide.special_outputs.read_length
57 #if str($option_set.options) == 'advanced':
58 -s '$option_set.name_prefix'
59 #end if
60 #if $guide.special_outputs.clustering:
61 -c
62 --legend ./legend.tsv
63
64 &&
65 sed -i.bak 's/,/\t/g' ./legend.tsv
66
67 #end if
68 &&
69 sed -i.bak 's/,/\t/g' transcripts_count_matrix.tsv
70 &&
71 sed -i.bak 's/,/\t/g' gene_cout_matrix.tsv
72 #end if
73 #end if
74
40 ]]> 75 ]]>
41 </command> 76 </command>
42 <inputs> 77 <inputs>
43 <param format="sam,bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" /> 78 <param format="sam,bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" />
44 <conditional name="guide"> 79 <conditional name="guide">
45 <param label="Use GFF file to guide assembly" name="use_guide" type="select"> 80 <param label="Use GFF file to guide assembly" name="use_guide" type="select">
46 <option value="yes">Use GFF</option> 81 <option value="yes">Use GFF/GTF</option>
47 <option selected="True" value="no">Do not use GFF</option> 82 <option selected="True" value="no">Do not use GFF/GTF</option>
48 </param> 83 </param>
49 <when value="no" /> 84 <when value="no" />
50 <when value="yes"> 85 <when value="yes">
51 <param argument="-G" format="gtf,gff3" help="" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" /> 86 <param argument="-G" format="gtf,gff3" name="guide_gff" type="data"
52 <param argument="-e" falsevalue="" help="" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" /> 87 help="" label="Reference annotation to use for guiding the assembly process" />
53 <param argument="-b" falsevalue="" help="" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" /> 88 <param argument="-e" name="input_estimation" truevalue="-e" type="boolean" falsevalue=""
89 help="" label="Perform abundance estimation only of input transcripts" />
90 <conditional name="special_outputs">
91 <param label="Output additional files for use in..." name="special_outputs_select" type="select">
92 <option value="ballgown">Ballgown</option>
93 <option selected="True" value="deseq2">DESeq2/EdgeR</option>
94 <option value="no">No addional output</option>
95 </param>
96 <when value="ballgown" />
97 <when value="deseq2">
98 <param label="Average read length" name="read_length" type="integer" value="75" help="" />
99 <param label="Whether to cluster genes that overlap with different gene IDs"
100 name="clustering"
101 truevalue="--cluster"
102 type="boolean" help="ignoring ones with geneID pattern" falsevalue="" />
103 </when>
104 </conditional>
54 </when> 105 </when>
55 </conditional> 106 </conditional>
56 <conditional name="option_set"> 107 <conditional name="option_set">
57 <param help="" label="Options" name="options" type="select"> 108 <param help="" label="Options" name="options" type="select">
58 <option selected="True" value="default">Use defaults</option> 109 <option selected="True" value="default">Use defaults</option>
59 <option value="advanced">Specify advanced options</option> 110 <option value="advanced">Specify advanced options</option>
60 </param> 111 </param>
61 <when value="default" /> 112 <when value="default" />
62 <when value="advanced"> 113 <when value="advanced">
63 <param argument="-t" falsevalue="" help="" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" /> 114 <param argument="-t" falsevalue="" name="disable_trimming" truevalue="-t" type="boolean"
64 <param argument="-S" falsevalue="" help="" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" /> 115 label="Disable trimming of predicted transcripts based on coverage" />
65 <param argument="-l" help="" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" /> 116 <param argument="-S" falsevalue=""
66 <param argument="-f" help="" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" /> 117 label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" />
67 <param argument="-m" help="" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" /> 118 <param argument="-l" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" />
68 <param argument="-a" help="" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" /> 119 <param argument="-f" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" />
69 <param argument="-j" help="" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" /> 120 <param argument="-m" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" />
70 <param argument="-c" help="" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" /> 121 <param argument="-a" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" />
71 <param argument="-g" help="" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" /> 122 <param argument="-j" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" />
72 <param argument="-M" help="" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" /> 123 <param argument="-c" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" />
73 <param argument="-x" help="e.g. chrM,chrX" label="Do not assemble any transcripts on these reference sequence(s)" name="omit_sequences" type="text" value="" /> 124 <param argument="-g" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" />
