Mercurial > repos > iuc > stringtie

comparison stringtie.xml @ 12:f70601406e0e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
author iuc
date Mon, 18 Jul 2016 06:53:19 -0400
parents 52f55ad3dee2
children 457d00d0005d
comparison
equal deleted inserted replaced
11:52f55ad3dee2 12:f70601406e0e
1 <tool id="stringtie" name="StringTie" version="1.1.0"> 1 <tool id="stringtie" name="StringTie" version="1.2.3">
2 <description>transcript assembly and quantification</description> 2 <description>transcript assembly and quantification</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="1.1.0">stringtie</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <command><![CDATA[ 6 <expand macro="requirements" />
7 stringtie "$input_bam" 7 <expand macro="stdio" />
8 -o "$output_gtf" 8 <expand macro="version_command" />
9 -p "\${GALAXY_SLOTS:-1}" 9 <command>
10 #if str($guide.use_guide) == 'yes': 10 <![CDATA[
11 -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation 11 #if $input_bam.metadata.ftype == 'sam':
12 #if str($guide.output_ballgown) == '-b': 12 samtools sort -@ \${GALAXY_SLOTS:-1} "$input_bam" | stringtie
13 $guide.output_ballgown `pwd` 13 #else
14 #end if 14 stringtie "$input_bam"
15 #end if
16 -o "$output_gtf"
17 -p "\${GALAXY_SLOTS:-1}"
18 #if str($guide.use_guide) == 'yes':
19 -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation
20 #if $guide.output_ballgown:
21 -b .
15 #end if 22 #end if
16 #if str($option_set.options) == 'advanced': 23 #end if
17 -l "$option_set.name_prefix" 24 #if str($option_set.options) == 'advanced':
18 -f "$option_set.fraction" 25 -l "$option_set.name_prefix"
19 -m "$option_set.min_tlen" 26 -f "$option_set.fraction"
20 -a "$option_set.min_anchor_len" 27 -m "$option_set.min_tlen"
21 -j "$option_set.min_anchor_cov" 28 -a "$option_set.min_anchor_len"
22 -c "$option_set.min_bundle_cov" 29 -j "$option_set.min_anchor_cov"
23 -g "$option_set.bdist" 30 -c "$option_set.min_bundle_cov"
24 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming 31 -g "$option_set.bdist"
25 #if $option_set.A: 32 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping
26 -A "$gene_abundance_estimation" 33 #if $option_set.abundance_estimation:
27 #end if 34 -A "$gene_abundance_estimation"
28 #if str($option_set.x).strip() != "":
29 -x "$option_set.x"
30 #end if
31 #end if 35 #end if
32 ]]> 36 #if str($option_set.omit_sequences).strip() != "":
33 </command> 37 -x "$option_set.omit_sequences"
38 #end if
39 #end if
40 ]]>
41 </command>
34 <inputs> 42 <inputs>
35 <param format="bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" /> 43 <param format="sam,bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" />
36 <conditional name="guide"> 44 <conditional name="guide">
37 <param label="Use GFF file to guide assembly" name="use_guide" type="select"> 45 <param label="Use GFF file to guide assembly" name="use_guide" type="select">
38 <option value="yes">Use GFF</option> 46 <option value="yes">Use GFF</option>
39 <option selected="True" value="no">Do not use GFF</option> 47 <option selected="True" value="no">Do not use GFF</option>
40 </param> 48 </param>
41 <when value="no" /> 49 <when value="no" />
42 <when value="yes"> 50 <when value="yes">
43 <param format="gtf,gff3" help="-G" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" /> 51 <param argument="-G" format="gtf,gff3" help="" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" />
44 <param falsevalue="" help="-e" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" /> 52 <param argument="-e" falsevalue="" help="" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" />
45 <param falsevalue="" help="-b" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" /> 53 <param argument="-b" falsevalue="" help="" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" />
46 </when> 54 </when>
47 </conditional> 55 </conditional>
48 <conditional name="option_set"> 56 <conditional name="option_set">
49 <param label="Options" name="options" type="select"> 57 <param help="" label="Options" name="options" type="select">
50 <option selected="True" value="default">Use defaults</option> 58 <option selected="True" value="default">Use defaults</option>
51 <option value="advanced">Specify advanced options</option> 59 <option value="advanced">Specify advanced options</option>
52 </param> 60 </param>
53 <when value="default" /> 61 <when value="default" />
54 <when value="advanced"> 62 <when value="advanced">
55 <param falsevalue="" help="-t" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" /> 63 <param argument="-t" falsevalue="" help="" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" />
56 <param falsevalue="" help="-S" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" /> 64 <param argument="-S" falsevalue="" help="" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" />
57 <param help="-l" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" /> 65 <param argument="-l" help="" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" />
58 <param help="-f" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" /> 66 <param argument="-f" help="" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" />
59 <param help="-m" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" /> 67 <param argument="-m" help="" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" />
60 <param help="-a" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" /> 68 <param argument="-a" help="" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" />
61 <param help="-j" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" /> 69 <param argument="-j" help="" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" />
62 <param help="-c" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" /> 70 <param argument="-c" help="" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" />
63 <param help="-g" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" /> 71 <param argument="-g" help="" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" />
64 <param help="-M" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" /> 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" />
65 <param argument="-x" type="text" value="" label="Do not assemble any transcripts on these reference sequence(s)" help="e.g. chrM,chrX" /> 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="" />
66 <param argument="-A" truevalue="-A" falsevalue="" type="boolean" help="" label="Additional gene abundance estimation output file" /> 74 <param argument="-A" falsevalue="" help="" label="Additional gene abundance estimation output file" name="abundance_estimation" truevalue="-A" type="boolean" />
75 <param argument="-u" falsevalue="" help="" label="Disable multi-mapping correction" name="multi_mapping" truevalue="-u" type="boolean" />
67 </when> 76 </when>
68 </conditional> 77 </conditional>
69 </inputs> 78 </inputs>
70 <outputs> 79 <outputs>
71 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" /> 80 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
72 <data format="tabular" label="${tool.name} on ${on_string}: Gene abundance estimates" name="gene_abundance_estimation"> 81 <data format="gtf" label="${tool.name} on ${on_string}: Gene abundance estimates" name="gene_abundance_estimation">
73 <filter>option_set['A']</filter> 82 <filter>option_set['options'] == 'advanced' and option_set['abundance_estimation']</filter>
74 </data> 83 </data>
75 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage"> 84 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
76 <filter>guide['use_guide'] == "yes"</filter> 85 <filter>guide['use_guide'] == 'yes'</filter>
77 </data> 86 </data>
78 <data format="tabular" from_work_dir="e_data.ctab" label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression"> 87 <data format="tabular" from_work_dir="e_data.ctab" label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression">
79 <filter>guide['output_ballgown']</filter> 88 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
80 </data> 89 </data>
81 <data format="tabular" from_work_dir="i_data.ctab" label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression"> 90 <data format="tabular" from_work_dir="i_data.ctab" label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression">
82 <filter>guide['output_ballgown']</filter> 91 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
83 </data> 92 </data>
84 <data format="tabular" from_work_dir="t_data.ctab" label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression"> 93 <data format="tabular" from_work_dir="t_data.ctab" label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression">
85 <filter>guide['output_ballgown']</filter> 94 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
86 </data> 95 </data>
87 <data format="tabular" from_work_dir="e2t.ctab" label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping"> 96 <data format="tabular" from_work_dir="e2t.ctab" label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping">
88 <filter>guide['output_ballgown']</filter> 97 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
89 </data> 98 </data>
90 <data format="tabular" from_work_dir="i2t.ctab" label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping"> 99 <data format="tabular" from_work_dir="i2t.ctab" label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping">
91 <filter>guide['output_ballgown']</filter> 100 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
92 </data> 101 </data>
93 </outputs> 102 </outputs>
94 <tests> 103 <tests>
95 <test> 104 <test>
96 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 105 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
97 <param name="use_guide" value="no" /> 106 <param name="use_guide" value="no" />
98 <param name="options" value="default" /> 107 <param name="options" value="default" />
99 <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> 108 <output file="stringtie_out1.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
100 </test> 109 </test>
101 <test> 110 <test>
102 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 111 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
103 <param name="use_guide" value="no" /> 112 <param name="use_guide" value="no" />
104 <param name="options" value="advanced" /> 113 <param name="options" value="advanced" />
105 <param name="fraction" value="0.17" /> 114 <param name="fraction" value="0.17" />
106 <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> 115 <output file="stringtie_out2.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
107 </test> 116 </test>
108 <test> 117 <test>
109 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 118 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
110 <param name="use_guide" value="yes" /> 119 <param name="use_guide" value="yes" />
111 <param name="guide_gff" value="stringtie_in.gtf" /> 120 <param name="guide_gff" value="stringtie_in.gtf" />
112 <param name="options" value="default" /> 121 <param name="options" value="default" />
113 <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> 122 <output file="stringtie_out3.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
114 </test> 123 </test>