74 <param argument="-A" falsevalue="" help="" label="Additional gene abundance estimation output file" name="abundance_estimation" truevalue="-A" type="boolean" /> 125 <param argument="-M" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" />
75 <param argument="-u" falsevalue="" help="" label="Disable multi-mapping correction" name="multi_mapping" truevalue="-u" type="boolean" /> 126 <param argument="-x" name="omit_sequences" type="text" value=""
127 help="e.g. chrM,chrX" label="Do not assemble any transcripts on these reference sequence(s)" />
128 <param argument="-A" falsevalue="" name="abundance_estimation" truevalue="-A" type="boolean"
129 label="Additional gene abundance estimation output file" />
130 <param argument="-u" falsevalue="" truevalue="-u" type="boolean"
131 label="Disable multi-mapping correction" name="multi_mapping" />
76 </when> 132 </when>
77 </conditional> 133 </conditional>
78 </inputs> 134 </inputs>
79 <outputs> 135 <outputs>
80 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" /> 136 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
82 <filter>option_set['options'] == 'advanced' and option_set['abundance_estimation']</filter> 138 <filter>option_set['options'] == 'advanced' and option_set['abundance_estimation']</filter>
83 </data> 139 </data>
84 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage"> 140 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
85 <filter>guide['use_guide'] == 'yes'</filter> 141 <filter>guide['use_guide'] == 'yes'</filter>
86 </data> 142 </data>
87 <data format="tabular" from_work_dir="e_data.ctab" label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression"> 143 <data format="tabular" from_work_dir="special_de_output/sample1/e_data.ctab"
88 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter> 144 label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression">
89 </data> 145 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
90 <data format="tabular" from_work_dir="i_data.ctab" label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression"> 146 </data>
91 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter> 147 <data format="tabular" from_work_dir="special_de_output/sample1/i_data.ctab"
92 </data> 148 label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression">
93 <data format="tabular" from_work_dir="t_data.ctab" label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression"> 149 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
94 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter> 150 </data>
95 </data> 151 <data format="tabular" from_work_dir="special_de_output/sample1/t_data.ctab"
96 <data format="tabular" from_work_dir="e2t.ctab" label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping"> 152 label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression">
97 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter> 153 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
98 </data> 154 </data>
99 <data format="tabular" from_work_dir="i2t.ctab" label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping"> 155 <data format="tabular" from_work_dir="special_de_output/sample1/e2t.ctab"
100 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter> 156 label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping">
157 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
158 </data>
159 <data format="tabular" from_work_dir="special_de_output/sample1/i2t.ctab"
160 label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping">
161 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
162 </data>
163
164 <data format="tabular" from_work_dir="gene_cout_matrix.tsv"
165 label="${tool.name} on ${on_string}: Gene counts" name="gene_counts">
166 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
167 </data>
168 <data format="tabular" from_work_dir="transcripts_count_matrix.tsv"
169 label="${tool.name} on ${on_string}: Transcript counts" name="transcript_counts">
170 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
171 </data>
172 <data format="tabular" from_work_dir="legend.tsv"
173 label="${tool.name} on ${on_string}: legend" name="legend">
174 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2' and guide['special_outputs']['clustering'] is True</filter>
101 </data> 175 </data>
102 </outputs> 176 </outputs>
103 <tests> 177 <tests>
104 <test> 178 <test>
105 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 179 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
115 <output file="stringtie_out2.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> 189 <output file="stringtie_out2.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
116 </test> 190 </test>
117 <test> 191 <test>
118 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 192 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
119 <param name="use_guide" value="yes" /> 193 <param name="use_guide" value="yes" />
194 <param name="special_outputs_select" value="no" />
120 <param name="guide_gff" value="stringtie_in.gtf" /> 195 <param name="guide_gff" value="stringtie_in.gtf" />
121 <param name="options" value="default" /> 196 <param name="options" value="default" />