115 <test> 124 <test>
116 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 125 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
117 <param name="use_guide" value="yes" /> 126 <param name="use_guide" value="yes" />
118 <param name="guide_gff" value="stringtie_in.gtf" /> 127 <param name="guide_gff" value="stringtie_in.gtf" />
119 <param name="options" value="advanced" /> 128 <param name="options" value="advanced" />
120 <param name="fraction" value="0.17" /> 129 <param name="fraction" value="0.17" />
121 <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> 130 <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
122 </test> 131 </test>
123 <test> 132 <test>
124 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 133 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
125 <param name="use_guide" value="yes" /> 134 <param name="use_guide" value="yes" />
126 <param name="output_ballgown" value="yes" /> 135 <param name="output_ballgown" value="yes" />
129 <output file="ballgown/e_data.ctab" ftype="tabular" name="exon_expression" /> 138 <output file="ballgown/e_data.ctab" ftype="tabular" name="exon_expression" />
130 <output file="ballgown/i_data.ctab" ftype="tabular" name="intron_expression" /> 139 <output file="ballgown/i_data.ctab" ftype="tabular" name="intron_expression" />
131 <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" /> 140 <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />
132 <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" /> 141 <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />
133 <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" /> 142 <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />
134 <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> 143 <output file="stringtie_out5.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
135 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" /> 144 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
136 </test> 145 </test>
137 <test> 146 <test>
138 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 147 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
139 <param name="use_guide" value="yes" /> 148 <param name="use_guide" value="yes" />
140 <param name="guide_gff" value="stringtie_in.gtf" /> 149 <param name="guide_gff" value="stringtie_in.gtf" />
141 <param name="options" value="advanced" /> 150 <param name="options" value="advanced" />
142 <param name="fraction" value="0.17" /> 151 <param name="fraction" value="0.17" />
143 <param name="A" value="True" /> 152 <param name="abundance_estimation" value="True" />
144 <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> 153 <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
145 <output file="stringtie_out6.gtf" ftype="tabular" name="gene_abundance_estimation" /> 154 <output file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" name="gene_abundance_estimation" />
146 </test> 155 </test>
147 <test> 156 <test>
148 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> 157 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
149 <param name="use_guide" value="yes" /> 158 <param name="use_guide" value="yes" />
150 <param name="guide_gff" value="stringtie_in.gtf" /> 159 <param name="guide_gff" value="stringtie_in.gtf" />
151 <param name="options" value="advanced" /> 160 <param name="options" value="advanced" />
152 <param name="fraction" value="0.15" /> 161 <param name="fraction" value="0.15" />
153 <param name="c" value="test_chromosome" /> 162 <param name="c" value="test_chromosome" />
154 <output file="stringtie_out7.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> 163 <output file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
155 </test> 164 </test>
156 </tests> 165 </tests>
157 <help> 166 <help>
158 <![CDATA[ 167 <![CDATA[
159 168
180 -v verbose (log bundle processing details) 189 -v verbose (log bundle processing details)
181 -g gap between read mappings triggering a new bundle (default: 50) 190 -g gap between read mappings triggering a new bundle (default: 50)
182 -C output file with reference transcripts that are covered by reads 191 -C output file with reference transcripts that are covered by reads
183 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95) 192 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
184 -p number of threads (CPUs) to use (default: 1) 193 -p number of threads (CPUs) to use (default: 1)
194 -A gene abundance estimation output file
185 -B enable output of Ballgown table files which will be created in the 195 -B enable output of Ballgown table files which will be created in the
186 same directory as the output GTF (requires -G, -o recommended) 196 same directory as the output GTF (requires -G, -o recommended)
187 -b enable output of Ballgown table files but these files will be 197 -b enable output of Ballgown table files but these files will be
188 created under the directory path given as <dir_path> 198 created under the directory path given as <dir_path>
189 -e only estimates the abundance of given reference transcripts (requires -G) 199 -e only estimates the abundance of given reference transcripts (requires -G)
190 -A gene abundance estimation output file
191 -x do not assemble any transcripts on these reference sequence(s) 200 -x do not assemble any transcripts on these reference sequence(s)
192 201 -u no multi-mapping correction default: false)
193 202
194 ]]> 203 ]]>
195 </help> 204 </help>
196 <citations> 205 <expand macro="citations" />
197 <citation type="doi">10.1038/nbt.3122</citation>
198 </citations>
199 </tool> 206 </tool>