122 <output file="stringtie_out3.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> 197 <output file="stringtie_out3.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
123 </test> 198 </test>
124 <test> 199 <test>
125 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 200 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
126 <param name="use_guide" value="yes" /> 201 <param name="use_guide" value="yes" />
202 <param name="special_outputs_select" value="no" />
127 <param name="guide_gff" value="stringtie_in.gtf" /> 203 <param name="guide_gff" value="stringtie_in.gtf" />
128 <param name="options" value="advanced" /> 204 <param name="options" value="advanced" />
129 <param name="fraction" value="0.17" /> 205 <param name="fraction" value="0.17" />
130 <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> 206 <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
131 </test> 207 </test>
132 <test> 208 <test>
133 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 209 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
134 <param name="use_guide" value="yes" /> 210 <param name="use_guide" value="yes" />
135 <param name="output_ballgown" value="yes" /> 211 <param name="special_outputs_select" value="ballgown" />
136 <param name="guide_gff" value="stringtie_in.gtf" /> 212 <param name="guide_gff" value="stringtie_in.gtf" />
137 <param name="options" value="default" /> 213 <param name="options" value="default" />
138 <output file="ballgown/e_data.ctab" ftype="tabular" name="exon_expression" /> 214 <output file="./ballgown/e_data.ctab" ftype="tabular" name="exon_expression" />
139 <output file="ballgown/i_data.ctab" ftype="tabular" name="intron_expression" /> 215 <output file="./ballgown/i_data.ctab" ftype="tabular" name="intron_expression" />
140 <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" /> 216 <output file="./ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />
141 <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" /> 217 <output file="./ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />
142 <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" /> 218 <output file="./ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />
143 <output file="stringtie_out5.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> 219 <output file="stringtie_out5.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
220 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
221 </test>
222 <test>
223 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
224 <param name="use_guide" value="yes" />
225 <param name="special_outputs_select" value="deseq2" />
226 <param name="input_estimation" value="True" />
227 <param name="guide_gff" value="stringtie_in.gtf" />
228 <param name="options" value="default" />
229 <param name="clustering" value="True" />
230 <output file="./deseq2/gene_counts.tsv" ftype="tabular" lines_diff="2" name="gene_counts" />
231 <output file="./deseq2/transcript_counts.tsv" ftype="tabular" name="transcript_counts" />
232 <output file="./deseq2/legend.tsv" ftype="tabular" name="legend" />
233 <output file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
144 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" /> 234 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
145 </test> 235 </test>
146 <test> 236 <test>
147 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 237 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
148 <param name="use_guide" value="yes" /> 238 <param name="use_guide" value="yes" />
149 <param name="guide_gff" value="stringtie_in.gtf" /> 239 <param name="guide_gff" value="stringtie_in.gtf" />
150 <param name="options" value="advanced" /> 240 <param name="options" value="advanced" />
151 <param name="fraction" value="0.17" /> 241 <param name="fraction" value="0.17" />
152 <param name="abundance_estimation" value="True" /> 242 <param name="abundance_estimation" value="True" />
153 <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> 243 <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
154 <output file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" name="gene_abundance_estimation" /> 244 <output file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" name="gene_abundance_estimation" />
155 </test> 245 </test>
156 <test> 246 <test>
157 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 247 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
158 <param name="use_guide" value="yes" /> 248 <param name="use_guide" value="yes" />
249 <param name="special_outputs_select" value="no" />
159 <param name="guide_gff" value="stringtie_in.gtf" /> 250 <param name="guide_gff" value="stringtie_in.gtf" />
160 <param name="options" value="advanced" /> 251 <param name="options" value="advanced" />
161 <param name="fraction" value="0.15" /> 252 <param name="fraction" value="0.15" />
162 <param name="c" value="test_chromosome" /> 253 <param name="c" value="test_chromosome" />
163 <output file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> 254 <output file="stringtie_out8.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
164 </test> 255 </test>
165 </tests> 256 </tests>
166 <help> 257 <help>
167 <![CDATA[ 258 <![CDATA[
168 259